BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161110_115511_263
Start time 2016-11-10 11:55:11
Run time 00:27:27.880
Tasks executed 2
Tasks failed 2
Tasks failed names 
bwa_sam rep1
markdup_bam_picard ctl1
Arguments* [-title, SRR1370891_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370891_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
* Values in global scope when program finished execution.

Timeline

Task Graph

Parallel (threads) details

Thread ID Parent Tasks
thread_Root None
thread_41 thread_Root 
 chipseq.bds.20161110_115511_263_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_11
thread_42 thread_Root 
 chipseq.bds.20161110_115511_263_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_10

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_10
Name markdup_bam_picard ctl1
Thread thread_42
PID 6613
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus 1
Mem
Start 2016-11-10 11:55:13
End 2016-11-10 11:55:13
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc
Dependencies 
 
# 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/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_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/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_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--------------------
42685 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Thu Nov 10 11:55:32 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Thu Nov 10 11:55:32 PST 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-10 11:55:32	MarkDuplicates	Start of doWork freeMemory: 254879344; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-10 11:55:32	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-10 11:55:32	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-11-10 11:55:40	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:07s.  Time for last 1,000,000:    7s.  Last read position: chr1:22,298,551
INFO	2016-11-10 11:55:40	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:55:46	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:13s.  Time for last 1,000,000:    5s.  Last read position: chr1:41,895,424
INFO	2016-11-10 11:55:46	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 11:55:58	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:26s.  Time for last 1,000,000:   12s.  Last read position: chr1:63,396,527
INFO	2016-11-10 11:55:58	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:56:07	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:34s.  Time for last 1,000,000:    8s.  Last read position: chr1:89,147,707
INFO	2016-11-10 11:56:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:56:18	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:   11s.  Last read position: chr1:115,615,553
INFO	2016-11-10 11:56:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:56:31	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:59s.  Time for last 1,000,000:   13s.  Last read position: chr1:164,468,682
INFO	2016-11-10 11:56:31	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 11:56:45	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:   13s.  Last read position: chr1:189,102,252
INFO	2016-11-10 11:56:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:57:04	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:31s.  Time for last 1,000,000:   18s.  Last read position: chr1:213,979,760
INFO	2016-11-10 11:57:04	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:57:17	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:01:44s.  Time for last 1,000,000:   13s.  Last read position: chr1:231,814,268
INFO	2016-11-10 11:57:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:57:37	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:02:04s.  Time for last 1,000,000:   20s.  Last read position: chr2:3,652,468
INFO	2016-11-10 11:57:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:57:53	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:02:21s.  Time for last 1,000,000:   16s.  Last read position: chr2:39,505,122
INFO	2016-11-10 11:57:53	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:58:05	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:   11s.  Last read position: chr2:73,561,393
INFO	2016-11-10 11:58:05	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:58:16	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:02:43s.  Time for last 1,000,000:   11s.  Last read position: chr2:120,526,571
INFO	2016-11-10 11:58:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:58:30	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:02:58s.  Time for last 1,000,000:   14s.  Last read position: chr2:160,316,783
INFO	2016-11-10 11:58:30	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:58:55	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:03:22s.  Time for last 1,000,000:   24s.  Last read position: chr2:195,549,735
INFO	2016-11-10 11:58:55	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 11:59:04	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:03:31s.  Time for last 1,000,000:    8s.  Last read position: chr2:230,358,034
INFO	2016-11-10 11:59:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 11:59:16	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:03:43s.  Time for last 1,000,000:   12s.  Last read position: chr3:16,305,780
INFO	2016-11-10 11:59:16	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 11:59:26	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:03:54s.  Time for last 1,000,000:   10s.  Last read position: chr3:49,251,279
INFO	2016-11-10 11:59:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 11:59:42	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:04:09s.  Time for last 1,000,000:   15s.  Last read position: chr3:84,621,225
