| Num | 2 | | ID | task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_11 | | Name | markdup_bam_picard ctl1 | | Thread | thread_42 | | PID | 6592 | | | OK | false | | Exit Code | 1 | | Retries | | | State | ERROR | | Dep. | ERROR | | Cpus | 1 | | Mem | | | | Start | 2016-11-10 11:54:40 | | End | 2016-11-10 11:54:40 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_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 ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 380
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
39523 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Thu Nov 10 11:54:45 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370874_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 11:54:45 PST 2016] Executing as imk1@surya on Linux 4.4.0-45-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO 2016-11-10 11:54:45 MarkDuplicates Start of doWork freeMemory: 254879344; totalMemory: 257425408; maxMemory: 3817865216
INFO 2016-11-10 11:54:45 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-11-10 11:54:45 MarkDuplicates Will retain up to 14684096 data points before spilling to disk.
INFO 2016-11-10 11:54:53 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 11:54:53 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 11:54:58 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 5s. Last read position: chr1:41,895,424
INFO 2016-11-10 11:54:58 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-10 11:55:04 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 6s. Last read position: chr1:63,396,527
INFO 2016-11-10 11:55:04 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 11:55:09 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 4s. Last read position: chr1:89,147,707
INFO 2016-11-10 11:55:09 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 11:55:15 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 6s. Last read position: chr1:115,615,553
INFO 2016-11-10 11:55:15 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 11:55:20 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 5s. Last read position: chr1:164,468,682
INFO 2016-11-10 11:55:20 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-10 11:55:26 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 5s. Last read position: chr1:189,102,252
INFO 2016-11-10 11:55:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 11:55:32 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 5s. Last read position: chr1:213,979,760
INFO 2016-11-10 11:55:32 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 11:55:37 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 5s. Last read position: chr1:231,814,268
INFO 2016-11-10 11:55:37 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 11:55:45 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 7s. Last read position: chr2:3,652,468
INFO 2016-11-10 11:55:45 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 11:55:52 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 6s. Last read position: chr2:39,505,122
INFO 2016-11-10 11:55:52 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 11:55:59 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 6s. Last read position: chr2:73,561,393
INFO 2016-11-10 11:55:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 11:56:07 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 8s. Last read position: chr2:120,526,571
INFO 2016-11-10 11:56:07 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 11:56:13 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 6s. Last read position: chr2:160,316,783
INFO 2016-11-10 11:56:13 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 11:56:41 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 27s. Last read position: chr2:195,549,735
INFO 2016-11-10 11:56:41 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 11:56:49 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 7s. Last read position: chr2:230,358,034
INFO 2016-11-10 11:56:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 11:56:57 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 8s. Last read position: chr3:16,305,780
INFO 2016-11-10 11:56:57 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-10 11:57:04 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 7s. Last read position: chr3:49,251,279
INFO 2016-11-10 11:57:04 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 11:57:12 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 7s. Last read position: chr3:84,621,225
INFO 2016-11-10 11:57:12 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 11:57:18 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 6s. Last read position: chr3:128,121,129
INFO 2016-11-10 11:57:18 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 11:57:24 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 5s. Last read position: chr3:165,373,238
INFO 2016-11-10 11:57:24 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 11:57:33 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 8s. Last read position: chr3:195,333,247
INFO 2016-11-10 11:57:33 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 11:57:39 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 6s. Last read position: chr4:37,752,582
INFO 2016-11-10 11:57:39 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 11:57:45 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 6s. Last read position: chr4:81,286,306
INFO 2016-11-10 11:57:45 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 11:57:52 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 6s. Last read position: chr4:119,339,736
INFO 2016-11-10 11:57:52 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 11:57:59 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 7s. Last read position: chr4:158,818,783
INFO 2016-11-10 11:57:59 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-10 11:58:09 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 9s. Last read position: chr5:6,447,551
INFO 2016-11-10 11:58:09 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO 2016-11-10 11:58:15 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 6s. Last read position: chr5:33,219,021
INFO 2016-11-10 11:58:15 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-10 11:58:22 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 6s. Last read position: chr5:60,694,078
INFO 2016-11-10 11:58:22 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 11:58:57 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 34s. Last read position: chr5:86,336,676
INFO 2016-11-10 11:58:57 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 11:59:02 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 5s. Last read position: chr5:112,930,184
INFO 2016-11-10 11:59:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-10 11:59:10 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 7s. Last read position: chr5:136,852,889
INFO 2016-11-10 11:59:10 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 11:59:16 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 6s. Last read position: chr5:160,271,193
INFO 2016-11-10 11:59:16 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 11:59:23 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 6s. Last read position: chr6:4,126,386
INFO 2016-11-10 11:59:23 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-10 11:59:29 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 6s. Last read position: chr6:28,666,579
INFO 2016-11-10 11:59:29 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 11:59:35 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 6s. Last read position: chr6:49,527,281
INFO 2016-11-10 11:59:35 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-10 11:59:42 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 6s. Last read position: chr6:81,728,195
INFO 2016-11-10 11:59:42 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 11:59:52 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 10s. Last read position: chr6:107,535,760
INFO 2016-11-10 11:59:52 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-10 12:00:00 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: |