Hello,I have set up an AWS instance with the Juicer AMI according to your documentation, and am having trouble getting it to work on the sample files.For example, from within the directory /opt/juicer/work/HIC003,I typed:source /opt/juicer/scripts/juicer.sh -d /opt/juicer/work/HIC003/ -p /opt/juicer/references/And got these messages:
(-: Looking for fastq files...fastq files existLSF daemon (LIM) not responding ... still tryingLSF daemon (LIM) not responding ... still tryingLSF daemon (LIM) not responding ... still trying
Please advise.Thank you!Richard
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cat aligned/a1516851053_msplit*_optdups.txt > aligned/opt_dups.txt; cat aligned/a1516851053_msplit*_dups.txt > aligned/dups.txt;cat aligned/a1516851053_msplit*_merged_nodups.txt > aligned/merged_nodups.txt;
juicer.sh -S final
1) After a day of running the alignment steps, Juicer stalled at a postproc job.
JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME
9504 ubuntu PEND long HEADNODE - a1516851053_postproc Jan 25 03:50
9505 ubuntu PEND normal HEADNODE - a1516851053_done Jan 25 03:50
9859 ubuntu PEND Merge HEADNODE - a1516885367_fragmerge1 Jan 25 15:18
9860 ubuntu PEND Merge HEADNODE - a1516885367_fragmerge Jan 25 15:18
9861 ubuntu PEND Clean3 HEADNODE - a1516885367_clean1 Jan 25 15:18
9862 ubuntu PEND Clean3 HEADNODE - a1516885367_osplit Jan 25 15:18
9863 ubuntu PEND Stat HEADNODE - a1516885367_clean2 Jan 25 15:18
9864 ubuntu PEND Stat HEADNODE - a1516885367_launch Jan 25 15:18
9865 ubuntu PEND Stat HEADNODE - a1516885367_postproc_wrap Jan 25 15:18
9866 ubuntu PEND CleanFnl HEADNODE - a1516885367_prep_done Jan 25 15:18
9867 ubuntu PEND Stat HEADNODE - #!/bin/bash; #BSUB -q Stat; #BSUB -W 1200; #BSUB -o /opt/juicer/work/NHCFV/NHCFV1/debug/finalclean-a1516885367.out ; #BSUB -e /opt/juicer/work/NHCFV/NHCFV1/debug/finalclean-a1516885367.err; #BSUB -w " done(a151688 Jan 25 15:18
2) Since it stalled, I followed the steps provided on the website, killing the jobs and then running these commands:
cat aligned/a1516851053_msplit*_optdups.txt > aligned/opt_dups.txt; cat aligned/a1516851053_msplit*_dups.txt > aligned/dups.txt;cat aligned/a1516851053_msplit*_merged_nodups.txt > aligned/merged_nodups.txt;
juicer.sh -S final
(-: Looking for fastq files...fastq files exist
Job <12850> is submitted to queue <normal>.
Job <12851> is submitted to queue <Stat>.
Job <12852> is submitted to queue <Stat>.
Job <12853> is submitted to queue <CleanFnl>.
Job <12854> is submitted to queue <Stat>.
