| Num | 2 | | ID | task.align_bwa.bwa_aln_rep1.line_108.id_11 | | Name | bwa_aln rep1 | | Thread | thread_41 | | PID | 5996 | | | OK | false | | Exit Code | 1 | | Retries | | | State | ERROR | | Dep. | ERROR | | Cpus | | | Mem | | | | Start | 2016-11-09 17:51:35 | | End | 2016-11-09 17:51:35 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370908_1.fastq.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_1/out/align/rep1/SRR1370908_1.sai
| | Dependencies | | |
# SYS command. line 110
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 113
bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/RawReadsFiles/SRR1370908_1.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_1/out/align/rep1/SRR1370908_1.sai
# SYS command. line 115
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
57230 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 155.26 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 115.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 110.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 113.57 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.63 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.78 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.10 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 112.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 99.02 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 100.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 98.81 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.26 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.40 sec
[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 1.1% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.15 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.82 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.01 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.21 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 105.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 104.66 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 120.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 114.24 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 107.89 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 111.64 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.00 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 103.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 109.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 106.92 sec
[bwa_aln_core] write to the disk... [fwrite] No space left on device
--------------------Post mortem info--------------------
==============================================================
job_number: 5996
exec_file: job_scripts/5996
submission_time: Wed Nov 9 17:51:35 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/SRR1370908_1
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_1/chipseq.bds.20161109_175131_705_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_11.stderr.cluster
mail_list: imk1@surya
notify: FALSE
job_name: STDIN
stdout_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_1/chipseq.bds.20161109_175131_705_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_11.stdout.cluster
jobshare: 0
env_list: MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 55144 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=3,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift,SSH_TTY=/dev/pts/4,ASCPKEY=/software/ascp/etc/asperaweb_id_dsa.openssh,_LMFILES_=/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/ascp/3.5.6,LOGNAME=imk1,_=/usr/bin/bds,XDG_SESSION_ID=20,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,PATH=/software/ascp/:/software/sratoolkit/2.5.2/bin/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=15402.SRR1370908_1.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_N5SeQf,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_1,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=modsappsdir/modsappsdir:sratoolkit/2.5.2:ascp/3.5.6,SSH_CONNECTION=171.65.77.8 55144 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,MODULEPATH=/usr/local/Modules/versions :/usr/local/Modules/$MODULE_VERSION/modulefiles :/modules/ :/software/modulefiles,MODULESAPPSDIR=/software,MODULESHOME=/software/env_module/3.2.10
script_file: STDIN
usage 1: cpu=00:59:44, mem=11352.31310 GBs, io=7.68428, vmem=27.129M, maxvmem=3.268G
scheduling info: queue instance "q@kadru" dropped because it is full
queue instance "q@nandi" dropped because it is full
queue instance "q@surya" dropped because it is full
queue instance "q@kali" dropped because it is full
queue instance "amd.q@wotan" dropped because it is full
|
| Num | 3 | | ID | task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_12 | | Name | markdup_bam_picard ctl1 | | Thread | thread_42 | | PID | 6256 | | | OK | false | | Exit Code | 0 | | Retries | | | State | RUNNING | | Dep. | WAIT | | Cpus | 1 | | Mem | | | | Start | 2016-11-09 18:32:25 | | End | 2016-11-09 18:32:25 | | Elapsed | 00:00:00 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_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 ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 380
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
25745 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 09 21:20:53 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370908_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 21:20:53 PST 2016] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO 2016-11-09 21:20:53 MarkDuplicates Start of doWork freeMemory: 254879328; totalMemory: 257425408; maxMemory: 3817865216
INFO 2016-11-09 21:20:53 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-11-09 21:20:53 MarkDuplicates Will retain up to 14684096 data points before spilling to disk.
INFO 2016-11-09 21:21:00 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 6s. Last read position: chr1:22,298,551
INFO 2016-11-09 21:21:00 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:21:06 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 2016-11-09 21:21:06 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 21:21:15 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 9s. Last read position: chr1:63,396,527
INFO 2016-11-09 21:21:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:21:21 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 6s. Last read position: chr1:89,147,707
INFO 2016-11-09 21:21:21 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:21:29 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 7s. Last read position: chr1:115,615,553
INFO 2016-11-09 21:21:29 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:21:34 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 5s. Last read position: chr1:164,468,682
INFO 2016-11-09 21:21:34 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 21:21:40 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 6s. Last read position: chr1:189,102,252
INFO 2016-11-09 21:21:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:21:46 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 5s. Last read position: chr1:213,979,760
INFO 2016-11-09 21:21:46 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:21:53 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 6s. Last read position: chr1:231,814,268
INFO 2016-11-09 21:21:53 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:21:58 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 5s. Last read position: chr2:3,652,468
INFO 2016-11-09 21:21:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:22:05 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 6s. Last read position: chr2:39,505,122
INFO 2016-11-09 21:22:05 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:22:13 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 7s. Last read position: chr2:73,561,393
INFO 2016-11-09 21:22:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:22:18 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 5s. Last read position: chr2:120,526,571
INFO 2016-11-09 21:22:18 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:22:25 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 6s. Last read position: chr2:160,316,783
INFO 2016-11-09 21:22:25 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:22:48 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 23s. Last read position: chr2:195,549,735
INFO 2016-11-09 21:22:48 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:22:55 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 7s. Last read position: chr2:230,358,034
INFO 2016-11-09 21:22:55 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:23:06 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 11s. Last read position: chr3:16,305,780
INFO 2016-11-09 21:23:06 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 21:23:14 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 7s. Last read position: chr3:49,251,279
INFO 2016-11-09 21:23:14 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:23:25 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 11s. Last read position: chr3:84,621,225
INFO 2016-11-09 21:23:25 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:23:35 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 10s. Last read position: chr3:128,121,129
INFO 2016-11-09 21:23:35 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:23:49 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 13s. Last read position: chr3:165,373,238
INFO 2016-11-09 21:23:49 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:24:00 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 10s. Last read position: chr3:195,333,247
INFO 2016-11-09 21:24:00 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:24:08 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 8s. Last read position: chr4:37,752,582
INFO 2016-11-09 21:24:08 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:24:16 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 8s. Last read position: chr4:81,286,306
INFO 2016-11-09 21:24:16 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:24:27 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 11s. Last read position: chr4:119,339,736
INFO 2016-11-09 21:24:27 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:24:35 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 7s. Last read position: chr4:158,818,783
INFO 2016-11-09 21:24:35 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 21:24:44 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 9s. Last read position: chr5:6,447,551
INFO 2016-11-09 21:24:44 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO 2016-11-09 21:24:54 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 9s. Last read position: chr5:33,219,021
INFO 2016-11-09 21:24:54 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 21:25:06 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 12s. Last read position: chr5:60,694,078
INFO 2016-11-09 21:25:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:25:24 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 17s. Last read position: chr5:86,336,676
INFO 2016-11-09 21:25:24 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:25:33 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 9s. Last read position: chr5:112,930,184
INFO 2016-11-09 21:25:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:25:44 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 11s. Last read position: chr5:136,852,889
INFO 2016-11-09 21:25:44 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:25:56 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 11s. Last read position: chr5:160,271,193
INFO 2016-11-09 21:25:56 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
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