BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20161109_220728_345
Start time 2016-11-09 22:07:28
Run time 01:10:17.440
Tasks executed 2
Tasks failed 1
Tasks failed names 
markdup_bam_picard ctl1
Arguments* [-title, SRR1370890_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370890_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_42 thread_Root 
 chipseq.bds.20161109_220728_345_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_10
thread_41 thread_Root 
 chipseq.bds.20161109_220728_345_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_11

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 6452
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus 1
Mem
Start 2016-11-09 22:07:31
End 2016-11-09 22:07:31
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_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/SRR1370890_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_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/SRR1370890_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_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
 
 
--------------------Error message--------------------
Task disappeared from cluster's queue. Task or node failure?
  
--------------------Stdout--------------------
3790 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 09 22:40:48 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Nov 09 22:40:48 PST 2016] Executing as imk1@nandi on Linux 4.4.0-38-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-11-09 22:40:50	MarkDuplicates	Start of doWork freeMemory: 254879344; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-11-09 22:40:50	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-11-09 22:40:50	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-11-09 22:41:21	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:   23s.  Last read position: chr1:22,298,551
INFO	2016-11-09 22:41:21	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:41:46	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:48s.  Time for last 1,000,000:   24s.  Last read position: chr1:41,895,424
INFO	2016-11-09 22:41:46	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:41:52	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    6s.  Last read position: chr1:63,396,527
INFO	2016-11-09 22:41:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:42:00	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:01:02s.  Time for last 1,000,000:    8s.  Last read position: chr1:89,147,707
INFO	2016-11-09 22:42:00	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:42:10	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    9s.  Last read position: chr1:115,615,553
INFO	2016-11-09 22:42:10	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:42:20	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:01:22s.  Time for last 1,000,000:   10s.  Last read position: chr1:164,468,682
INFO	2016-11-09 22:42:20	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:42:24	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:01:26s.  Time for last 1,000,000:    4s.  Last read position: chr1:189,102,252
INFO	2016-11-09 22:42:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:42:45	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:01:47s.  Time for last 1,000,000:   20s.  Last read position: chr1:213,979,760
INFO	2016-11-09 22:42:45	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:42:58	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:02:00s.  Time for last 1,000,000:   13s.  Last read position: chr1:231,814,268
INFO	2016-11-09 22:42:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:43:06	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:02:08s.  Time for last 1,000,000:    7s.  Last read position: chr2:3,652,468
INFO	2016-11-09 22:43:06	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:43:12	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:02:14s.  Time for last 1,000,000:    6s.  Last read position: chr2:39,505,122
INFO	2016-11-09 22:43:12	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:43:22	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:02:24s.  Time for last 1,000,000:    9s.  Last read position: chr2:73,561,393
INFO	2016-11-09 22:43:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:43:31	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:02:33s.  Time for last 1,000,000:    9s.  Last read position: chr2:120,526,571
INFO	2016-11-09 22:43:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:43:39	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:02:41s.  Time for last 1,000,000:    7s.  Last read position: chr2:160,316,783
INFO	2016-11-09 22:43:39	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:44:05	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:   26s.  Last read position: chr2:195,549,735