3) Issuing those commands caused two new commands (stats and hic30) to run:
JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME
12855 ubuntu RUN long HEADNODE HEADNODE a1517075571_stats Jan 27 17:52
12857 ubuntu RUN long HEADNODE HEADNODE a1517075571_hic30 Jan 27 17:52
9504 ubuntu PEND long HEADNODE - a1516851053_postproc Jan 25 03:50
9505 ubuntu PEND normal HEADNODE - a1516851053_done Jan 25 03:50
9859 ubuntu PEND Merge HEADNODE - a1516885367_fragmerge1 Jan 25 15:18
9860 ubuntu PEND Merge HEADNODE - a1516885367_fragmerge Jan 25 15:18
9861 ubuntu PEND Clean3 HEADNODE - a1516885367_clean1 Jan 25 15:18
9862 ubuntu PEND Clean3 HEADNODE - a1516885367_osplit Jan 25 15:18
9863 ubuntu PEND Stat HEADNODE - a1516885367_clean2 Jan 25 15:18
9864 ubuntu PEND Stat HEADNODE - a1516885367_launch Jan 25 15:18
9865 ubuntu PEND Stat HEADNODE - a1516885367_postproc_wrap Jan 25 15:18
9866 ubuntu PEND CleanFnl HEADNODE - a1516885367_prep_done Jan 25 15:18
9867 ubuntu PEND Stat HEADNODE - #!/bin/bash; #BSUB -q Stat; #BSUB -W 1200; #BSUB -o /opt/juicer/work/NHCFV/NHCFV1/debug/finalclean-a1516885367.out ; #BSUB -e /opt/juicer/work/NHCFV/NHCFV1/debug/finalclean-a1516885367.err; #BSUB -w " done(a151688 Jan 25 15:18
12856 ubuntu PEND long HEADNODE - a1517075571_hic Jan 27 17:52
12858 ubuntu PEND long HEADNODE - a1517075571_postproc Jan 27 17:52
12859 ubuntu PEND normal HEADNODE - a1517075571_clean3 Jan 27 17:52
12860 ubuntu PEND normal HEADNODE - a1517075571_done Jan 27 17:52
4) But once those commands finished running, Juicer was stalled again, this time at a done step:
JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME
9505 ubuntu PEND normal HEADNODE - a1516851053_done Jan 25 03:50
9859 ubuntu PEND Merge HEADNODE - a1516885367_fragmerge1 Jan 25 15:18
9860 ubuntu PEND Merge HEADNODE - a1516885367_fragmerge Jan 25 15:18
9861 ubuntu PEND Clean3 HEADNODE - a1516885367_clean1 Jan 25 15:18
9862 ubuntu PEND Clean3 HEADNODE - a1516885367_osplit Jan 25 15:18
9863 ubuntu PEND Stat HEADNODE - a1516885367_clean2 Jan 25 15:18
9864 ubuntu PEND Stat HEADNODE - a1516885367_launch Jan 25 15:18
9865 ubuntu PEND Stat HEADNODE - a1516885367_postproc_wrap Jan 25 15:18
9867 ubuntu PEND Stat HEADNODE - #!/bin/bash; #BSUB -q Stat; #BSUB -W 1200; #BSUB -o /opt/juicer/work/NHCFV/NHCFV1/debug/finalclean-a1516885367.out ; #BSUB -e /opt/juicer/work/NHCFV/NHCFV1/debug/finalclean-a1516885367.err; #BSUB -w " done(a151688 Jan 25 15:18
12860 ubuntu PEND normal HEADNODE - a1517075571_done Jan 27 17:52
5) I tried killing jobs and once again running juicer.sh -S final, which started stats and hic30 jobs with different prefixes:
JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME
12966 ubuntu RUN long HEADNODE HEADNODE a1517097868_stats Jan 28 00:04
12968 ubuntu RUN long HEADNODE HEADNODE a1517097868_hic30 Jan 28 00:04
9505 ubuntu PEND normal HEADNODE - a1516851053_done Jan 25 03:50
9859 ubuntu PEND Merge HEADNODE - a1516885367_fragmerge1 Jan 25 15:18
9860 ubuntu PEND Merge HEADNODE - a1516885367_fragmerge Jan 25 15:18
9861 ubuntu PEND Clean3 HEADNODE - a1516885367_clean1 Jan 25 15:18
9862 ubuntu PEND Clean3 HEADNODE - a1516885367_osplit Jan 25 15:18
9863 ubuntu PEND Stat HEADNODE - a1516885367_clean2 Jan 25 15:18
9864 ubuntu PEND Stat HEADNODE - a1516885367_launch Jan 25 15:18
9865 ubuntu PEND Stat HEADNODE - a1516885367_postproc_wrap Jan 25 15:18
9867 ubuntu PEND Stat HEADNODE - #!/bin/bash; #BSUB -q Stat; #BSUB -W 1200; #BSUB -o /opt/juicer/work/NHCFV/NHCFV1/debug/finalclean-a1516885367.out ; #BSUB -e /opt/juicer/work/NHCFV/NHCFV1/debug/finalclean-a1516885367.err; #BSUB -w " done(a151688 Jan 25 15:18
