| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161109_175126_129 |
| Start time | 2016-11-09 17:51:26 |
| Run time | 05:04:58.605 |
| Tasks executed | 4 |
| Tasks failed | 2 |
| Tasks failed names | markdup_bam_picard ctl1 bwa_sam rep1 |
| Arguments* | [-title, SRR1370899_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370899_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_175126_129_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_11 chipseq.bds.20161109_175126_129_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_12 |
| thread_41 | thread_Root | chipseq.bds.20161109_175126_129_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10 chipseq.bds.20161109_175126_129_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_13 |
| 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/SRR1370899_1.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out/align/rep1/SRR1370899_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-------------------- 39926 (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... 48.34 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.76 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.78 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.64 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.19 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.34 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.46 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.30 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.37 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.26 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.36 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.39 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.22 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.08 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.27 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.48 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.05 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.84 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.27 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.22 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.63 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.93 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.85 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.54 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.15 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.09 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.07 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.95 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.53 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... 47.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.78 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.42 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.86 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.67 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.98 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.28 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.92 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.48 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.93 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.49 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... 48.43 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... 50.48 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.38 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.93 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.95 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.81 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.71 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.88 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.11 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.4% 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] 14155776 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.96 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.81 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.85 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.60 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.64 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.51 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... 50.96 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.64 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.22 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.81 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.46 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.96 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.32 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... 49.22 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.85 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.44 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.55 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.61 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.26 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.07 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.73 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 19892923 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/SRR1370899_1.fastq.gz [main] Real time: 3811.327 sec; CPU: 3801.596 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/SRR1370899_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out/align/ctl1/ss_50M_2000_GRCh38.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 22142 (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/SRR1370899_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_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/SRR1370899_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_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
--------------------Stdout--------------------
46975 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 09 21:20:30 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_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
[Wed Nov 09 21:20:30 PST 2016] Executing as imk1@nandi on Linux 4.4.0-38-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO 2016-11-09 21:20:30 MarkDuplicates Start of doWork freeMemory: 254879344; totalMemory: 257425408; maxMemory: 3817865216
INFO 2016-11-09 21:20:30 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-11-09 21:20:30 MarkDuplicates Will retain up to 14684096 data points before spilling to disk.
INFO 2016-11-09 21:20:41 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
