Juicer on AWS failure: Error: Unable to access jarfile ./juicer_tools.7.0.jar
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Darya
Jun 23, 2017, 1:08:04 AM6/23/17
to 3D Genomics
Hi!
I'm trying to use your AWS AMI ami-458fc22f to run an analysis. I'm getting the following error:
Error: Unable to access jarfile /opt/juicer/scripts/juicer_tools.7.0.jar
The following is the first mention of this in the lsf.out:
Job <a1498176700_hic> 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/a1> was used as the working directory.
Started at Fri Jun 23 03:41:06 2017
Results reported at Fri Jun 23 03:41:06 2017
Your job looked like:
------------------------------------------------------------
# LSBATCH: User input
df -h;export _JAVA_OPTIONS=-Xmx16384m; if [ "0" -eq 1 ]; then /opt/juicer/scripts/juicer_tools pre -s /opt/juicer/work/a1/aligned/inter.txt -g /opt/juicer/work/a1/aligned/inter_hists.m -q 1 /opt/juicer/work/a1/aligned/merged_nodups.txt /opt/juicer/work/a1/aligned/inter.hic hg19; else /opt/juicer/scripts/juicer_tools pre -f /opt/juicer/restriction_sites/hg19_HindIII.txt -s /opt/juicer/work/a1/aligned/inter.txt -g /opt/juicer/work/a1/aligned/inter_hists.m -q 1 /opt/juicer/work/a1/aligned/merged_nodups.txt /opt/juicer/work/a1/aligned/inter.hic hg19; fi ;
------------------------------------------------------------
Exited
The output (if any) follows:
Filesystem Size Used Avail Use% Mounted on
/dev/xvda1 7.9G 5.0G 2.6G 67% /
udev 15G 12K 15G 1% /dev
tmpfs 3.0G 260K 3.0G 1% /run
none 5.0M 0 5.0M 0% /run/lock
none 15G 0 15G 0% /run/shm
/dev/xvdb 3.4T 190G 3.1T 6% /opt
Error: Unable to access jarfile /opt/juicer/scripts/juicer_tools.7.0.jar
When I ls the /opt/juicer/scripts directory, such a file is indeed not found:
ls /opt/juicer/scripts
abnormal.awk chimeric_blacklist.awk collisions.awk dups.awk fragment.pl hicInternalMenu.properties juicebox_tools.jar juicer_hiccups.sh juicer.sh lib64 LibraryComplexity.java mega.sh split_rmdups.awk stats_sub.awk
check.sh cleanup.sh countligations.sh fragment_4dnpairs.pl juicebox juicer_arrowhead.sh juicer_postprocessing.sh juicer_tools LibraryComplexity.class makemega_addstats.awk relaunch_prep.sh statistics.pl
My aligned folder so far contains the following:
ubuntu@HEADNODE /opt/juicer/work/a1> ls aligned/
abnormal.sam collisions.txt dups.txt inter_30_hists.m inter_30.txt inter_hists.m inter.txt merged_nodups.txt merged_sort.txt opt_dups.txt stats_dups_hists.m stats_dups.txt unmapped.sam
How do I get around this problem?
Thanks in advance!
Muhammad Saad Shamim
Jun 23, 2017, 1:20:38 AM6/23/17
to Darya, 3D Genomics
Hi Darya,
We'll look into the AWS scripts regarding this issue.
In the meantime, you can directly download the jar from this page:
And move it into the scripts folder.
Example:
mv juicer_tools.1.6.2_jcuda.0.7.0.jar /opt/juicer/scripts/juicer_tools.7.0.jar
And then run juicer.sh with the -S stage flag.
[stage]: must be one of "merge", "dedup", "final", "postproc" or "early".
Use "merge" when alignment has finished but the merged_sort file has not yet been created.
Use "dedup" when the files have been merged into merged_sort but merged_nodups has not yet been created.
Use "final" when the reads have been deduped into merged_nodups but the final stats and hic files have not yet been created.
Use "early" for an early exit, before the final creation of the stats and hic files
So something like
/opt/juicer/scripts/juicer.sh -g hg19 -s DpnII -S final
(with the appropriate genome and restriction enzyme that you're using)
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Neva Durand
Jun 23, 2017, 1:43:55 AM6/23/17
to Muhammad Saad Shamim, Darya, 3D Genomics
Muhammad gave a great answer. I will just add that if you look at the requirements on the wiki:
You will see that you need to install the Juicer tools jar. We no longer store the jars in the scripts folders as it's bad practice.
Best
Neva
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Darya
Jun 23, 2017, 1:51:20 AM6/23/17
to 3D Genomics, sa50...@gmail.com, d.vani...@gmail.com
Hi Neva,
I'm using your AMI - I thought that was supposed to have all of the tools already properly preconfigured/installed for use? Do you know whether there is anything else I have to manually install/reconfigure to get it to work correctly?
Thanks in advance,
Darya
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Neva Durand
Jun 23, 2017, 1:52:04 AM6/23/17
to Darya, 3D Genomics, Muhammad Shamim (via Google Docs)
Ah, indeed the AMI should have everything needed. We will look into it.
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Muhammad Saad Shamim
Jun 23, 2017, 1:58:38 AM6/23/17
to Neva Durand, Darya, 3D Genomics
I've updated the instructions under AWS first-time tweaks to resolve this:
There should be no additional changes needed that I am aware of.
Please do let us know if any other bugs are encountered!
Muhammad Saad Shamim
Jun 23, 2017, 2:03:04 AM6/23/17
to Neva Durand, Darya, 3D Genomics
Note that the AMI does have everything including the jar and scripts initially.
The jar is removed when updating to the latest version of the juicer scripts (since the latest scripts no longer contain the jar by default).
It's technically ok to run without updating to the latest scripts, and juicer would run fine.
Best,
Darya
Jun 26, 2017, 12:19:53 AM6/26/17
to 3D Genomics, ne...@broadinstitute.org, d.vani...@gmail.com
Continuing with implementing on AWS:
cd /opt/juicer/scripts
> ./juicer_tools arrowhead
Usage: juicebox arrowhead [-c chromosome(s)] [-m matrix size] [-r resolution] [-k normalization (NONE/VC/VC_SQRT/KR)] [--ignore_sparsity flag] <hicFile(s)> <output_file> [feature_list] [control_list]
> ./juicebox arrowhead
Usage: juicebox arrowhead [-c chromosome(s)] [-m matrix size] [-r resolution] [-k normalization (NONE/VC/VC_SQRT/KR)] <HiC file(s)> <output_file> [feature_list] [control_list]
Thanks in advance!
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Neva Durand
Jun 26, 2017, 3:36:04 AM6/26/17
to Darya, 3D Genomics
Hello Darya,
Thanks for pointing this out - there should be only one, juicer_tools. It is also surprising because this indicates they are calling different jar files. We will look into the discrepancy but for now just run juicer_tools for Arrowhead.
Best
Neva
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