INFO	2016-11-09 22:44:05	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:44:11	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:03:13s.  Time for last 1,000,000:    6s.  Last read position: chr2:230,358,034
INFO	2016-11-09 22:44:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:44:22	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:03:24s.  Time for last 1,000,000:   10s.  Last read position: chr3:16,305,780
INFO	2016-11-09 22:44:22	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:44:29	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:03:31s.  Time for last 1,000,000:    7s.  Last read position: chr3:49,251,279
INFO	2016-11-09 22:44:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:44:37	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:03:39s.  Time for last 1,000,000:    7s.  Last read position: chr3:84,621,225
INFO	2016-11-09 22:44:37	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:44:48	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:03:49s.  Time for last 1,000,000:   10s.  Last read position: chr3:128,121,129
INFO	2016-11-09 22:44:48	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:44:58	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:04:00s.  Time for last 1,000,000:   10s.  Last read position: chr3:165,373,238
INFO	2016-11-09 22:44:58	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:45:04	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:04:06s.  Time for last 1,000,000:    5s.  Last read position: chr3:195,333,247
INFO	2016-11-09 22:45:04	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:45:15	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:04:17s.  Time for last 1,000,000:   11s.  Last read position: chr4:37,752,582
INFO	2016-11-09 22:45:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:45:26	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:04:27s.  Time for last 1,000,000:   10s.  Last read position: chr4:81,286,306
INFO	2016-11-09 22:45:26	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:45:34	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:04:36s.  Time for last 1,000,000:    8s.  Last read position: chr4:119,339,736
INFO	2016-11-09 22:45:34	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:45:42	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:04:44s.  Time for last 1,000,000:    7s.  Last read position: chr4:158,818,783
INFO	2016-11-09 22:45:42	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:45:50	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:04:52s.  Time for last 1,000,000:    7s.  Last read position: chr5:6,447,551
INFO	2016-11-09 22:45:50	MarkDuplicates	Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO	2016-11-09 22:45:58	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:05:00s.  Time for last 1,000,000:    8s.  Last read position: chr5:33,219,021
INFO	2016-11-09 22:45:58	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:46:09	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:05:11s.  Time for last 1,000,000:   11s.  Last read position: chr5:60,694,078
INFO	2016-11-09 22:46:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:46:34	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:05:35s.  Time for last 1,000,000:   24s.  Last read position: chr5:86,336,676
INFO	2016-11-09 22:46:34	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:46:46	MarkDuplicates	Read    31,000,000 records.  Elapsed time: 00:05:48s.  Time for last 1,000,000:   12s.  Last read position: chr5:112,930,184
INFO	2016-11-09 22:46:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:46:52	MarkDuplicates	Read    32,000,000 records.  Elapsed time: 00:05:54s.  Time for last 1,000,000:    5s.  Last read position: chr5:136,852,889
INFO	2016-11-09 22:46:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:47:00	MarkDuplicates	Read    33,000,000 records.  Elapsed time: 00:06:02s.  Time for last 1,000,000:    8s.  Last read position: chr5:160,271,193
INFO	2016-11-09 22:47:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:47:07	MarkDuplicates	Read    34,000,000 records.  Elapsed time: 00:06:09s.  Time for last 1,000,000:    7s.  Last read position: chr6:4,126,386
INFO	2016-11-09 22:47:07	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:47:17	MarkDuplicates	Read    35,000,000 records.  Elapsed time: 00:06:19s.  Time for last 1,000,000:    9s.  Last read position: chr6:28,666,579
INFO	2016-11-09 22:47:17	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:47:24	MarkDuplicates	Read    36,000,000 records.  Elapsed time: 00:06:25s.  Time for last 1,000,000:    6s.  Last read position: chr6:49,527,281