12860 ubuntu PEND normal HEADNODE - a1517075571_done Jan 27 17:52
12967 ubuntu PEND long HEADNODE - a1517097868_hic Jan 28 00:04
12969 ubuntu PEND long HEADNODE - a1517097868_postproc Jan 28 00:04
12970 ubuntu PEND normal HEADNODE - a1517097868_clean3 Jan 28 00:04
12971 ubuntu PEND normal HEADNODE - a1517097868_done Jan 28 00:04
6) But once they finished, Juicer was once again stalled at the same done step:
JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME
9505 ubuntu PEND normal HEADNODE - a1516851053_done Jan 25 03:50
9859 ubuntu PEND Merge HEADNODE - a1516885367_fragmerge1 Jan 25 15:18
9860 ubuntu PEND Merge HEADNODE - a1516885367_fragmerge Jan 25 15:18
9861 ubuntu PEND Clean3 HEADNODE - a1516885367_clean1 Jan 25 15:18
9862 ubuntu PEND Clean3 HEADNODE - a1516885367_osplit Jan 25 15:18
9863 ubuntu PEND Stat HEADNODE - a1516885367_clean2 Jan 25 15:18
9864 ubuntu PEND Stat HEADNODE - a1516885367_launch Jan 25 15:18
9865 ubuntu PEND Stat HEADNODE - a1516885367_postproc_wrap Jan 25 15:18
9867 ubuntu PEND Stat HEADNODE - #!/bin/bash; #BSUB -q Stat; #BSUB -W 1200; #BSUB -o /opt/juicer/work/NHCFV/NHCFV1/debug/finalclean-a1516885367.out ; #BSUB -e /opt/juicer/work/NHCFV/NHCFV1/debug/finalclean-a1516885367.err; #BSUB -w " done(a151688 Jan 25 15:18
12860 ubuntu PEND normal HEADNODE - a1517075571_done Jan 27 17:52
12971 ubuntu PEND normal HEADNODE - a1517097868_done Jan 28 00:04
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Experiment description: Juicer version 1.5.6; BWA 0.7.12-r1039; 8 threads; splitsize 90000000; java version "1.7.0_79"; /opt/juicer/scripts/juicer.sh -S final
Sequenced Read Pairs: 2,372,999,927
Normal Paired: 802,630,753 (33.82%)
Chimeric Paired: 1,182,415,488 (49.83%)
Chimeric Ambiguous: 374,179,723 (15.77%)
Unmapped: 13,773,963 (0.58%)
Ligation Motif Present: 1,977,990,097 (83.35%)
Alignable (Normal+Chimeric Paired): 1,985,046,241 (83.65%)
stats-a1517122532.err
Exception in thread "main" java.lang.UnsupportedClassVersionError: LibraryComplexity : Unsupported major.minor version 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
stats30hic30-a1517122532.err
Picked up _JAVA_OPTIONS: -Xmx16384m
Exception in thread "main" java.lang.UnsupportedClassVersionError: LibraryComplexity : Unsupported major.minor version 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Picked up _JAVA_OPTIONS: -Xmx8192m
Problem with creating fragment-delimited maps, NullPointerException.
This could be due to a null fragment map or to a mismatch in the chromosome name in the fragment map vis-a-vis the input file or chrom.sizes file.
Exiting.
cat stats-a1517122532.out
Sender: LSF System <genome@HEADNODE>
Subject: Job 13073: <a1517122532_launch> Done
Job <a1517122532_launch> was submitted from host <HEADNODE> by user <ubuntu>.
Job was executed on host(s) <HEADNODE>, in queue <Stat>, as user <ubuntu>.
</home/ubuntu> was used as the home directory.
</opt/juicer/work/NHCFV> was used as the working directory.
Started at Sun Jan 28 06:55:33 2018
Results reported at Sun Jan 28 06:55:33 2018
Your job looked like:
------------------------------------------------------------
# LSBATCH: User input
#!/bin/bash
#BSUB -q Stat
#BSUB -W 1200
#BSUB -o /opt/juicer/work/NHCFV/debug/stats-a1517122532.out
#BSUB -e /opt/juicer/work/NHCFV/debug/stats-a1517122532.err
#BSUB -J "a1517122532_launch"
echo "(-: Alignment and merge done, launching other jobs."
