[Iplant-api-dev] Error with InterProScan via DE

Fri Jun 27 11:05:30 MST 2014

Is there anyone who has access to this script (since we don't here at UA)
who might be able to help us get this fixed?

On Thu, Jun 26, 2014 at 1:58 PM, Ghiban, Cornel <ghiban at cshl.edu> wrote:

> Adding this should work (at least on lonestar):
>
> load java64/1.7.0
>
> Cornel
>
> On Thu, 2014-06-26 at 13:58 -0500, Cathy Gresham wrote:
> >
> > Do not know if this helps but one of the out files from the failed job
> > lists the env settings that you set up for
> > interproscan:
> >
> > OUT TEXT FILE:
> > # Environmental settings for interproscan-5.44.0u1:
> > module purge
> > module load TACC
> > module swap intel gcc
> > module load iRODS
> > module load perl
> > module load launcher
> > THREADS=1
> > OWD=$PWD
> >
> > # Unpack bin directory
> > tar -zxf bin.tgz
> > PATH=${PATH}:${OWD}/bin
> > # Deployed in the TACC scratch projects space dedicated to iPlant
> > # until we can develop a module for InterproScan
> >
> IPRSCAN="/scratch/projects/tacc/iplant/interproscan/5/interproscan-5-44.0/"
> > PATH=${PATH}:${IPRSCAN}:${IPRSCAN}/bin
> >
> >
> > interproscan.sh which is throwing the java error has this code to
> > identify java:
> >
> > JAVA=$(type -p java)
> >
> > if [[ "$JAVA" == "" ]]; then
> >     printf 'Java not found. Please install java\n'
> >     printf 'and place it on your path,\n'
> >     printf 'or edit the interproscan.sh script to refer to your java
> > installation.\n'.
> >     exit 1
> > fi
> > VERSION=$("$JAVA" -Xms32M -Xmx32M -version 2>&1 | { read X; printf '%
> > s' "${X#*\"}"; } )
> > MAJOR_VERSION=${VERSION%%.*}
> > MINOR_VERSION=${VERSION#*.}
> > MINOR_VERSION=${MINOR_VERSION%%.*}
> >
> > if [[ "${MAJOR_VERSION}" == "1" && "${MINOR_VERSION}" -lt "6" ]];
> > then
> >     printf 'Java version 1.6 or above required\n'
> >     printf 'Detected version %s.%s\n' "${MAJOR_VERSION}"
> > "${MINOR_VERSION}"
> >     printf 'Install the correct version \n'
> >     printf 'or edit the interproscan.sh script to disable version
> > check.\n'
> >     exit 1
> > fi
> >
> > "$JAVA" -XX:+UseParallelGC -XX:ParallelGCThreads=2 -XX:+AggressiveOpts
> > -XX:+UseFastAccessorMethods -Xms128M -Xmx2048M -jar
> > interproscan-5.jar $@ -u $USER_DIR
> >
> >
> >
> > >>> "Barthelson, Roger A - (rogerab)" <rogerab at email.arizona.edu>
> > 6/26/2014 1:42 PM >>>
> >
> > Java is generally loaded as a module on TACC machines. It is possible
> > that the java module on Lonestar or Stampede (wherever it runs) was
> > updated and that the name change rendered the app inoperable. I have
> > run into this sort of problem before with e.g. irods.
> >
> >
> > Roger
> > --
> > Roger Barthelson Ph.D.
> > Scientific Analyst
> > iPlant Collaborative
> > BIO5 Institute, University of Arizona
> > Phone: 520-977-5249
> > Email: rogerab at email.arizona.edu
> > Web: www.iplantcollaborative.org/
> >
> > On June 26, 2014 at 11:38:53 AM, Dennis Roberts
> > (dennis at iplantcollaborative.org) wrote:
> >
> > >
> > > Hi Nicole,
> > >
> > >
> > > It appears that the issue is that Java isn’t available in the
> > > location where the app is being executed. If this is the case then
> > > this isn’t something that can be fixed in the DE.
> > >
> > >
> > > Thanks,
> > > Dennis
> > >
> > >
> > > On Jun 26, 2014, at 11:30 AM, Nicole Hopkins
> > > <nicole at iplantcollaborative.org> wrote:
> > >
> > > > Up until a few weeks ago, the InterProScan5-44.0 tool in the DE
> > > > was working quite well. Fiona and Cathy have been using it, and
> > > > have recently had jobs complete, but with empty datasets
> > > > returned.
> > > > A look at the .out log from the tool gives this error message:
> > > >
> > > >
> > > > TACC Launcher -> Iniating task 1 on c339-104.ls4.tacc.utexas.edu
> > > > (time
> /scratch/projects/tacc/iplant/interproscan/5/interproscan-5-44.0/interproscan.sh
> --formats tsv,gff3,xml --iprlookup --goterms --pathways --tempdir /tmp
> --output-dir output --input split_fasta/seqfile.0 )
> > > > Java not found. Please install java
> > > > and place it on your path,
> > > > or edit the interproscan.sh script to refer to your java
> > > > installation.
> > > > .TACC: Shutting down parallel environment.
> > > > TACC: Shutdown complete. Exiting.
> > > >
> {"status":"success","message":"","result":{"id":54209,"name":"InterproScan5-44.0_example_test2-2014-06-26-16-50-
> > > >
> > > >
> > > > This is running via on v1 of the API. I am assuming it will be
> > > > running via Agave as well, but is there a fix that can be put in
> > > > place near term?
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Nicole Hopkins
> > > > Scientific Initiatives Coordinator
> > > > iPlant Collaborative- University of Arizona
> > > > (520) 626-7390
> > > >
> > > > _______________________________________________
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> > > >
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> > >
> > >
> > > _______________________________________________
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> > >
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> > >
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-- 
Nicole Hopkins
Scientific Initiatives Coordinator
iPlant Collaborative- University of Arizona
(520) 626-7390
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