INFO	2016-11-09 22:47:24	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:47:34	MarkDuplicates	Read    37,000,000 records.  Elapsed time: 00:06:36s.  Time for last 1,000,000:   10s.  Last read position: chr6:81,728,195
INFO	2016-11-09 22:47:34	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:47:45	MarkDuplicates	Read    38,000,000 records.  Elapsed time: 00:06:47s.  Time for last 1,000,000:   11s.  Last read position: chr6:107,535,760
INFO	2016-11-09 22:47:45	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:47:55	MarkDuplicates	Read    39,000,000 records.  Elapsed time: 00:06:57s.  Time for last 1,000,000:   10s.  Last read position: chr6:132,364,408
INFO	2016-11-09 22:47:55	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:48:05	MarkDuplicates	Read    40,000,000 records.  Elapsed time: 00:07:07s.  Time for last 1,000,000:    9s.  Last read position: chr6:156,918,595
INFO	2016-11-09 22:48:05	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:48:16	MarkDuplicates	Read    41,000,000 records.  Elapsed time: 00:07:18s.  Time for last 1,000,000:   11s.  Last read position: chr7:18,636,743
INFO	2016-11-09 22:48:16	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:48:31	MarkDuplicates	Read    42,000,000 records.  Elapsed time: 00:07:33s.  Time for last 1,000,000:   15s.  Last read position: chr7:53,850,313
INFO	2016-11-09 22:48:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:48:43	MarkDuplicates	Read    43,000,000 records.  Elapsed time: 00:07:45s.  Time for last 1,000,000:   11s.  Last read position: chr7:96,503,433
INFO	2016-11-09 22:48:43	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:48:56	MarkDuplicates	Read    44,000,000 records.  Elapsed time: 00:07:58s.  Time for last 1,000,000:   13s.  Last read position: chr7:120,651,846
INFO	2016-11-09 22:48:56	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:49:07	MarkDuplicates	Read    45,000,000 records.  Elapsed time: 00:08:09s.  Time for last 1,000,000:   11s.  Last read position: chr7:146,401,497
INFO	2016-11-09 22:49:07	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:49:15	MarkDuplicates	Read    46,000,000 records.  Elapsed time: 00:08:17s.  Time for last 1,000,000:    7s.  Last read position: chr8:17,030,519
INFO	2016-11-09 22:49:15	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:49:25	MarkDuplicates	Read    47,000,000 records.  Elapsed time: 00:08:27s.  Time for last 1,000,000:   10s.  Last read position: chr8:42,750,671
INFO	2016-11-09 22:49:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:49:31	MarkDuplicates	Read    48,000,000 records.  Elapsed time: 00:08:32s.  Time for last 1,000,000:    5s.  Last read position: chr8:85,385,487
INFO	2016-11-09 22:49:31	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:49:39	MarkDuplicates	Read    49,000,000 records.  Elapsed time: 00:08:41s.  Time for last 1,000,000:    8s.  Last read position: chr8:124,358,985
INFO	2016-11-09 22:49:39	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:49:46	MarkDuplicates	Read    50,000,000 records.  Elapsed time: 00:08:48s.  Time for last 1,000,000:    7s.  Last read position: chr9:18,183,883
INFO	2016-11-09 22:49:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:49:51	MarkDuplicates	Read    51,000,000 records.  Elapsed time: 00:08:53s.  Time for last 1,000,000:    5s.  Last read position: chr9:84,163,983
INFO	2016-11-09 22:49:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:49:57	MarkDuplicates	Read    52,000,000 records.  Elapsed time: 00:08:59s.  Time for last 1,000,000:    5s.  Last read position: chr9:119,875,535
INFO	2016-11-09 22:49:57	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:50:11	MarkDuplicates	Read    53,000,000 records.  Elapsed time: 00:09:13s.  Time for last 1,000,000:   13s.  Last read position: chr10:5,661,683
INFO	2016-11-09 22:50:11	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:50:18	MarkDuplicates	Read    54,000,000 records.  Elapsed time: 00:09:20s.  Time for last 1,000,000:    7s.  Last read position: chr10:29,748,948
INFO	2016-11-09 22:50:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:50:29	MarkDuplicates	Read    55,000,000 records.  Elapsed time: 00:09:31s.  Time for last 1,000,000:   10s.  Last read position: chr10:61,280,221
INFO	2016-11-09 22:50:29	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:50:39	MarkDuplicates	Read    56,000,000 records.  Elapsed time: 00:09:41s.  Time for last 1,000,000:    9s.  Last read position: chr10:85,305,552
INFO	2016-11-09 22:50:39	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:50:50	MarkDuplicates	Read    57,000,000 records.  Elapsed time: 00:09:52s.  Time for last 1,000,000:   10s.  Last read position: chr10:108,129,202