INFO	2016-11-10 11:59:42	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:00:04	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:04:31s.  Time for last 1,000,000:   22s.  Last read position: chr3:128,121,129
INFO	2016-11-10 12:00:04	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:00:14	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:04:41s.  Time for last 1,000,000:   10s.  Last read position: chr3:165,373,238
INFO	2016-11-10 12:00:14	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:00:24	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:04:51s.  Time for last 1,000,000:    9s.  Last read position: chr3:195,333,247
INFO	2016-11-10 12:00:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:00:35	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:05:03s.  Time for last 1,000,000:   11s.  Last read position: chr4:37,752,582
INFO	2016-11-10 12:00:35	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:00:45	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:05:12s.  Time for last 1,000,000:    9s.  Last read position: chr4:81,286,306
INFO	2016-11-10 12:00:45	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:01:04	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:05:31s.  Time for last 1,000,000:   18s.  Last read position: chr4:119,339,736
INFO	2016-11-10 12:01:04	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:01:14	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:05:42s.  Time for last 1,000,000:   10s.  Last read position: chr4:158,818,783
INFO	2016-11-10 12:01:14	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:01:27	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:   12s.  Last read position: chr5:6,447,551
INFO	2016-11-10 12:01:27	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-10 12:01:42	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:06:09s.  Time for last 1,000,000:   15s.  Last read position: chr5:33,219,021
INFO	2016-11-10 12:01:42	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:01:57	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:06:25s.  Time for last 1,000,000:   15s.  Last read position: chr5:60,694,078
INFO	2016-11-10 12:01:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:02:19	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:06:46s.  Time for last 1,000,000:   21s.  Last read position: chr5:86,336,676
INFO	2016-11-10 12:02:19	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:02:27	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:06:55s.  Time for last 1,000,000:    8s.  Last read position: chr5:112,930,184
INFO	2016-11-10 12:02:27	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:02:36	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:07:03s.  Time for last 1,000,000:    8s.  Last read position: chr5:136,852,889
INFO	2016-11-10 12:02:36	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:02:45	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:07:13s.  Time for last 1,000,000:    9s.  Last read position: chr5:160,271,193
INFO	2016-11-10 12:02:45	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:03:01	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:07:28s.  Time for last 1,000,000:   15s.  Last read position: chr6:4,126,386
INFO	2016-11-10 12:03:01	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:03:14	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:07:41s.  Time for last 1,000,000:   13s.  Last read position: chr6:28,666,579
INFO	2016-11-10 12:03:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:03:23	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:07:50s.  Time for last 1,000,000:    8s.  Last read position: chr6:49,527,281
INFO	2016-11-10 12:03:23	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:03:32	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:08:00s.  Time for last 1,000,000:    9s.  Last read position: chr6:81,728,195
INFO	2016-11-10 12:03:32	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:03:41	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:08:08s.  Time for last 1,000,000:    8s.  Last read position: chr6:107,535,760
INFO	2016-11-10 12:03:41	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:03:55	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:08:23s.  Time for last 1,000,000:   14s.  Last read position: chr6:132,364,408
INFO	2016-11-10 12:03:55	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:04:12	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:08:39s.  Time for last 1,000,000:   16s.  Last read position: chr6:156,918,595
INFO	2016-11-10 12:04:12	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:04:26	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:08:53s.  Time for last 1,000,000:   13s.  Last read position: chr7:18,636,743
INFO	2016-11-10 12:04:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:04:41	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:09:08s.  Time for last 1,000,000:   15s.  Last read position: chr7:53,850,313
INFO	2016-11-10 12:04:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:04:53	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:09:20s.  Time for last 1,000,000:   12s.  Last read position: chr7:96,503,433
INFO	2016-11-10 12:04:53	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:05:01	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:09:28s.  Time for last 1,000,000:    8s.  Last read position: chr7:120,651,846
INFO	2016-11-10 12:05:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:05:15	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:09:42s.  Time for last 1,000,000:   14s.  Last read position: chr7:146,401,497
INFO	2016-11-10 12:05:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:05:26	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:09:53s.  Time for last 1,000,000:   11s.  Last read position: chr8:17,030,519