INFO 2016-11-09 21:20:41 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:20:49 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 8s. Last read position: chr1:41,895,424
INFO 2016-11-09 21:20:49 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 21:20:57 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 7s. Last read position: chr1:63,396,527
INFO 2016-11-09 21:20:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:21:04 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 7s. Last read position: chr1:89,147,707
INFO 2016-11-09 21:21:04 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:21:10 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 5s. Last read position: chr1:115,615,553
INFO 2016-11-09 21:21:10 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:21:17 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 6s. Last read position: chr1:164,468,682
INFO 2016-11-09 21:21:17 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 21:21:26 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 8s. Last read position: chr1:189,102,252
INFO 2016-11-09 21:21:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:21:35 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 9s. Last read position: chr1:213,979,760
INFO 2016-11-09 21:21:35 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:21:44 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 9s. Last read position: chr1:231,814,268
INFO 2016-11-09 21:21:44 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:21:52 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 7s. Last read position: chr2:3,652,468
INFO 2016-11-09 21:21:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:22:02 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 9s. Last read position: chr2:39,505,122
INFO 2016-11-09 21:22:02 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:22:11 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 8s. Last read position: chr2:73,561,393
INFO 2016-11-09 21:22:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:22:17 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 6s. Last read position: chr2:120,526,571
INFO 2016-11-09 21:22:17 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:22:34 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 17s. Last read position: chr2:160,316,783
INFO 2016-11-09 21:22:34 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:22:58 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 24s. Last read position: chr2:195,549,735
INFO 2016-11-09 21:22:58 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:23:11 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 13s. Last read position: chr2:230,358,034
INFO 2016-11-09 21:23:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:23:27 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 15s. Last read position: chr3:16,305,780
INFO 2016-11-09 21:23:27 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 21:23:41 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 13s. Last read position: chr3:49,251,279
INFO 2016-11-09 21:23:41 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:23:54 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 13s. Last read position: chr3:84,621,225
INFO 2016-11-09 21:23:54 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:24:05 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 11s. Last read position: chr3:128,121,129
INFO 2016-11-09 21:24:05 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:24:19 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 13s. Last read position: chr3:165,373,238
INFO 2016-11-09 21:24:19 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:24:31 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 11s. Last read position: chr3:195,333,247
INFO 2016-11-09 21:24:31 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:24:44 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 13s. Last read position: chr4:37,752,582
INFO 2016-11-09 21:24:44 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:24:59 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 14s. Last read position: chr4:81,286,306
INFO 2016-11-09 21:24:59 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:25:15 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 15s. Last read position: chr4:119,339,736
INFO 2016-11-09 21:25:15 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:25:28 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 13s. Last read position: chr4:158,818,783
INFO 2016-11-09 21:25:28 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 21:25:46 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 17s. Last read position: chr5:6,447,551
INFO 2016-11-09 21:25:46 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO 2016-11-09 21:25:59 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 13s. Last read position: chr5:33,219,021
INFO 2016-11-09 21:25:59 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 21:26:12 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 13s. Last read position: chr5:60,694,078
INFO 2016-11-09 21:26:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:26:37 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 25s. Last read position: chr5:86,336,676
INFO 2016-11-09 21:26:37 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:26:51 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 13s. Last read position: chr5:112,930,184
INFO 2016-11-09 21:26:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:27:09 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 17s. Last read position: chr5:136,852,889
INFO 2016-11-09 21:27:09 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:27:26 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 17s. Last read position: chr5:160,271,193
INFO 2016-11-09 21:27:26 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:27:38 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 11s. Last read position: chr6:4,126,386
INFO 2016-11-09 21:27:38 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 21:27:55 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 16s. Last read position: chr6:28,666,579
INFO 2016-11-09 21:27:55 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:28:07 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 12s. Last read position: chr6:49,527,281
INFO 2016-11-09 21:28:07 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:28:26 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 19s. Last read position: chr6:81,728,195
INFO 2016-11-09 21:28:26 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:28:46 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 20s. Last read position: chr6:107,535,760