INFO	2016-11-09 22:50:50	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:51:01	MarkDuplicates	Read    58,000,000 records.  Elapsed time: 00:10:03s.  Time for last 1,000,000:   11s.  Last read position: chr10:132,730,123
INFO	2016-11-09 22:51:01	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:51:20	MarkDuplicates	Read    59,000,000 records.  Elapsed time: 00:10:21s.  Time for last 1,000,000:   18s.  Last read position: chr11:35,359,267
INFO	2016-11-09 22:51:20	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:51:30	MarkDuplicates	Read    60,000,000 records.  Elapsed time: 00:10:32s.  Time for last 1,000,000:   10s.  Last read position: chr11:75,696,431
INFO	2016-11-09 22:51:30	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:51:44	MarkDuplicates	Read    61,000,000 records.  Elapsed time: 00:10:46s.  Time for last 1,000,000:   13s.  Last read position: chr11:114,414,621
INFO	2016-11-09 22:51:44	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:51:55	MarkDuplicates	Read    62,000,000 records.  Elapsed time: 00:10:57s.  Time for last 1,000,000:   10s.  Last read position: chr12:8,900,276
INFO	2016-11-09 22:51:55	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:52:01	MarkDuplicates	Read    63,000,000 records.  Elapsed time: 00:11:03s.  Time for last 1,000,000:    5s.  Last read position: chr12:38,863,889
INFO	2016-11-09 22:52:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:52:07	MarkDuplicates	Read    64,000,000 records.  Elapsed time: 00:11:09s.  Time for last 1,000,000:    6s.  Last read position: chr12:60,598,824
INFO	2016-11-09 22:52:07	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:52:15	MarkDuplicates	Read    65,000,000 records.  Elapsed time: 00:11:17s.  Time for last 1,000,000:    8s.  Last read position: chr12:88,520,538
INFO	2016-11-09 22:52:15	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:52:23	MarkDuplicates	Read    66,000,000 records.  Elapsed time: 00:11:25s.  Time for last 1,000,000:    8s.  Last read position: chr12:112,268,437
INFO	2016-11-09 22:52:23	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:52:36	MarkDuplicates	Read    67,000,000 records.  Elapsed time: 00:11:37s.  Time for last 1,000,000:   12s.  Last read position: chr13:23,999,632
INFO	2016-11-09 22:52:36	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:52:43	MarkDuplicates	Read    68,000,000 records.  Elapsed time: 00:11:45s.  Time for last 1,000,000:    7s.  Last read position: chr13:51,165,870
INFO	2016-11-09 22:52:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:52:49	MarkDuplicates	Read    69,000,000 records.  Elapsed time: 00:11:51s.  Time for last 1,000,000:    5s.  Last read position: chr13:88,986,369
INFO	2016-11-09 22:52:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:52:57	MarkDuplicates	Read    70,000,000 records.  Elapsed time: 00:11:59s.  Time for last 1,000,000:    8s.  Last read position: chr14:23,149,367
INFO	2016-11-09 22:52:57	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:53:05	MarkDuplicates	Read    71,000,000 records.  Elapsed time: 00:12:07s.  Time for last 1,000,000:    7s.  Last read position: chr14:58,140,905
INFO	2016-11-09 22:53:05	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:53:18	MarkDuplicates	Read    72,000,000 records.  Elapsed time: 00:12:20s.  Time for last 1,000,000:   12s.  Last read position: chr14:91,912,553
INFO	2016-11-09 22:53:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:53:30	MarkDuplicates	Read    73,000,000 records.  Elapsed time: 00:12:32s.  Time for last 1,000,000:   12s.  Last read position: chr15:38,895,095
INFO	2016-11-09 22:53:30	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:53:46	MarkDuplicates	Read    74,000,000 records.  Elapsed time: 00:12:48s.  Time for last 1,000,000:   16s.  Last read position: chr15:68,188,367
INFO	2016-11-09 22:53:46	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:53:52	MarkDuplicates	Read    75,000,000 records.  Elapsed time: 00:12:54s.  Time for last 1,000,000:    5s.  Last read position: chr15:87,921,272
INFO	2016-11-09 22:53:52	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:54:00	MarkDuplicates	Read    76,000,000 records.  Elapsed time: 00:13:02s.  Time for last 1,000,000:    7s.  Last read position: chr16:11,143,813
INFO	2016-11-09 22:54:00	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:54:09	MarkDuplicates	Read    77,000,000 records.  Elapsed time: 00:13:11s.  Time for last 1,000,000:    9s.  Last read position: chr16:51,391,437
INFO	2016-11-09 22:54:09	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:54:18	MarkDuplicates	Read    78,000,000 records.  Elapsed time: 00:13:20s.  Time for last 1,000,000:    9s.  Last read position: chr16:84,928,458