INFO	2016-11-10 12:05:26	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:05:37	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:10:05s.  Time for last 1,000,000:   11s.  Last read position: chr8:42,750,671
INFO	2016-11-10 12:05:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:05:47	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:10:14s.  Time for last 1,000,000:    9s.  Last read position: chr8:85,385,487
INFO	2016-11-10 12:05:47	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:06:01	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:10:28s.  Time for last 1,000,000:   13s.  Last read position: chr8:124,358,985
INFO	2016-11-10 12:06:01	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:06:10	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:10:37s.  Time for last 1,000,000:    9s.  Last read position: chr9:18,183,883
INFO	2016-11-10 12:06:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:06:26	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:10:53s.  Time for last 1,000,000:   16s.  Last read position: chr9:84,163,983
INFO	2016-11-10 12:06:26	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:06:37	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:11:04s.  Time for last 1,000,000:   10s.  Last read position: chr9:119,875,535
INFO	2016-11-10 12:06:37	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:06:50	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:11:17s.  Time for last 1,000,000:   13s.  Last read position: chr10:5,661,683
INFO	2016-11-10 12:06:50	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:07:07	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:11:34s.  Time for last 1,000,000:   17s.  Last read position: chr10:29,748,948
INFO	2016-11-10 12:07:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:07:16	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:11:44s.  Time for last 1,000,000:    9s.  Last read position: chr10:61,280,221
INFO	2016-11-10 12:07:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:07:28	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:11:56s.  Time for last 1,000,000:   12s.  Last read position: chr10:85,305,552
INFO	2016-11-10 12:07:28	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:07:41	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:12:09s.  Time for last 1,000,000:   13s.  Last read position: chr10:108,129,202
INFO	2016-11-10 12:07:41	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:07:52	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:12:19s.  Time for last 1,000,000:   10s.  Last read position: chr10:132,730,123
INFO	2016-11-10 12:07:52	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:08:12	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:12:39s.  Time for last 1,000,000:   20s.  Last read position: chr11:35,359,267
INFO	2016-11-10 12:08:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:08:23	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:12:50s.  Time for last 1,000,000:   11s.  Last read position: chr11:75,696,431
INFO	2016-11-10 12:08:23	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:08:35	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:13:02s.  Time for last 1,000,000:   11s.  Last read position: chr11:114,414,621
INFO	2016-11-10 12:08:35	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:08:55	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:13:22s.  Time for last 1,000,000:   19s.  Last read position: chr12:8,900,276
INFO	2016-11-10 12:08:55	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:09:04	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:13:31s.  Time for last 1,000,000:    9s.  Last read position: chr12:38,863,889
INFO	2016-11-10 12:09:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:09:12	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:13:40s.  Time for last 1,000,000:    8s.  Last read position: chr12:60,598,824
INFO	2016-11-10 12:09:12	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:09:22	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:13:50s.  Time for last 1,000,000:   10s.  Last read position: chr12:88,520,538
INFO	2016-11-10 12:09:22	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:09:34	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:14:01s.  Time for last 1,000,000:   11s.  Last read position: chr12:112,268,437
INFO	2016-11-10 12:09:34	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:09:41	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:14:08s.  Time for last 1,000,000:    7s.  Last read position: chr13:23,999,632
INFO	2016-11-10 12:09:41	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:09:50	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:14:17s.  Time for last 1,000,000:    8s.  Last read position: chr13:51,165,870
INFO	2016-11-10 12:09:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:10:07	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:14:34s.  Time for last 1,000,000:   17s.  Last read position: chr13:88,986,369
INFO	2016-11-10 12:10:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:10:16	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:14:43s.  Time for last 1,000,000:    8s.  Last read position: chr14:23,149,367
INFO	2016-11-10 12:10:16	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:10:29	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:14:56s.  Time for last 1,000,000:   13s.  Last read position: chr14:58,140,905
INFO	2016-11-10 12:10:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:10:41	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:15:08s.  Time for last 1,000,000:   12s.  Last read position: chr14:91,912,553