INFO 2016-11-09 21:28:46 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:29:02 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 15s. Last read position: chr6:132,364,408
INFO 2016-11-09 21:29:02 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 21:29:19 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 17s. Last read position: chr6:156,918,595
INFO 2016-11-09 21:29:19 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:29:38 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 18s. Last read position: chr7:18,636,743
INFO 2016-11-09 21:29:38 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:29:54 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 16s. Last read position: chr7:53,850,313
INFO 2016-11-09 21:29:54 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:30:17 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 22s. Last read position: chr7:96,503,433
INFO 2016-11-09 21:30:17 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:30:42 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 25s. Last read position: chr7:120,651,846
INFO 2016-11-09 21:30:42 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:30:58 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 15s. Last read position: chr7:146,401,497
INFO 2016-11-09 21:30:58 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:31:18 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 20s. Last read position: chr8:17,030,519
INFO 2016-11-09 21:31:18 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:31:37 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 18s. Last read position: chr8:42,750,671
INFO 2016-11-09 21:31:37 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:31:59 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 21s. Last read position: chr8:85,385,487
INFO 2016-11-09 21:31:59 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:32:31 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 32s. Last read position: chr8:124,358,985
INFO 2016-11-09 21:32:31 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:33:07 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 35s. Last read position: chr9:18,183,883
INFO 2016-11-09 21:33:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:33:37 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 30s. Last read position: chr9:84,163,983
INFO 2016-11-09 21:33:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:34:05 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 27s. Last read position: chr9:119,875,535
INFO 2016-11-09 21:34:05 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:34:27 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 21s. Last read position: chr10:5,661,683
INFO 2016-11-09 21:34:27 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 21:34:59 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:14:28s. Time for last 1,000,000: 32s. Last read position: chr10:29,748,948
INFO 2016-11-09 21:34:59 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:35:22 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:14:51s. Time for last 1,000,000: 23s. Last read position: chr10:61,280,221
INFO 2016-11-09 21:35:22 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:35:53 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:15:22s. Time for last 1,000,000: 30s. Last read position: chr10:85,305,552
INFO 2016-11-09 21:35:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:36:18 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:15:46s. Time for last 1,000,000: 24s. Last read position: chr10:108,129,202
INFO 2016-11-09 21:36:18 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:36:53 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:16:21s. Time for last 1,000,000: 34s. Last read position: chr10:132,730,123
INFO 2016-11-09 21:36:53 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:37:41 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:17:09s. Time for last 1,000,000: 48s. Last read position: chr11:35,359,267
INFO 2016-11-09 21:37:41 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:38:14 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:17:43s. Time for last 1,000,000: 33s. Last read position: chr11:75,696,431
INFO 2016-11-09 21:38:14 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:38:51 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:18:19s. Time for last 1,000,000: 36s. Last read position: chr11:114,414,621
INFO 2016-11-09 21:38:51 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 21:39:20 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:18:49s. Time for last 1,000,000: 29s. Last read position: chr12:8,900,276
INFO 2016-11-09 21:39:20 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 21:40:02 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:19:31s. Time for last 1,000,000: 41s. Last read position: chr12:38,863,889
INFO 2016-11-09 21:40:02 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:40:35 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:20:04s. Time for last 1,000,000: 33s. Last read position: chr12:60,598,824
INFO 2016-11-09 21:40:35 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:41:05 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:20:33s. Time for last 1,000,000: 29s. Last read position: chr12:88,520,538
INFO 2016-11-09 21:41:05 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 21:41:42 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:21:11s. Time for last 1,000,000: 37s. Last read position: chr12:112,268,437
INFO 2016-11-09 21:41:42 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:42:19 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:21:48s. Time for last 1,000,000: 36s. Last read position: chr13:23,999,632
INFO 2016-11-09 21:42:19 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:42:42 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:22:11s. Time for last 1,000,000: 23s. Last read position: chr13:51,165,870
INFO 2016-11-09 21:42:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:43:19 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:22:48s. Time for last 1,000,000: 37s. Last read position: chr13:88,986,369
INFO 2016-11-09 21:43:19 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:43:56 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:23:25s. Time for last 1,000,000: 36s. Last read position: chr14:23,149,367
INFO 2016-11-09 21:43:56 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 21:44:26 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:23:54s. Time for last 1,000,000: 29s. Last read position: chr14:58,140,905