bsub -o /opt/juicer/work/NHCFV/debug/stats-a1517122532.out -e /opt/juicer/work/NHCFV/debug/stats-a1517122532.err -q long -W 3600 -R "rusage[mem=16000]" -J "a1517122532_stats" "df -h;_JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; tail -n1 /opt/juicer/work/NHCFV/debug/head-a1517122532.out | awk '{printf\"%-1000s\n\", \$0}' > /opt/juicer/work/NHCFV/aligned/inter.txt; /opt/juicer/scripts/statistics.pl -s /opt/juicer/restriction_sites/hg38_DpnII.txt -l GATCGATC -o /opt/juicer/work/NHCFV/aligned/stats_dups.txt /opt/juicer/work/NHCFV/aligned/dups.txt; cat /opt/juicer/work/NHCFV/splits/*.res.txt | awk -f /opt/juicer/scripts/stats_sub.awk >> /opt/juicer/work/NHCFV/aligned/inter.txt; java -cp /opt/juicer/scripts/ LibraryComplexity /opt/juicer/work/NHCFV/aligned inter.txt >> /opt/juicer/work/NHCFV/aligned/inter.txt; /opt/juicer/scripts/statistics.pl -s /opt/juicer/restriction_sites/hg38_DpnII.txt -l GATCGATC -o /opt/juicer/work/NHCFV/aligned/inter.txt -q 1 /opt/juicer/work/NHCFV/aligned/merged_nodups.txt; cat /opt/juicer/work/NHCFV/splits/*_abnorm.sam > /opt/juicer/work/NHCFV/aligned/abnormal.sam; cat /opt/juicer/work/NHCFV/splits/*_unmapped.sam > /opt/juicer/work/NHCFV/aligned/unmapped.sam; awk -f /opt/juicer/scripts/collisions.awk /opt/juicer/work/NHCFV/aligned/abnormal.sam > /opt/juicer/work/NHCFV/aligned/collisions.txt"
bsub -o /opt/juicer/work/NHCFV/debug/hic-a1517122532.out -e /opt/juicer/work/NHCFV/debug/hic-a1517122532.err -q long -W 3600 -R "rusage[mem=16000]" -w "done(a1517122532_stats)" -J "a1517122532_hic" "df -h;export _JAVA_OPTIONS=-Xmx16384m; if [ \"0\" -eq 1 ]; then /opt/juicer/scripts/juicer_tools pre -s /opt/juicer/work/NHCFV/aligned/inter.txt -g /opt/juicer/work/NHCFV/aligned/inter_hists.m -q 1 /opt/juicer/work/NHCFV/aligned/merged_nodups.txt /opt/juicer/work/NHCFV/aligned/inter.hic hg38; else /opt/juicer/scripts/juicer_tools pre -f /opt/juicer/restriction_sites/hg38_DpnII.txt -s /opt/juicer/work/NHCFV/aligned/inter.txt -g /opt/juicer/work/NHCFV/aligned/inter_hists.m -q 1 /opt/juicer/work/NHCFV/aligned/merged_nodups.txt /opt/juicer/work/NHCFV/aligned/inter.hic hg38; fi ;"
bsub -o /opt/juicer/work/NHCFV/debug/stats30hic30-a1517122532.out -e /opt/juicer/work/NHCFV/debug/stats30hic30-a1517122532.err -q long -W 3600 -R "rusage[mem=16000]" -J "a1517122532_hic30" "df -h;export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; tail -n1 /opt/juicer/work/NHCFV/debug/head-a1517122532.out | awk '{printf\"%-1000s\n\", \$0}' > /opt/juicer/work/NHCFV/aligned/inter_30.txt; cat /opt/juicer/work/NHCFV/splits/*.res.txt | awk -f /opt/juicer/scripts/stats_sub.awk >> /opt/juicer/work/NHCFV/aligned/inter_30.txt; java -cp /opt/juicer/scripts/ LibraryComplexity /opt/juicer/work/NHCFV/aligned inter_30.txt >> /opt/juicer/work/NHCFV/aligned/inter_30.txt; /opt/juicer/scripts/statistics.pl -s /opt/juicer/restriction_sites/hg38_DpnII.txt -l GATCGATC -o /opt/juicer/work/NHCFV/aligned/inter_30.txt -q 30 /opt/juicer/work/NHCFV/aligned/merged_nodups.txt; export _JAVA_OPTIONS=-Xmx8192m; if [ \"0\" -eq 1 ]; then /opt/juicer/scripts/juicer_tools pre -s /opt/juicer/work/NHCFV/aligned/inter_30.txt -g /opt/juicer/work/NHCFV/aligned/inter_30_hists.m -q 30 /opt/juicer/work/NHCFV/aligned/merged_nodups.txt /opt/juicer/work/NHCFV/aligned/inter_30.hic hg38; else /opt/juicer/scripts/juicer_tools pre -f /opt/juicer/restriction_sites/hg38_DpnII.txt -s /opt/juicer/work/NHCFV/aligned/inter_30.txt -g /opt/juicer/work/NHCFV/aligned/inter_30_hists.m -q 30 /opt/juicer/work/NHCFV/aligned/merged_nodups.txt /opt/juicer/work/NHCFV/aligned/inter_30.hic hg38; fi"
echo
------------------------------------------------------------
Exited
The output (if any) follows:
(-: Alignment and merge done, launching other jobs.
Job <13077> is submitted to queue <long>.
Job <13078> is submitted to queue <long>.
Job <13079> is submitted to queue <long>.
PS:
Read file </opt/juicer/work/NHCFV/debug/stats-a1517122532.err> for stderr output of this job.
Sender: LSF System <genome@HEADNODE>
Subject: Job 13077: <a1517122532_stats> Exited
Job <a1517122532_stats> was submitted from host <HEADNODE> by user <ubuntu>.
Job was executed on host(s) <HEADNODE>, in queue <long>, as user <ubuntu>.
</home/ubuntu> was used as the home directory.
</opt/juicer/work/NHCFV> was used as the working directory.
Started at Sun Jan 28 06:55:34 2018
Results reported at Sun Jan 28 12:39:19 2018
Your job looked like:
------------------------------------------------------------
# LSBATCH: User input
df -h;_JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; tail -n1 /opt/juicer/work/NHCFV/debug/head-a1517122532.out | awk '{printf"%-1000s\n", $0}' > /opt/juicer/work/NHCFV/aligned/inter.txt; /opt/juicer/scripts/statistics.pl -s /opt/juicer/restriction_sites/hg38_DpnII.txt -l GATCGATC -o /opt/juicer/work/NHCFV/aligned/stats_dups.txt /opt/juicer/work/NHCFV/aligned/dups.txt; cat /opt/juicer/work/NHCFV/splits/*.res.txt | awk -f /opt/juicer/scripts/stats_sub.awk >> /opt/juicer/work/NHCFV/aligned/inter.txt; java -cp /opt/juicer/scripts/ LibraryComplexity /opt/juicer/work/NHCFV/aligned inter.txt >> /opt/juicer/work/NHCFV/aligned/inter.txt; /opt/juicer/scripts/statistics.pl -s /opt/juicer/restriction_sites/hg38_DpnII.txt -l GATCGATC -o /opt/juicer/work/NHCFV/aligned/inter.txt -q 1 /opt/juicer/work/NHCFV/aligned/merged_nodups.txt; cat /opt/juicer/work/NHCFV/splits/*_abnorm.sam > /opt/juicer/work/NHCFV/aligned/abnormal.sam; cat /opt/juicer/work/NHCFV/splits/*_unmapped.sam > /opt/juicer/work/NHCFV/aligned/unmapped.sam; awk -f /opt/juicer/scripts/collisions.awk /opt/juicer/work/NHCFV/aligned/abnormal.sam > /opt/juicer/work/NHCFV/aligned/collisions.txt
------------------------------------------------------------
Exited with signal termination: Killed.
Resource usage summary:
CPU time : 0.01 sec.
Max Memory : 770 MB
Max Swap : 808 MB
Max Processes : 3
The output (if any) follows:
Filesystem Size Used Avail Use% Mounted on
/dev/xvda1 20G 5.6G 14G 30% /
udev 30G 12K 30G 1% /dev
tmpfs 6.0G 256K 6.0G 1% /run
none 5.0M 0 5.0M 0% /run/lock
none 30G 0 30G 0% /run/shm
/dev/xvdb 15T 8.9T 4.9T 65% /opt
PS:
Read file </opt/juicer/work/NHCFV/debug/stats-a1517122532.err> for stderr output of this job.
stats30hic30-a1517122532.out
Sender: LSF System <genome@HEADNODE>
Subject: Job 13079: <a1517122532_hic30> Exited
Job <a1517122532_hic30> was submitted from host <HEADNODE> by user <ubuntu>.