INFO	2016-11-10 12:10:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:10:52	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:15:19s.  Time for last 1,000,000:   11s.  Last read position: chr15:38,895,095
INFO	2016-11-10 12:10:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:11:10	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:15:37s.  Time for last 1,000,000:   17s.  Last read position: chr15:68,188,367
INFO	2016-11-10 12:11:10	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:11:17	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:15:44s.  Time for last 1,000,000:    7s.  Last read position: chr15:87,921,272
INFO	2016-11-10 12:11:17	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:11:31	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:15:58s.  Time for last 1,000,000:   13s.  Last read position: chr16:11,143,813
INFO	2016-11-10 12:11:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:11:46	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:16:13s.  Time for last 1,000,000:   15s.  Last read position: chr16:51,391,437
INFO	2016-11-10 12:11:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:11:58	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:16:26s.  Time for last 1,000,000:   12s.  Last read position: chr16:84,928,458
INFO	2016-11-10 12:11:58	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:12:06	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:16:34s.  Time for last 1,000,000:    8s.  Last read position: chr17:18,368,935
INFO	2016-11-10 12:12:06	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:12:18	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:16:45s.  Time for last 1,000,000:   11s.  Last read position: chr17:44,246,522
INFO	2016-11-10 12:12:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:12:27	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:16:54s.  Time for last 1,000,000:    9s.  Last read position: chr17:66,172,158
INFO	2016-11-10 12:12:27	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 12:12:38	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:17:06s.  Time for last 1,000,000:   11s.  Last read position: chr18:5,619,614
INFO	2016-11-10 12:12:38	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:12:50	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:17:17s.  Time for last 1,000,000:   11s.  Last read position: chr18:46,152,631
INFO	2016-11-10 12:12:50	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:12:58	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:17:25s.  Time for last 1,000,000:    8s.  Last read position: chr19:1,328,731
INFO	2016-11-10 12:12:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:13:07	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:17:35s.  Time for last 1,000,000:    9s.  Last read position: chr19:28,148,444
INFO	2016-11-10 12:13:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:13:24	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:17:51s.  Time for last 1,000,000:   16s.  Last read position: chr19:40,341,579
INFO	2016-11-10 12:13:24	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:13:35	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:18:02s.  Time for last 1,000,000:   10s.  Last read position: chr20:3,222,035
INFO	2016-11-10 12:13:35	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:13:46	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:18:13s.  Time for last 1,000,000:   11s.  Last read position: chr20:37,218,903
INFO	2016-11-10 12:13:46	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:14:07	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:18:35s.  Time for last 1,000,000:   21s.  Last read position: chr20:62,871,367
INFO	2016-11-10 12:14:07	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-10 12:14:21	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:18:48s.  Time for last 1,000,000:   13s.  Last read position: chr21:39,474,524
INFO	2016-11-10 12:14:21	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:14:38	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:19:05s.  Time for last 1,000,000:   17s.  Last read position: chr22:31,346,944
INFO	2016-11-10 12:14:38	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-10 12:14:52	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:19:19s.  Time for last 1,000,000:   14s.  Last read position: chrX:6,235,951
INFO	2016-11-10 12:14:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:15:04	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:19:31s.  Time for last 1,000,000:   11s.  Last read position: chrX:38,820,975
INFO	2016-11-10 12:15:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-10 12:15:14	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:19:41s.  Time for last 1,000,000:   10s.  Last read position: chrX:69,473,954
INFO	2016-11-10 12:15:14	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:15:29	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:19:57s.  Time for last 1,000,000:   15s.  Last read position: chrX:92,683,143
INFO	2016-11-10 12:15:29	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-10 12:15:43	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:20:10s.  Time for last 1,000,000:   13s.  Last read position: chrX:118,447,518
INFO	2016-11-10 12:15:43	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-10 12:15:52	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:20:19s.  Time for last 1,000,000:    8s.  Last read position: chrX:142,819,613
INFO	2016-11-10 12:15:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-10 12:16:01	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:20:28s.  Time for last 1,000,000:    9s.  Last read position: chrM:3,995
INFO	2016-11-10 12:16:01	MarkDuplicates	Tracking 7472 as yet unmatched pairs. 7472 records in RAM.
INFO	2016-11-10 12:16:12	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:20:40s.  Time for last 1,000,000:   11s.  Last read position: chrM:11,775
INFO	2016-11-10 12:16:12	MarkDuplicates	Tracking 14000 as yet unmatched pairs. 14000 records in RAM.
INFO	2016-11-10 12:16:21	MarkDuplicates	Read 99989486 records. 0 pairs never matched.
INFO	2016-11-10 12:16:28	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2913601568; totalMemory: 2941255680; maxMemory: 3817865216
INFO	2016-11-10 12:16:28	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-10 12:16:28	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-10 12:16:47	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-10 12:17:18	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-10 12:17:18	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2006469808; totalMemory: 2988441600; maxMemory: 3817865216
INFO	2016-11-10 12:17:18	MarkDuplicates	Marking 496224 records as duplicates.
INFO	2016-11-10 12:17:18	MarkDuplicates	Found 42648 optical duplicate clusters.
[Thu Nov 10 12:19:15 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 23.72 minutes.
Runtime.totalMemory()=3019898880
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/SRR1370891_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:160)
	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:                 6613
exec_file:                  job_scripts/6613
submission_time:            Thu Nov 10 11:55:13 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/SRR1370891_1
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/chipseq.bds.20161110_115511_263_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_10.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/chipseq.bds.20161110_115511_263_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_10.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=41335.SRR1370891_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/SRR1370891_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=00:15:32, mem=2716.03229 GBs, io=20.37517, vmem=2.968G, maxvmem=2.968G
scheduling info:            queue instance "amd.q@wotan" dropped because it is full
                            queue instance "q@nandi" dropped because it is full
                            queue instance "q@kadru" dropped because it is full
                            queue instance "q@kali" dropped because it is full
                            queue instance "q@surya" dropped because it is full
Num 2
ID task.align_bwa.bwa_sam_rep1.line_140.id_11
Name bwa_sam rep1
Thread thread_41
PID 6614
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus 1
Mem
Start 2016-11-10 11:55:14
End 2016-11-10 11:55:14
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370891_1.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/rep1/SRR1370891_1.sai
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/rep1/SRR1370891_1.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/qc/rep1/SRR1370891_1.flagstat.qc
Dependencies 
 
# 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/SRR1370891_1/out/align/rep1/SRR1370891_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370891_1.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/rep1/SRR1370891_1.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/align/rep1/SRR1370891_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out/qc/rep1/SRR1370891_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--------------------
42683 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.34 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.65 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.82 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.54 sec
[bwa_aln_core] refine gapped alignments... 2.79 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.75 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.28 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.71 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.81 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.79 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.95 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.93 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.79 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.07 sec
[bwa_aln_core] refine gapped alignments... 1.02 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.98 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.83 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.36 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.54 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.72 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.85 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.08 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.29 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.86 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.64 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.18 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.11 sec
[bwa_aln_core] refine gapped alignments... 1.47 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.99 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.29 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.27 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.92 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.10 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.20 sec
[bwa_aln_core] refine gapped alignments... 4.52 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.02 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.94 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.57 sec
[bwa_aln_core] refine gapped alignments... 0.54 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.00 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.94 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.67 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.85 sec