INFO	2016-11-09 22:54:18	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:54:25	MarkDuplicates	Read    79,000,000 records.  Elapsed time: 00:13:27s.  Time for last 1,000,000:    6s.  Last read position: chr17:18,368,935
INFO	2016-11-09 22:54:25	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:54:34	MarkDuplicates	Read    80,000,000 records.  Elapsed time: 00:13:35s.  Time for last 1,000,000:    8s.  Last read position: chr17:44,246,522
INFO	2016-11-09 22:54:34	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:54:38	MarkDuplicates	Read    81,000,000 records.  Elapsed time: 00:13:40s.  Time for last 1,000,000:    4s.  Last read position: chr17:66,172,158
INFO	2016-11-09 22:54:38	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-09 22:54:49	MarkDuplicates	Read    82,000,000 records.  Elapsed time: 00:13:51s.  Time for last 1,000,000:   10s.  Last read position: chr18:5,619,614
INFO	2016-11-09 22:54:49	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:54:55	MarkDuplicates	Read    83,000,000 records.  Elapsed time: 00:13:57s.  Time for last 1,000,000:    5s.  Last read position: chr18:46,152,631
INFO	2016-11-09 22:54:55	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:55:01	MarkDuplicates	Read    84,000,000 records.  Elapsed time: 00:14:03s.  Time for last 1,000,000:    5s.  Last read position: chr19:1,328,731
INFO	2016-11-09 22:55:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:55:06	MarkDuplicates	Read    85,000,000 records.  Elapsed time: 00:14:08s.  Time for last 1,000,000:    4s.  Last read position: chr19:28,148,444
INFO	2016-11-09 22:55:06	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:55:13	MarkDuplicates	Read    86,000,000 records.  Elapsed time: 00:14:15s.  Time for last 1,000,000:    7s.  Last read position: chr19:40,341,579
INFO	2016-11-09 22:55:13	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:55:22	MarkDuplicates	Read    87,000,000 records.  Elapsed time: 00:14:23s.  Time for last 1,000,000:    8s.  Last read position: chr20:3,222,035
INFO	2016-11-09 22:55:22	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:55:26	MarkDuplicates	Read    88,000,000 records.  Elapsed time: 00:14:28s.  Time for last 1,000,000:    4s.  Last read position: chr20:37,218,903
INFO	2016-11-09 22:55:26	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:55:44	MarkDuplicates	Read    89,000,000 records.  Elapsed time: 00:14:46s.  Time for last 1,000,000:   18s.  Last read position: chr20:62,871,367
INFO	2016-11-09 22:55:44	MarkDuplicates	Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO	2016-11-09 22:55:52	MarkDuplicates	Read    90,000,000 records.  Elapsed time: 00:14:54s.  Time for last 1,000,000:    8s.  Last read position: chr21:39,474,524
INFO	2016-11-09 22:55:52	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:55:58	MarkDuplicates	Read    91,000,000 records.  Elapsed time: 00:14:59s.  Time for last 1,000,000:    5s.  Last read position: chr22:31,346,944
INFO	2016-11-09 22:55:58	MarkDuplicates	Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO	2016-11-09 22:56:03	MarkDuplicates	Read    92,000,000 records.  Elapsed time: 00:15:05s.  Time for last 1,000,000:    5s.  Last read position: chrX:6,235,951
INFO	2016-11-09 22:56:03	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:56:10	MarkDuplicates	Read    93,000,000 records.  Elapsed time: 00:15:12s.  Time for last 1,000,000:    6s.  Last read position: chrX:38,820,975
INFO	2016-11-09 22:56:10	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-11-09 22:56:22	MarkDuplicates	Read    94,000,000 records.  Elapsed time: 00:15:24s.  Time for last 1,000,000:   12s.  Last read position: chrX:69,473,954
INFO	2016-11-09 22:56:22	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:56:26	MarkDuplicates	Read    95,000,000 records.  Elapsed time: 00:15:28s.  Time for last 1,000,000:    4s.  Last read position: chrX:92,683,143
INFO	2016-11-09 22:56:26	MarkDuplicates	Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO	2016-11-09 22:56:33	MarkDuplicates	Read    96,000,000 records.  Elapsed time: 00:15:35s.  Time for last 1,000,000:    6s.  Last read position: chrX:118,447,518
INFO	2016-11-09 22:56:33	MarkDuplicates	Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO	2016-11-09 22:56:37	MarkDuplicates	Read    97,000,000 records.  Elapsed time: 00:15:39s.  Time for last 1,000,000:    4s.  Last read position: chrX:142,819,613
INFO	2016-11-09 22:56:37	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-11-09 22:56:42	MarkDuplicates	Read    98,000,000 records.  Elapsed time: 00:15:43s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,995
INFO	2016-11-09 22:56:42	MarkDuplicates	Tracking 7472 as yet unmatched pairs. 7472 records in RAM.