INFO 2016-11-09 21:44:26 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:45:00 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:24:29s. Time for last 1,000,000: 34s. Last read position: chr14:91,912,553
INFO 2016-11-09 21:45:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:45:29 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:24:57s. Time for last 1,000,000: 28s. Last read position: chr15:38,895,095
INFO 2016-11-09 21:45:29 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:46:11 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:25:40s. Time for last 1,000,000: 42s. Last read position: chr15:68,188,367
INFO 2016-11-09 21:46:11 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 21:46:37 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:26:06s. Time for last 1,000,000: 26s. Last read position: chr15:87,921,272
INFO 2016-11-09 21:46:37 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:47:03 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:26:32s. Time for last 1,000,000: 25s. Last read position: chr16:11,143,813
INFO 2016-11-09 21:47:03 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:47:33 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:27:02s. Time for last 1,000,000: 30s. Last read position: chr16:51,391,437
INFO 2016-11-09 21:47:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:48:02 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:27:30s. Time for last 1,000,000: 28s. Last read position: chr16:84,928,458
INFO 2016-11-09 21:48:02 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:48:35 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:28:04s. Time for last 1,000,000: 33s. Last read position: chr17:18,368,935
INFO 2016-11-09 21:48:35 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:49:07 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:28:36s. Time for last 1,000,000: 32s. Last read position: chr17:44,246,522
INFO 2016-11-09 21:49:07 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:49:40 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:29:09s. Time for last 1,000,000: 32s. Last read position: chr17:66,172,158
INFO 2016-11-09 21:49:40 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO 2016-11-09 21:50:14 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:29:43s. Time for last 1,000,000: 34s. Last read position: chr18:5,619,614
INFO 2016-11-09 21:50:14 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:50:59 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:30:27s. Time for last 1,000,000: 44s. Last read position: chr18:46,152,631
INFO 2016-11-09 21:50:59 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:51:33 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:31:02s. Time for last 1,000,000: 34s. Last read position: chr19:1,328,731
INFO 2016-11-09 21:51:33 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:52:02 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:31:31s. Time for last 1,000,000: 29s. Last read position: chr19:28,148,444
INFO 2016-11-09 21:52:02 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:52:39 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:32:08s. Time for last 1,000,000: 36s. Last read position: chr19:40,341,579
INFO 2016-11-09 21:52:39 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 21:53:19 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:32:48s. Time for last 1,000,000: 40s. Last read position: chr20:3,222,035
INFO 2016-11-09 21:53:19 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:54:19 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:33:47s. Time for last 1,000,000: 59s. Last read position: chr20:37,218,903
INFO 2016-11-09 21:54:19 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:54:53 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:34:22s. Time for last 1,000,000: 34s. Last read position: chr20:62,871,367
INFO 2016-11-09 21:54:53 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO 2016-11-09 21:55:29 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:34:58s. Time for last 1,000,000: 36s. Last read position: chr21:39,474,524
INFO 2016-11-09 21:55:29 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:56:01 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:35:30s. Time for last 1,000,000: 31s. Last read position: chr22:31,346,944
INFO 2016-11-09 21:56:01 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 21:56:33 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:36:02s. Time for last 1,000,000: 32s. Last read position: chrX:6,235,951
INFO 2016-11-09 21:56:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:57:09 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:36:38s. Time for last 1,000,000: 35s. Last read position: chrX:38,820,975
INFO 2016-11-09 21:57:09 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:57:43 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:37:11s. Time for last 1,000,000: 33s. Last read position: chrX:69,473,954
INFO 2016-11-09 21:57:43 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:58:20 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:37:48s. Time for last 1,000,000: 36s. Last read position: chrX:92,683,143
INFO 2016-11-09 21:58:20 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:58:52 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:38:20s. Time for last 1,000,000: 32s. Last read position: chrX:118,447,518
INFO 2016-11-09 21:58:52 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 21:59:29 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:38:58s. Time for last 1,000,000: 37s. Last read position: chrX:142,819,613
INFO 2016-11-09 21:59:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:00:14 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:39:43s. Time for last 1,000,000: 44s. Last read position: chrM:3,995
INFO 2016-11-09 22:00:14 MarkDuplicates Tracking 7472 as yet unmatched pairs. 7472 records in RAM.
INFO 2016-11-09 22:00:40 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:40:08s. Time for last 1,000,000: 25s. Last read position: chrM:11,775
INFO 2016-11-09 22:00:40 MarkDuplicates Tracking 14000 as yet unmatched pairs. 14000 records in RAM.
INFO 2016-11-09 22:01:10 MarkDuplicates Read 99989486 records. 0 pairs never matched.
INFO 2016-11-09 22:01:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 2700102224; totalMemory: 2727870464; maxMemory: 3817865216
INFO 2016-11-09 22:01:17 MarkDuplicates Will retain up to 119308288 duplicate indices before spilling to disk.
INFO 2016-11-09 22:01:17 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2016-11-09 22:01:35 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2016-11-09 22:02:09 MarkDuplicates Sorting list of duplicate records.
INFO 2016-11-09 22:02:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 1794152960; totalMemory: 2776104960; maxMemory: 3817865216
INFO 2016-11-09 22:02:09 MarkDuplicates Marking 496224 records as duplicates.
INFO 2016-11-09 22:02:09 MarkDuplicates Found 42648 optical duplicate clusters.
INFO 2016-11-09 22:21:20 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:17:00s. Time for last 10,000,000: 1,020s. Last read position: chr2:3,652,468
INFO 2016-11-09 22:28:57 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:24:37s. Time for last 10,000,000: 457s. Last read position: chr3:128,121,129
INFO 2016-11-09 22:32:35 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:28:15s. Time for last 10,000,000: 217s. Last read position: chr5:86,336,676
INFO 2016-11-09 22:36:11 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:31:51s. Time for last 10,000,000: 216s. Last read position: chr6:156,918,595
INFO 2016-11-09 22:40:46 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:36:27s. Time for last 10,000,000: 275s. Last read position: chr9:18,183,883
INFO 2016-11-09 22:45:45 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:41:25s. Time for last 10,000,000: 298s. Last read position: chr11:75,696,431
INFO 2016-11-09 22:52:05 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:47:45s. Time for last 10,000,000: 380s. Last read position: chr14:23,149,367
[Wed Nov 09 22:54:25 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 93.91 minutes.
Runtime.totalMemory()=2845835264
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; file: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam
at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:208)
at htsjdk.samtools.util.BlockCompressedOutputStream.writeGzipBlock(BlockCompressedOutputStream.java:331)
at htsjdk.samtools.util.BlockCompressedOutputStream.deflateBlock(BlockCompressedOutputStream.java:294)
at htsjdk.samtools.util.BlockCompressedOutputStream.write(BlockCompressedOutputStream.java:194)
at java.io.DataOutputStream.write(DataOutputStream.java:107)
at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:206)
at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:198)
at htsjdk.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:154)
at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:127)
at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:177)
at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:194)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:326)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.write(BufferedOutputStream.java:126)
at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:206)
... 13 more
--------------------Post mortem info--------------------
==============================================================
job_number: 6254
exec_file: job_scripts/6254
submission_time: Wed Nov 9 18:32:06 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/SRR1370899_1
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/chipseq.bds.20161109_175126_129_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.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/SRR1370899_1/chipseq.bds.20161109_175126_129_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.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=14548.SRR1370899_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/SRR1370899_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=00:30:15, mem=5291.50433 GBs, io=65.45171, vmem=27.129M, maxvmem=2.969G
scheduling info: queue instance "amd.q@wotan" dropped because it is full
queue instance "q@kali" dropped because it is full
queue instance "q@kadru" dropped because it is full
queue instance "q@surya" dropped because it is full
queue instance "q@nandi" 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; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 147
bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out/align/rep1/SRR1370899_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370899_1.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out/align/rep1/SRR1370899_1.bam
# SYS command. line 149
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out/align/rep1/SRR1370899_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out/qc/rep1/SRR1370899_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--------------------
27326 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.55 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.48 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.68 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.87 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.74 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.57 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.74 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.22 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.25 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.00 sec
[bwa_aln_core] refine gapped alignments... 2.42 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.75 sec
[bwa_aln_core] refine gapped alignments... 4.76 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.52 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.66 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.39 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 36.79 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.46 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.62 sec
[bwa_aln_core] refine gapped alignments... 3.21 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.40 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.35 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.13 sec
[bwa_aln_core] refine gapped alignments... 0.87 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.96 sec
[bwa_aln_core] refine gapped alignments... 1.24 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.65 sec
[bwa_aln_core] refine gapped alignments... 1.65 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.19 sec
[bwa_aln_core] refine gapped alignments... 1.68 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.66 sec
[bwa_aln_core] refine gapped alignments... 1.90 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.72 sec
[bwa_aln_core] refine gapped alignments... 2.37 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.75 sec
[bwa_aln_core] refine gapped alignments... 2.70 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.53 sec