[bwa_aln_core] refine gapped alignments... 5.50 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.17 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.84 sec
[bwa_aln_core] refine gapped alignments... 3.08 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 9.10 sec
[bwa_aln_core] refine gapped alignments... 1.70 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.63 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.41 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.01 sec
[bwa_aln_core] refine gapped alignments... 2.59 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.21 sec
[bwa_aln_core] refine gapped alignments... 2.33 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.15 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.87 sec
[bwa_aln_core] refine gapped alignments... 0.62 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.79 sec
[bwa_aln_core] refine gapped alignments... 2.01 sec
[bwa_aln_core] print alignments... 0.86 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.61 sec
[bwa_aln_core] refine gapped alignments... 2.51 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.70 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.68 sec
[bwa_aln_core] refine gapped alignments... 0.59 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.75 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.84 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.02 sec
[bwa_aln_core] refine gapped alignments... 3.55 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 51.31 sec
[bwa_aln_core] refine gapped alignments... 0.68 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.19 sec
[bwa_aln_core] refine gapped alignments... 1.55 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.55 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.00 sec
[bwa_aln_core] refine gapped alignments... 0.67 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... 40.61 sec
[bwa_aln_core] refine gapped alignments... 4.14 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.26 sec
[bwa_aln_core] refine gapped alignments... 3.36 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.21 sec
[bwa_aln_core] refine gapped alignments... 2.82 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.40 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.18 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.56 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.83 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.69 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 5.62 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 4.05 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.87 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.72 sec
[bwa_aln_core] refine gapped alignments... 0.56 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.71 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.13 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.15 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.78 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.08 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.30 sec
[bwa_aln_core] 19293935 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/SRR1370891_1/out/align/rep1/SRR1370891_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370891_1.fastq.gz
[main] Real time: 1468.413 sec; CPU: 1212.996 sec

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 6614
exec_file:                  job_scripts/6614
submission_time:            Thu Nov 10 11:55:14 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/SRR1370891_1
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/chipseq.bds.20161110_115511_263_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_11.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/chipseq.bds.20161110_115511_263_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_11.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=41335.SRR1370891_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/SRR1370891_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=00:25:52, mem=2432.55150 GBs, io=809.85092, vmem=845.195M, maxvmem=5.350G
scheduling info:            queue instance "q@kali" dropped because it is full
                            queue instance "q@kadru" 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 "amd.q@wotan" dropped because it is full

Global scope

Note: Global scope when program finished execution.
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, SRR1370891_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370891_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370891_1.fastq.gz, -ctl_bam, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.bam, -final_stage, xcor, $]
string ASCPKEY /software/ascp/etc/asperaweb_id_dsa.openssh
bool canFail false
int cpus -1
int cpusLocal 56
int day 86400
string DEEPLIFT_DIR /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift
string DERBY_HOME /usr/lib/jvm/java-8-oracle/db
string DISPLAY localhost:12.0
real E 2.718281828459045
string ENHANCER_SCRIPTS_DIR /srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
int G 1073741824
string HOME /users/imk1/
int hour 3600
string J2REDIR /usr/lib/jvm/java-8-oracle/jre
string J2SDKDIR /usr/lib/jvm/java-8-oracle
string JAVA_HOME /usr/lib/jvm/java-8-oracle
int K 1024
string KERAS_DIR /users/imk1/.local/lib/python2.7/site-packages/keras/
string KRB5CCNAME FILE:/tmp/krb5cc_1048_N5SeQf
string LANG en_US.UTF-8
string LOADEDMODULES modsappsdir/modsappsdir:sratoolkit/2.5.2:ascp/3.5.6
string LOGNAME imk1
int M 1048576
string MAIL /var/mail/imk1
int mem -1
int minute 60
string MODULE_VERSION 3.2.10
string MODULE_VERSION_STACK 3.2.10
string MODULEPATH /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$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/SRR1370891_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/SRR1370891_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 41335.SRR1370891_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