INFO	2016-11-09 22:56:48	MarkDuplicates	Read    99,000,000 records.  Elapsed time: 00:15:50s.  Time for last 1,000,000:    6s.  Last read position: chrM:11,775
INFO	2016-11-09 22:56:48	MarkDuplicates	Tracking 14000 as yet unmatched pairs. 14000 records in RAM.
INFO	2016-11-09 22:56:56	MarkDuplicates	Read 99989486 records. 0 pairs never matched.
INFO	2016-11-09 22:57:03	MarkDuplicates	After buildSortedReadEndLists freeMemory: 2884202736; totalMemory: 2911895552; maxMemory: 3817865216
INFO	2016-11-09 22:57:03	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-11-09 22:57:03	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-11-09 22:57:16	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-11-09 22:57:40	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-11-09 22:57:40	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1872603200; totalMemory: 2854748160; maxMemory: 3817865216
INFO	2016-11-09 22:57:40	MarkDuplicates	Marking 496224 records as duplicates.
INFO	2016-11-09 22:57:40	MarkDuplicates	Found 42648 optical duplicate clusters.
INFO	2016-11-09 23:01:02	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:03:19s.  Time for last 10,000,000:  199s.  Last read position: chr2:3,652,468
INFO	2016-11-09 23:03:35	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:05:52s.  Time for last 10,000,000:  152s.  Last read position: chr3:128,121,129
INFO	2016-11-09 23:06:40	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:08:57s.  Time for last 10,000,000:  185s.  Last read position: chr5:86,336,676
INFO	2016-11-09 23:09:08	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:11:25s.  Time for last 10,000,000:  147s.  Last read position: chr6:156,918,595
INFO	2016-11-09 23:11:29	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:13:46s.  Time for last 10,000,000:  140s.  Last read position: chr9:18,183,883
INFO	2016-11-09 23:13:49	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:16:06s.  Time for last 10,000,000:  139s.  Last read position: chr11:75,696,431
[Wed Nov 09 23:14:24 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 33.59 minutes.
Runtime.totalMemory()=2975334400
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/SRR1370890_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
Num 2
ID task.align_bwa.bwa_sam_rep1.line_140.id_11
Name bwa_sam rep1
Thread thread_41
PID 6453
OK false
Exit Code 0
Retries
State RUNNING
Dep. WAIT
Cpus 1
Mem
Start 2016-11-09 22:07:31
End 2016-11-09 22:07:31
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370890_1.fastq.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_1/out/align/rep1/SRR1370890_1.sai
Output files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_1/out/align/rep1/SRR1370890_1.bam /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_1/out/qc/rep1/SRR1370890_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/SRR1370890_1/out/align/rep1/SRR1370890_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370890_1.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_1/out/align/rep1/SRR1370890_1.bam

# SYS command. line 149

 sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_1/out/align/rep1/SRR1370890_1.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_1/out/qc/rep1/SRR1370890_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--------------------
3976 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.08 sec
[bwa_aln_core] refine gapped alignments... 1.51 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.57 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.86 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.08 sec
[bwa_aln_core] refine gapped alignments... 2.59 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.32 sec
[bwa_aln_core] refine gapped alignments... 3.42 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.26 sec
[bwa_aln_core] refine gapped alignments... 3.48 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.00 sec
[bwa_aln_core] refine gapped alignments... 1.25 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 14.17 sec
[bwa_aln_core] refine gapped alignments... 1.51 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 23.50 sec
[bwa_aln_core] refine gapped alignments... 1.37 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.72 sec
[bwa_aln_core] refine gapped alignments... 1.52 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.08 sec
[bwa_aln_core] refine gapped alignments... 2.11 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.14 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.60 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.63 sec
[bwa_aln_core] refine gapped alignments... 2.75 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.47 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.15 sec
[bwa_aln_core] refine gapped alignments... 1.65 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.02 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.35 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.05 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.85 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 13.01 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.23 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.15 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 16.52 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.13 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.59 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 17.30 sec
[bwa_aln_core] refine gapped alignments... 0.96 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.56 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.41 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.22 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.16 sec
[bwa_aln_core] refine gapped alignments... 0.47 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.26 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.84 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.15 sec
[bwa_aln_core] refine gapped alignments... 4.82 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.13 sec
[bwa_aln_core] refine gapped alignments... 2.77 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.95 sec
[bwa_aln_core] refine gapped alignments... 0.81 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.95 sec
[bwa_aln_core] refine gapped alignments... 2.85 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.88 sec
[bwa_aln_core] refine gapped alignments... 4.64 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 18.51 sec
[bwa_aln_core] refine gapped alignments... 2.50 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.88 sec
[bwa_aln_core] refine gapped alignments... 0.57 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.80 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.03 sec
[bwa_aln_core] refine gapped alignments... 0.64 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.82 sec
[bwa_aln_core] refine gapped alignments... 3.08 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.08 sec
[bwa_aln_core] refine gapped alignments... 5.21 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 20.98 sec
[bwa_aln_core] refine gapped alignments... 3.27 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.66 sec
[bwa_aln_core] refine gapped alignments... 3.34 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.58 sec
[bwa_aln_core] refine gapped alignments... 0.45 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 7.53 sec
[bwa_aln_core] refine gapped alignments... 5.11 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 12.02 sec
[bwa_aln_core] refine gapped alignments... 0.87 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.84 sec
[bwa_aln_core] refine gapped alignments... 4.93 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.12 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 8.62 sec
[bwa_aln_core] refine gapped alignments... 0.80 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 11.43 sec
[bwa_aln_core] refine gapped alignments... 2.26 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.99 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.60 sec
[bwa_aln_core] refine gapped alignments... 0.79 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 10.26 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 21.88 sec
[bwa_aln_core] refine gapped alignments... 4.26 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.00 sec
[bwa_aln_core] refine gapped alignments... 4.09 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.46 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 19.59 sec
[bwa_aln_core] refine gapped alignments... 4.78 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.74 sec
[bwa_aln_core] refine gapped alignments... 4.59 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.36 sec
[bwa_aln_core] refine gapped alignments... 1.53 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... 27.57 sec
[bwa_aln_core] refine gapped alignments... 5.09 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 58.01 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.53 sec
[bwa_aln_core] refine gapped alignments... 4.26 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.91 sec
[bwa_aln_core] refine gapped alignments... 4.12 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.08 sec
[bwa_aln_core] refine gapped alignments... 4.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.09 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 6.34 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 15.28 sec
[bwa_aln_core] refine gapped alignments... 2.14 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.75 sec
[bwa_aln_core] refine gapped alignments... 1.81 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.47 sec
[bwa_aln_core] refine gapped alignments... 1.68 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 18572862 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/SRR1370890_1/out/align/rep1/SRR1370890_1.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370890_1.fastq.gz
[main] Real time: 1970.323 sec; CPU: 1797.864 sec

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, SRR1370890_1, -nth, 5, -macs2_for_pooled_rep_only, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370890_1/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370890_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