| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161113_130809_674 |
| Start time | 2016-11-13 13:08:09 |
| Run time | 07:25:57.315 |
| Tasks executed | 9 |
| Tasks failed | 1 |
| Tasks failed names | xcor rep1 |
| Arguments* | [-title, SRR1370902_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370902_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.20161113_130809_674_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_11 chipseq.bds.20161113_130809_674_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_505.id_13 |
| thread_41 | thread_Root | chipseq.bds.20161113_130809_674_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_10 chipseq.bds.20161113_130809_674_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_12 chipseq.bds.20161113_130809_674_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_14 chipseq.bds.20161113_130809_674_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_15 chipseq.bds.20161113_130809_674_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_16 chipseq.bds.20161113_130809_674_parallel_41/task.postalign_bed.spr_rep1.line_255.id_17 chipseq.bds.20161113_130809_674_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_18 |
| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr | ||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 105
if [[ 0 > 0 ]]; then \
sambamba sort -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.bam | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.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-------------------- 11793 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 146
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 150
samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
# SYS command. line 153
sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam
# SYS command. line 155
sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/qc/ctl1/ss_50M_2000_GRCh38.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
grep -v 'chrM' | sort | uniq -c | \
awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/qc/ctl1/ss_50M_2000_GRCh38.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 56703 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 350
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 354
export _JAVA_OPTIONS="-Xms256M -Xmx12G -XX:ParallelGCThreads=1"
# SYS command. line 360
if [ -f "${PICARDROOT}/picard.jar" ]; then \
MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
fi
# SYS command. line 369
if [ -f "${MARKDUP}" ]; then \
java -Xmx4G -jar ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/qc/rep1/SRR1370902_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/qc/rep1/SRR1370902_1.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 381
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 20180 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1 [Sun Nov 13 15:25:50 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/qc/rep1/SRR1370902_1.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 [Sun Nov 13 15:25:50 PST 2016] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater INFO 2016-11-13 15:25:51 MarkDuplicates Start of doWork freeMemory: 254879472; totalMemory: 257425408; maxMemory: 11453595648 INFO 2016-11-13 15:25:51 MarkDuplicates Reading input file and constructing read end information. INFO 2016-11-13 15:25:51 MarkDuplicates Will retain up to 44052290 data points before spilling to disk. INFO 2016-11-13 15:26:02 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 9s. Last read position: chr1:113,406,284 INFO 2016-11-13 15:26:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:26:09 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 6s. Last read position: chr1:242,572,952 INFO 2016-11-13 15:26:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:26:15 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 6s. Last read position: chr2:179,974,937 INFO 2016-11-13 15:26:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:26:21 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 6s. Last read position: chr3:99,856,183 INFO 2016-11-13 15:26:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:26:25 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 3s. Last read position: chr4:85,400,811 INFO 2016-11-13 15:26:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:26:33 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 7s. Last read position: chr5:51,613,490 INFO 2016-11-13 15:26:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:26:38 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 4s. Last read position: chr5:170,177,307 INFO 2016-11-13 15:26:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:26:43 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 5s. Last read position: chr6:111,624,800 INFO 2016-11-13 15:26:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:26:50 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 6s. Last read position: chr7:93,199,168 INFO 2016-11-13 15:26:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:26:53 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 2s. Last read position: chr8:74,137,422 INFO 2016-11-13 15:26:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:27:01 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 7s. Last read position: chr9:130,521,647 INFO 2016-11-13 15:27:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:27:07 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 6s. Last read position: chr10:114,535,960 INFO 2016-11-13 15:27:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:27:10 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 3s. Last read position: chr12:11,858,010 INFO 2016-11-13 15:27:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:27:26 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 16s. Last read position: chr12:132,629,816 INFO 2016-11-13 15:27:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:27:30 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 3s. Last read position: chr14:88,630,635 INFO 2016-11-13 15:27:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:27:36 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 6s. Last read position: chr16:52,041,672 INFO 2016-11-13 15:27:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:27:40 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 3s. Last read position: chr18:9,650,892 INFO 2016-11-13 15:27:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:27:43 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 3s. Last read position: chr20:11,997,903 INFO 2016-11-13 15:27:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:27:48 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 5s. Last read position: chrX:15,141,651 INFO 2016-11-13 15:27:48 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:27:51 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 3s. Last read position: chrX:153,347,979 INFO 2016-11-13 15:27:51 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-11-13 15:27:58 MarkDuplicates Read 20058721 records. 