[bwa_aln_core] refine gapped alignments... 3.13 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.63 sec
[bwa_aln_core] refine gapped alignments... 3.74 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.76 sec
[bwa_aln_core] refine gapped alignments... 4.05 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.13 sec
[bwa_aln_core] refine gapped alignments... 5.37 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.86 sec
[bwa_aln_core] refine gapped alignments... 4.85 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.90 sec
[bwa_aln_core] refine gapped alignments... 5.33 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.70 sec
[bwa_aln_core] refine gapped alignments... 5.34 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.10 sec
[bwa_aln_core] refine gapped alignments... 5.40 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.47 sec
[bwa_aln_core] refine gapped alignments... 5.23 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.21 sec
[bwa_aln_core] refine gapped alignments... 5.20 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.24 sec
[bwa_aln_core] refine gapped alignments... 4.75 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.07 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.34 sec
[bwa_aln_core] refine gapped alignments... 3.46 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.22 sec
[bwa_aln_core] refine gapped alignments... 0.80 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.50 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.12 sec
[bwa_aln_core] refine gapped alignments... 1.36 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.96 sec
[bwa_aln_core] refine gapped alignments... 2.03 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.00 sec
[bwa_aln_core] refine gapped alignments... 1.19 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.01 sec
[bwa_aln_core] refine gapped alignments... 1.91 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.23 sec
[bwa_aln_core] refine gapped alignments... 3.17 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.08 sec
[bwa_aln_core] refine gapped alignments... 3.46 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.24 sec
[bwa_aln_core] refine gapped alignments... 2.62 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.82 sec
[bwa_aln_core] refine gapped alignments... 1.80 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.12 sec
[bwa_aln_core] refine gapped alignments... 2.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.78 sec
[bwa_aln_core] refine gapped alignments... 1.30 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.31 sec
[bwa_aln_core] refine gapped alignments... 1.62 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.29 sec
[bwa_aln_core] refine gapped alignments... 5.03 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.86 sec
[bwa_aln_core] refine gapped alignments... 4.52 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.72 sec
[bwa_aln_core] refine gapped alignments... 0.76 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.58 sec
[bwa_aln_core] refine gapped alignments... 3.23 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.36 sec
[bwa_aln_core] refine gapped alignments... 4.56 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.15 sec
[bwa_aln_core] refine gapped alignments... 0.78 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.20 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.58 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.68 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.81 sec
[bwa_aln_core] refine gapped alignments... 1.51 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.14 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.47 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.75 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.90 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.06 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.21 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.73 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.08 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.76 sec
[bwa_aln_core] refine gapped alignments... 1.47 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.07 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.58 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.30 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.85 sec
[bwa_aln_core] refine gapped alignments... 1.32 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.97 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.59 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 19892923 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out/align/rep1/SRR1370899_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370899_1.fastq.gz
[main] Real time: 2368.699 sec; CPU: 2261.220 sec
sambamba-sort: Unable to write to stream
--------------------Post mortem info--------------------
==============================================================
job_number: 6414
exec_file: job_scripts/6414
submission_time: Wed Nov 9 21:02:34 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/SRR1370899_1
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/chipseq.bds.20161109_175126_129_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_13.stderr.cluster
mail_list: imk1@surya
notify: FALSE
job_name: STDIN
stdout_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/chipseq.bds.20161109_175126_129_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_13.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=14548.SRR1370899_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/SRR1370899_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=00:42:22, mem=4618.36249 GBs, io=835.83406, vmem=834.789M, maxvmem=5.163G
scheduling info: queue instance "amd.q@wotan" dropped because it is full
queue instance "q@surya" dropped because it is full
queue instance "q@nandi" dropped because it is full
queue instance "q@kali" dropped because it is full
queue instance "q@kadru" dropped because it is full
|
| 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, SRR1370899_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370899_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370899_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/SRR1370899_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/SRR1370899_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 | 14548.SRR1370899_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 |