| Num | 1 | | ID | task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_10 | | Name | markdup_bam_picard ctl1 | | Thread | thread_42 | | PID | 6450 | | | OK | false | | Exit Code | 1 | | Retries | | | State | ERROR | | Dep. | ERROR | | Cpus | 1 | | Mem | | | | Start | 2016-11-09 22:07:27 | | End | 2016-11-09 22:07:27 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_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 ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 380
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
3611 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 09 22:39:33 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370886_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 22:39:33 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 22:39:34 MarkDuplicates Start of doWork freeMemory: 254879344; totalMemory: 257425408; maxMemory: 3817865216
INFO 2016-11-09 22:39:34 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-11-09 22:39:34 MarkDuplicates Will retain up to 14684096 data points before spilling to disk.
INFO 2016-11-09 22:39:55 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 9s. Last read position: chr1:22,298,551
INFO 2016-11-09 22:39:55 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:40:08 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 12s. Last read position: chr1:41,895,424
INFO 2016-11-09 22:40:08 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 22:40:23 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 15s. Last read position: chr1:63,396,527
INFO 2016-11-09 22:40:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:40:55 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 31s. Last read position: chr1:89,147,707
INFO 2016-11-09 22:40:55 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:41:05 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 10s. Last read position: chr1:115,615,553
INFO 2016-11-09 22:41:05 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:41:14 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 8s. Last read position: chr1:164,468,682
INFO 2016-11-09 22:41:14 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 22:41:25 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 11s. Last read position: chr1:189,102,252
INFO 2016-11-09 22:41:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:41:45 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 19s. Last read position: chr1:213,979,760
INFO 2016-11-09 22:41:45 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:41:52 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 7s. Last read position: chr1:231,814,268
INFO 2016-11-09 22:41:52 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:41:59 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 6s. Last read position: chr2:3,652,468
INFO 2016-11-09 22:41:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:42:16 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 16s. Last read position: chr2:39,505,122
INFO 2016-11-09 22:42:16 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:42:27 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 11s. Last read position: chr2:73,561,393
INFO 2016-11-09 22:42:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:42:36 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 8s. Last read position: chr2:120,526,571
INFO 2016-11-09 22:42:36 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:42:56 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 20s. Last read position: chr2:160,316,783
INFO 2016-11-09 22:42:56 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:43:15 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 19s. Last read position: chr2:195,549,735
INFO 2016-11-09 22:43:15 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:43:25 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 9s. Last read position: chr2:230,358,034
INFO 2016-11-09 22:43:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:43:33 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 8s. Last read position: chr3:16,305,780
INFO 2016-11-09 22:43:33 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 22:43:39 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 5s. Last read position: chr3:49,251,279
INFO 2016-11-09 22:43:39 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:43:54 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 14s. Last read position: chr3:84,621,225
INFO 2016-11-09 22:43:54 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:44:03 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 9s. Last read position: chr3:128,121,129
INFO 2016-11-09 22:44:03 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:44:09 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 6s. Last read position: chr3:165,373,238
INFO 2016-11-09 22:44:09 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:44:23 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 13s. Last read position: chr3:195,333,247
INFO 2016-11-09 22:44:23 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:44:30 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 7s. Last read position: chr4:37,752,582
INFO 2016-11-09 22:44:30 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:44:41 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 10s. Last read position: chr4:81,286,306
INFO 2016-11-09 22:44:41 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:44:52 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 10s. Last read position: chr4:119,339,736
INFO 2016-11-09 22:44:52 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:45:01 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 9s. Last read position: chr4:158,818,783
INFO 2016-11-09 22:45:01 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 22:45:12 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 10s. Last read position: chr5:6,447,551
INFO 2016-11-09 22:45:12 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO 2016-11-09 22:45:20 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 8s. Last read position: chr5:33,219,021
INFO 2016-11-09 22:45:20 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 22:45:30 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 9s. Last read position: chr5:60,694,078
INFO 2016-11-09 22:45:30 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:45:52 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 22s. Last read position: chr5:86,336,676
INFO 2016-11-09 22:45:52 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:46:03 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 11s. Last read position: chr5:112,930,184
INFO 2016-11-09 22:46:03 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:46:15 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 11s. Last read position: chr5:136,852,889
INFO 2016-11-09 22:46:15 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:46:22 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 6s. Last read position: chr5:160,271,193
INFO 2016-11-09 22:46:22 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:46:26 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 4s. Last read position: chr6:4,126,386
INFO 2016-11-09 22:46:26 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 22:46:40 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 13s. Last read position: chr6:28,666,579
INFO 2016-11-09 22:46:40 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:46:50 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 9s. Last read position: chr6:49,527,281
INFO 2016-11-09 22:46:50 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:46:56 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 5s. Last read position: chr6:81,728,195
INFO 2016-11-09 22:46:56 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:47:05 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 9s. Last read position: chr6:107,535,760
INFO 2016-11-09 22:47:05 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:47:12 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 6s. Last read position: chr6:132,364,408
INFO 2016-11-09 22:47:12 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 22:47:22 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 9s. Last read position: chr6:156,918,595
INFO 2016-11-09 22:47:22 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:47:31 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 9s. Last read position: chr7:18,636,743
INFO 2016-11-09 22:47:31 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:47:42 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 10s. Last read position: chr7:53,850,313
INFO 2016-11-09 22:47:42 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:47:53 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 10s. Last read position: chr7:96,503,433