Job was executed on host(s) <HEADNODE>, in queue <long>, as user <ubuntu>.
</home/ubuntu> was used as the home directory.
</opt/juicer/work/NHCFV> was used as the working directory.
Started at Sun Jan 28 06:55:34 2018
Results reported at Sun Jan 28 12:38:31 2018
Your job looked like:
------------------------------------------------------------
# LSBATCH: User input
df -h;export _JAVA_OPTIONS=-Xmx16384m; export LC_ALL=en_US.UTF-8; tail -n1 /opt/juicer/work/NHCFV/debug/head-a1517122532.out | awk '{printf"%-1000s\n", $0}' > /opt/juicer/work/NHCFV/aligned/inter_30.txt; cat /opt/juicer/work/NHCFV/splits/*.res.txt | awk -f /opt/juicer/scripts/stats_sub.awk >> /opt/juicer/work/NHCFV/aligned/inter_30.txt; java -cp /opt/juicer/scripts/ LibraryComplexity /opt/juicer/work/NHCFV/aligned inter_30.txt >> /opt/juicer/work/NHCFV/aligned/inter_30.txt; /opt/juicer/scripts/statistics.pl -s /opt/juicer/restriction_sites/hg38_DpnII.txt -l GATCGATC -o /opt/juicer/work/NHCFV/aligned/inter_30.txt -q 30 /opt/juicer/work/NHCFV/aligned/merged_nodups.txt; export _JAVA_OPTIONS=-Xmx8192m; if [ "0" -eq 1 ]; then /opt/juicer/scripts/juicer_tools pre -s /opt/juicer/work/NHCFV/aligned/inter_30.txt -g /opt/juicer/work/NHCFV/aligned/inter_30_hists.m -q 30 /opt/juicer/work/NHCFV/aligned/merged_nodups.txt /opt/juicer/work/NHCFV/aligned/inter_30.hic hg38; else /opt/juicer/scripts/juicer_tools pre -f /opt/juicer/restriction_sites/hg38_DpnII.txt -s /opt/juicer/work/NHCFV/aligned/inter_30.txt -g /opt/juicer/work/NHCFV/aligned/inter_30_hists.m -q 30 /opt/juicer/work/NHCFV/aligned/merged_nodups.txt /opt/juicer/work/NHCFV/aligned/inter_30.hic hg38; fi
------------------------------------------------------------
Exited with exit code 63.
Resource usage summary:
CPU time : 20418.05 sec.
Max Memory : 768 MB
Max Swap : 806 MB
Max Processes : 3
The output (if any) follows:
Filesystem Size Used Avail Use% Mounted on
/dev/xvda1 20G 5.6G 14G 30% /
udev 30G 12K 30G 1% /dev
tmpfs 6.0G 256K 6.0G 1% /run
none 5.0M 0 5.0M 0% /run/lock
none 30G 0 30G 0% /run/shm
/dev/xvdb 15T 8.9T 4.9T 65% /opt
PS:
Read file </opt/juicer/work/NHCFV/debug/stats30hic30-a1517122532.err> for stderr output of this job.
sudo add-apt-repository ppa:webupd8team/java
sudo apt-get update
sudo apt-get install oracle-java8-installer
Best,
David.
To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/06ef2dc2-a687-4146-a731-fae6a27104b4%40googlegroups.com.
...
[Message clipped]
Hi David,sudo apt-get update gets hung up because it cannot update R. It turns out most mirrors no longer host R for Ubuntu 12.04 (Precise).Without getting past this hurdle, I can't update Java on the Juicer AMI.Please advise.Thanks,
Richard
On Wednesday, February 7, 2018 at 6:13:51 PM UTC-5, Richard Gill wrote:
Thanks David. I will give that a try. I updated the juicer_tools jar and the pipeline ran until the done step and generated a .hic file.Richard
Please advise.<div style="font-family:arial