| Num | 1 | | ID | task.align_bwa.bwa_aln_rep1.line_108.id_10 | | Name | bwa_aln rep1 | | Thread | thread_41 | | PID | 5998 | | | 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/SRR1370910_1.fastq.gz
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_1/out/align/rep1/SRR1370910_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/SRR1370910_1.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_1/out/align/rep1/SRR1370910_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--------------------
11854 (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] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.79 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.00 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.38 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.72 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.08 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.65 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.56 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.56 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.94 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 48.93 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.50 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.50 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.53 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.15 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.02 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.10 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 49.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.04 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.40 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.13 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.79 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.47 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61.21 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 62.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.85 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 54.33 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.57 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.93 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.89 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59.58 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 56.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.46 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.30 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.3% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 51.18 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.27 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 52.21 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 73.87 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 72.97 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 65.68 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.90 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.82 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.39 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.09 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.64 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.41 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.13 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58.77 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 67.13 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 64.58 sec
[bwa_aln_core] write to the disk... [fwrite] No space left on device
--------------------Post mortem info--------------------
==============================================================
job_number: 5998
exec_file: job_scripts/5998
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/SRR1370910_1
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_1/chipseq.bds.20161109_175132_706_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10.stderr.cluster
mail_list: imk1@surya
notify: FALSE
job_name: STDIN
stdout_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_1/chipseq.bds.20161109_175132_706_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10.stdout.cluster
jobshare: 0
env_list: MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 55144 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=3,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift,SSH_TTY=/dev/pts/4,ASCPKEY=/software/ascp/etc/asperaweb_id_dsa.openssh,_LMFILES_=/software/modulefiles/modsappsdir/modsappsdir:/software/modulefiles/sratoolkit/2.5.2:/software/modulefiles/ascp/3.5.6,LOGNAME=imk1,_=/usr/bin/bds,XDG_SESSION_ID=20,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,PATH=/software/ascp/:/software/sratoolkit/2.5.2/bin/:/users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/srv/scratch/imk1/TFBindingPredictionProject/src/R-3.2.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=15511.SRR1370910_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/SRR1370910_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=00:48:34, mem=9103.92169 GBs, io=4.24891, vmem=3.168G, maxvmem=3.172G
scheduling info: queue instance "q@nandi" dropped because it is full
queue instance "q@kadru" dropped because it is full
queue instance "q@kali" dropped because it is full
queue instance "q@surya" dropped because it is full
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 | 6276 | | | OK | true | | Exit Code | 0 | | Retries | | | State | FINISHED | | Dep. | OK | | Cpus | 1 | | Mem | | | | Start | 2016-11-09 18:49:12 | | End | 2016-11-09 22:34:43 | | Elapsed | 03:45:30 | | Timeout | 00:00:-1 | | Wall Timeout | 100 days | | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam
| | Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_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 ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_1/out/qc/ctl1/ss_50M_2000_GRCh38.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 380
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
40369 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Nov 09 21:22:01 PST 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_1/out/align/ctl1/ss_50M_2000_GRCh38.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_1/out/align/ctl1/ss_50M_2000_GRCh38.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/HughesZnfData/SRR1370910_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 21:22:01 PST 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO 2016-11-09 21:22:03 MarkDuplicates Start of doWork freeMemory: 254879344; totalMemory: 257425408; maxMemory: 3817865216
INFO 2016-11-09 21:22:03 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-11-09 21:22:03 MarkDuplicates Will retain up to 14684096 data points before spilling to disk.
INFO 2016-11-09 21:22:23 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 18s. Last read position: chr1:22,298,551
INFO 2016-11-09 21:22:23 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:22:44 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 21s. Last read position: chr1:41,895,424
INFO 2016-11-09 21:22:44 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 21:23:00 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 15s. Last read position: chr1:63,396,527
INFO 2016-11-09 21:23:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:23:11 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 10s. Last read position: chr1:89,147,707
INFO 2016-11-09 21:23:11 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:23:20 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 9s. Last read position: chr1:115,615,553
INFO 2016-11-09 21:23:20 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:23:32 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 11s. Last read position: chr1:164,468,682
INFO 2016-11-09 21:23:32 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 21:23:46 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 13s. Last read position: chr1:189,102,252
INFO 2016-11-09 21:23:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:24:03 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 17s. Last read position: chr1:213,979,760
INFO 2016-11-09 21:24:03 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:24:16 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 12s. Last read position: chr1:231,814,268
INFO 2016-11-09 21:24:16 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:24:29 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 13s. Last read position: chr2:3,652,468
INFO 2016-11-09 21:24:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:24:43 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 13s. Last read position: chr2:39,505,122
INFO 2016-11-09 21:24:43 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:25:02 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 19s. Last read position: chr2:73,561,393
INFO 2016-11-09 21:25:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:25:21 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 19s. Last read position: chr2:120,526,571
INFO 2016-11-09 21:25:21 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:25:38 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 16s. Last read position: chr2:160,316,783
INFO 2016-11-09 21:25:38 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:26:10 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 32s. Last read position: chr2:195,549,735
INFO 2016-11-09 21:26:10 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:26:27 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 16s. Last read position: chr2:230,358,034
INFO 2016-11-09 21:26:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:26:47 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 19s. Last read position: chr3:16,305,780
INFO 2016-11-09 21:26:47 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 21:27:09 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 22s. Last read position: chr3:49,251,279
INFO 2016-11-09 21:27:09 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:27:30 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 21s. Last read position: chr3:84,621,225
INFO 2016-11-09 21:27:30 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:27:49 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 18s. Last read position: chr3:128,121,129
INFO 2016-11-09 21:27:49 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:28:07 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 17s. Last read position: chr3:165,373,238
INFO 2016-11-09 21:28:07 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:28:28 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 20s. Last read position: chr3:195,333,247
INFO 2016-11-09 21:28:28 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:28:49 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 21s. Last read position: chr4:37,752,582
INFO 2016-11-09 21:28:49 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:29:08 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 19s. Last read position: chr4:81,286,306
INFO 2016-11-09 21:29:08 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:29:38 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 29s. Last read position: chr4:119,339,736
INFO 2016-11-09 21:29:38 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:29:59 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 20s. Last read position: chr4:158,818,783
INFO 2016-11-09 21:29:59 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 21:30:26 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 26s. Last read position: chr5:6,447,551
INFO 2016-11-09 21:30:26 MarkDuplicates Tracking 16 as yet unmatched pairs. 16 records in RAM.
INFO 2016-11-09 21:30:51 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 25s. Last read position: chr5:33,219,021
INFO 2016-11-09 21:30:51 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 21:31:11 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 19s. Last read position: chr5:60,694,078
INFO 2016-11-09 21:31:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:31:56 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 45s. Last read position: chr5:86,336,676
INFO 2016-11-09 21:31:56 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:32:28 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 32s. Last read position: chr5:112,930,184
INFO 2016-11-09 21:32:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO 2016-11-09 21:32:58 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 29s. Last read position: chr5:136,852,889
INFO 2016-11-09 21:32:58 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:33:21 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 23s. Last read position: chr5:160,271,193
INFO 2016-11-09 21:33:21 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:33:53 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 31s. Last read position: chr6:4,126,386
INFO 2016-11-09 21:33:53 MarkDuplicates Tracking 6 as yet unmatched pairs. 6 records in RAM.
INFO 2016-11-09 21:34:16 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 23s. Last read position: chr6:28,666,579
INFO 2016-11-09 21:34:16 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:34:41 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 25s. Last read position: chr6:49,527,281
INFO 2016-11-09 21:34:41 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:35:08 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:13:03s. Time for last 1,000,000: 27s. Last read position: chr6:81,728,195
INFO 2016-11-09 21:35:08 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:35:31 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 22s. Last read position: chr6:107,535,760
INFO 2016-11-09 21:35:31 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:36:03 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 32s. Last read position: chr6:132,364,408
INFO 2016-11-09 21:36:03 MarkDuplicates Tracking 8 as yet unmatched pairs. 8 records in RAM.
INFO 2016-11-09 21:36:24 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:14:19s. Time for last 1,000,000: 21s. Last read position: chr6:156,918,595
INFO 2016-11-09 21:36:24 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:36:57 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:14:52s. Time for last 1,000,000: 32s. Last read position: chr7:18,636,743
INFO 2016-11-09 21:36:57 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:37:39 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:15:34s. Time for last 1,000,000: 42s. Last read position: chr7:53,850,313
INFO 2016-11-09 21:37:39 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:38:20 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:16:14s. Time for last 1,000,000: 40s. Last read position: chr7:96,503,433
INFO 2016-11-09 21:38:20 MarkDuplicates Tracking 4 as yet unmatched pairs. 4 records in RAM.
INFO 2016-11-09 21:38:47 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:16:42s. Time for last 1,000,000: 27s. Last read position: chr7:120,651,846
INFO 2016-11-09 21:38:47 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:39:19 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:17:14s. Time for last 1,000,000: 31s. Last read position: chr7:146,401,497
INFO 2016-11-09 21:39:19 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:39:54 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:17:49s. Time for last 1,000,000: 34s. Last read position: chr8:17,030,519
INFO 2016-11-09 21:39:54 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:40:25 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:18:20s. Time for last 1,000,000: 31s. Last read position: chr8:42,750,671
INFO 2016-11-09 21:40:25 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO 2016-11-09 21:40:48 MarkDuplicates |