INFO 2016-11-09 22:47:53 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:48:02 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 9s. Last read position: chr7:120,651,846
INFO 2016-11-09 22:48:02 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:48:18 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 15s. Last read position: chr7:146,401,497
INFO 2016-11-09 22:48:18 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:48:33 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 14s. Last read position: chr8:17,030,519
INFO 2016-11-09 22:48:33 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:48:43 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 10s. Last read position: chr8:42,750,671
INFO 2016-11-09 22:48:43 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:48:56 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 12s. Last read position: chr8:85,385,487
INFO 2016-11-09 22:48:56 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:49:02 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 5s. Last read position: chr8:124,358,985
INFO 2016-11-09 22:49:02 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:49:11 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 8s. Last read position: chr9:18,183,883
INFO 2016-11-09 22:49:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:49:16 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 5s. Last read position: chr9:84,163,983
INFO 2016-11-09 22:49:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:49:26 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 9s. Last read position: chr9:119,875,535
INFO 2016-11-09 22:49:26 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:49:31 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 5s. Last read position: chr10:5,661,683
INFO 2016-11-09 22:49:31 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 22:49:39 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 7s. Last read position: chr10:29,748,948
INFO 2016-11-09 22:49:39 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:49:44 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 5s. Last read position: chr10:61,280,221
INFO 2016-11-09 22:49:44 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:49:49 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 4s. Last read position: chr10:85,305,552
INFO 2016-11-09 22:49:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:50:05 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 15s. Last read position: chr10:108,129,202
INFO 2016-11-09 22:50:05 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:50:15 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 10s. Last read position: chr10:132,730,123
INFO 2016-11-09 22:50:15 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:50:33 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 17s. Last read position: chr11:35,359,267
INFO 2016-11-09 22:50:33 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:50:44 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 11s. Last read position: chr11:75,696,431
INFO 2016-11-09 22:50:44 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:50:57 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 13s. Last read position: chr11:114,414,621
INFO 2016-11-09 22:50:57 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 22:51:07 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 9s. Last read position: chr12:8,900,276
INFO 2016-11-09 22:51:07 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 22:51:14 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 7s. Last read position: chr12:38,863,889
INFO 2016-11-09 22:51:14 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:51:22 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 7s. Last read position: chr12:60,598,824
INFO 2016-11-09 22:51:22 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:51:32 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 10s. Last read position: chr12:88,520,538
INFO 2016-11-09 22:51:32 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 22:51:47 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 15s. Last read position: chr12:112,268,437
INFO 2016-11-09 22:51:47 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:51:57 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 9s. Last read position: chr13:23,999,632
INFO 2016-11-09 22:51:57 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:52:02 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 4s. Last read position: chr13:51,165,870
INFO 2016-11-09 22:52:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:52:08 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 6s. Last read position: chr13:88,986,369
INFO 2016-11-09 22:52:08 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:52:16 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:12:30s. Time for last 1,000,000: 7s. Last read position: chr14:23,149,367
INFO 2016-11-09 22:52:16 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 22:52:23 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 7s. Last read position: chr14:58,140,905
INFO 2016-11-09 22:52:23 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:52:35 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:12:50s. Time for last 1,000,000: 12s. Last read position: chr14:91,912,553
INFO 2016-11-09 22:52:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:52:45 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:12:59s. Time for last 1,000,000: 9s. Last read position: chr15:38,895,095
INFO 2016-11-09 22:52:45 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:52:57 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 11s. Last read position: chr15:68,188,367
INFO 2016-11-09 22:52:57 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 22:53:04 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 7s. Last read position: chr15:87,921,272
INFO 2016-11-09 22:53:04 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:53:17 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:13:31s. Time for last 1,000,000: 12s. Last read position: chr16:11,143,813
INFO 2016-11-09 22:53:17 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:53:28 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 11s. Last read position: chr16:51,391,437
INFO 2016-11-09 22:53:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:53:36 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 7s. Last read position: chr16:84,928,458
INFO 2016-11-09 22:53:36 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:53:47 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:14:01s. Time for last 1,000,000: 10s. Last read position: chr17:18,368,935
INFO 2016-11-09 22:53:47 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:53:52 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:14:06s. Time for last 1,000,000: 5s. Last read position: chr17:44,246,522
INFO 2016-11-09 22:53:52 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:54:00 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:14:14s. Time for last 1,000,000: 7s. Last read position: chr17:66,172,158
INFO 2016-11-09 22:54:00 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO 2016-11-09 22:54:09 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:14:23s. Time for last 1,000,000: 8s. Last read position: chr18:5,619,614
INFO 2016-11-09 22:54:09 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:54:16 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:14:31s. Time for last 1,000,000: 7s. Last read position: chr18:46,152,631
INFO 2016-11-09 22:54:16 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:54:24 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:14:39s. Time for last 1,000,000: 7s. Last read position: chr19:1,328,731
INFO 2016-11-09 22:54:24 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:54:29 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:14:43s. Time for last 1,000,000: 4s. Last read position: chr19:28,148,444
INFO 2016-11-09 22:54:29 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:54:36 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:14:51s. Time for last 1,000,000: 7s. Last read position: chr19:40,341,579
INFO 2016-11-09 22:54:36 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 22:54:48 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:15:02s. Time for last 1,000,000: 11s. Last read position: chr20:3,222,035
INFO 2016-11-09 22:54:48 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:54:53 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:15:07s. Time for last 1,000,000: 5s. Last read position: chr20:37,218,903
INFO 2016-11-09 22:54:53 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:55:09 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:15:23s. Time for last 1,000,000: 16s. Last read position: chr20:62,871,367
INFO 2016-11-09 22:55:09 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM.