0 pairs never matched. INFO 2016-11-13 15:28:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 4183254320; totalMemory: 5898764288; maxMemory: 11453595648 INFO 2016-11-13 15:28:01 MarkDuplicates Will retain up to 357924864 duplicate indices before spilling to disk. INFO 2016-11-13 15:28:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-11-13 15:28:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-11-13 15:28:02 MarkDuplicates Sorting list of duplicate records. INFO 2016-11-13 15:28:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 6008816840; totalMemory: 8950644736; maxMemory: 11453595648 INFO 2016-11-13 15:28:32 MarkDuplicates Marking 1205292 records as duplicates. INFO 2016-11-13 15:28:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-11-13 15:30:17 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:45s. Time for last 10,000,000: 105s. Last read position: chr8:74,137,422 INFO 2016-11-13 15:32:05 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:03:33s. Time for last 10,000,000: 108s. Last read position: chrX:153,347,979 INFO 2016-11-13 15:32:06 MarkDuplicates Before output close freeMemory: 8885272048; totalMemory: 8966373376; maxMemory: 11453595648 INFO 2016-11-13 15:32:07 MarkDuplicates After output close freeMemory: 8757868904; totalMemory: 8838971392; maxMemory: 11453595648 [Sun Nov 13 15:32:08 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 6.29 minutes. Runtime.totalMemory()=8838971392 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 507
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 510
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 36837 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 146
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 150
samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.nodup.bam
# SYS command. line 153
sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.nodup.bam
# SYS command. line 155
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/qc/rep1/SRR1370902_1.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.dupmark.bam | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
grep -v 'chrM' | sort | uniq -c | \
awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/qc/rep1/SRR1370902_1.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 54360 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
|
|
|
|
# SYS command. line 507
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 510
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.nodup.tagAlign.gz
# SYS command. line 512
echo
# SYS command. line 514
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 17951 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
|
|
|
|
# SYS command. line 47
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 50
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.nodup.tagAlign.gz | \
grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.nodup.15M.tagAlign.gz
# SYS command. line 53
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 28465 (process ID) old priority 0, new priority 10 Waiting for 27 seconds. | ||||||||||||||||||||||||||||||||||||||||
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|
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|
# SYS command. line 257
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 260
nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.nodup.tagAlign.gz | wc -l )
# SYS command. line 261
nlines=$(( (nlines + 1) / 2 ))
# SYS command. line 265
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.
# SYS command. line 268
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.pr1.tagAlign.gz
# SYS command. line 269
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.00
# SYS command. line 270
gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/pseudo_reps/rep1/pr2/SRR1370902_1.nodup.pr2.tagAlign.gz
# SYS command. line 271
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/pseudo_reps/rep1/pr1/SRR1370902_1.nodup.01
# SYS command. line 273
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 10748 (process ID) old priority 0, new priority 10 | ||||||||||||||||||||||||||||||||||||||||
|
|
|
|
# SYS command. line 214
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 217
if [[ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]]; then RUN_SPP=$(which run_spp_nodups.R); \
else RUN_SPP=$(which run_spp.R); \
fi
# SYS command. line 223
Rscript ${RUN_SPP} -rf \
-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/align/rep1/SRR1370902_1.nodup.15M.tagAlign.gz -p=1 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/qc/rep1/SRR1370902_1.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/qc/rep1/SRR1370902_1.nodup.15M.cc.qc
# SYS command. line 226
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/qc/rep1/SRR1370902_1.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/qc/rep1/SRR1370902_1.nodup.15M.cc.qc.tmp
# SYS command. line 227
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/qc/rep1/SRR1370902_1.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out/qc/rep1/SRR1370902_1.nodup.15M.cc.qc
# SYS command. line 229
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Post mortem info--------------------
==============================================================
job_number: 9915
exec_file: job_scripts/9915
submission_time: Sun Nov 13 20:24:25 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/SRR1370902_1
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/chipseq.bds.20161113_130809_674_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_18.stderr.cluster
mail_list: imk1@surya
notify: FALSE
job_name: STDIN
stdout_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/chipseq.bds.20161113_130809_674_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_18.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=9842.SRR1370902_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/SRR1370902_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
usage 1: cpu=00:00:00, mem=0.02653 GBs, io=0.00786, vmem=181.852M, maxvmem=181.852M
scheduling info: queue instance "q@kali" dropped because it is full
queue instance "q@nandi" dropped because it is full
queue instance "q@surya" dropped because it is full
queue instance "q@kadru" dropped because it is full
queue instance "amd.q@wotan" 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, SRR1370902_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370902_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/SRR1370902_1 |
| string | programName | chipseq.bds |
| string | programPath | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds |
| string | PWD | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370902_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 | 9842.SRR1370902_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 |