Question: Snpeff build error
2
gravatar for v4savaishnavi
5 months ago by
v4savaishnavi30 wrote:

Hi,

I am trying to do exome analysis among Solanum lycopersicum leaf curl mutants. I have followed exome analysis pipeline using Varscan in galaxy and obtained a VCF file. For doing annotation I need to build a Snpeff database for that I have uploaded an annotation file with genbank format 'GCF_000188115.3_SL2.50_genomic (5).gbff'. The following error has been shown while building SnpEff database:

Fatal error: Exit code 255 (Error)
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/019/427/19427315/_job_tmp -Xmx7g  -Xms256m
00:00:00    SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00    Command: 'build'
00:00:00    Building database for 'SoLy'
00:00:00    Reading configuration file 'snpEff.config'. Genome: 'SoLy'
00:00:00    Reading config file: /galaxy-repl/main/jobdir/019/427/19427315/working/snpEff.config
00:00:00    Reading config file: /cvmfs/main.galaxyproject.org/deps/_conda/pkgs/snpeff-4.3.1t-0/share/snpeff-4.3.1t-0/snpEff.config
00:00:02    done
java.lang.RuntimeException: Cannot find sequence for 'SoLy'
    at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.sequence(SnpEffPredictorFactoryFeatures.java:467)
    at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.addFeatures(SnpEffPredictorFactoryFeatures.java:111)
    at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.create(SnpEffPredictorFactoryFeatures.java:330)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:369)
    at org.snpeff.SnpEff.run(SnpEff.java:1183)
    at org.snpeff.SnpEff.main(SnpEff.java:162)
java.lang.RuntimeException: Error reading file '/galaxy-repl/main/jobdir/019/427/19427315/dataset_25181627_files/SoLy/genes.gbk'
java.lang.RuntimeException: Cannot find sequence for 'SoLy'
    at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.create(SnpEffPredictorFactoryFeatures.java:344)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:369)
    at org.snpeff.SnpEff.run(SnpEff.java:1183)
    at org.snpeff.SnpEff.main(SnpEff.java:162)
00:00:09    Logging
00:00:10    Checking for updates...
00:00:11    Done.

Please help me regarding this query.Thanks in advance.

ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson25k • written 5 months ago by v4savaishnavi30
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

If working at Galaxy Main https://usegalaxy.org, try this again as there have been recent server updates as the 18.05 pre-release nears completion.

Should the job error again, please send in a bug report. There have been problems with SnpEff tools, updated versions have been created and added to the server, but there could still be a few issues with the tool suite.

If working somewhere else, you might try to see if the problem can be reproduced at Galaxy Main, then submit the bug report.

Make sure that the input and output datasets are left undeleted and include a link to your question here in the comments.

FAQ https://galaxyproject.org/support/#unexpected-results >> https://galaxyproject.org/issues/

I'll also run an independent test to review the current functionality for build tool to see if I can reproduce this.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson25k
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