INFO 2016-11-09 22:55:15 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:15:29s. Time for last 1,000,000: 5s. Last read position: chr21:39,474,524
INFO 2016-11-09 22:55:15 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:55:21 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:15:35s. Time for last 1,000,000: 5s. Last read position: chr22:31,346,944
INFO 2016-11-09 22:55:21 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 22:55:25 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:15:39s. Time for last 1,000,000: 4s. Last read position: chrX:6,235,951
INFO 2016-11-09 22:55:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:55:33 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:15:47s. Time for last 1,000,000: 7s. Last read position: chrX:38,820,975
INFO 2016-11-09 22:55:33 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 22:55:39 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:15:53s. Time for last 1,000,000: 5s. Last read position: chrX:69,473,954
INFO 2016-11-09 22:55:39 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:55:47 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:16:01s. Time for last 1,000,000: 8s. Last read position: chrX:92,683,143
INFO 2016-11-09 22:55:47 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 22:55:54 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:16:08s. Time for last 1,000,000: 6s. Last read position: chrX:118,447,518
INFO 2016-11-09 22:55:54 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 22:55:58 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:16:12s. Time for last 1,000,000: 4s. Last read position: chrX:142,819,613
INFO 2016-11-09 22:55:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 22:56:02 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:16:16s. Time for last 1,000,000: 4s. Last read position: chrM:3,995
INFO 2016-11-09 22:56:02 MarkDuplicates Tracking 7472 as yet unmatched pairs. 7472 records in RAM.
INFO 2016-11-09 22:56:07 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:16:21s. Time for last 1,000,000: 4s. Last read position: chrM:11,775
INFO 2016-11-09 22:56:07 MarkDuplicates Tracking 14000 as yet unmatched pairs. 14000 records in RAM.
INFO 2016-11-09 22:56:19 MarkDuplicates Read 99989486 records. 0 pairs never matched.
INFO 2016-11-09 22:56:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 3312098952; totalMemory: 3339714560; maxMemory: 3817865216
INFO 2016-11-09 22:56:26 MarkDuplicates Will retain up to 119308288 duplicate indices before spilling to disk.
INFO 2016-11-09 22:56:26 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2016-11-09 22:56:41 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2016-11-09 22:57:04 MarkDuplicates Sorting list of duplicate records.
INFO 2016-11-09 22:57:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 2299398800; totalMemory: 3281518592; maxMemory: 3817865216
INFO 2016-11-09 22:57:04 MarkDuplicates Marking 496224 records as duplicates.
INFO 2016-11-09 22:57:04 MarkDuplicates Found 42648 optical duplicate clusters.
INFO 2016-11-09 23:00:04 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:02:58s. Time for last 10,000,000: 178s. Last read position: chr2:3,652,468
INFO 2016-11-09 23:03:08 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:06:01s. Time for last 10,000,000: 183s. Last read position: chr3:128,121,129
[Wed Nov 09 23:04:51 PST 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 25.31 minutes.
Runtime.totalMemory()=3400007680
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/SRR1370886_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.util.BinaryCodec.writeString(BinaryCodec.java:305)
at htsjdk.samtools.util.BinaryCodec.writeString(BinaryCodec.java:292)
at htsjdk.samtools.BinaryTagCodec.writeTag(BinaryTagCodec.java:193)
at htsjdk.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:163)
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)
... 16 more
--------------------Post mortem info--------------------
==============================================================
job_number: 6450
exec_file: job_scripts/6450
submission_time: Wed Nov 9 22:07:27 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/SRR1370886_1
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch |