Question: SnpEff error and problems downloading genome
0
gravatar for carey.lambert
16 months ago by
carey.lambert0 wrote:

Running SnpEff generates the following error: Fatal error: Exit code 1 (Error) Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/016/025/16025586/_galaxy_tmp -Xmx7680m -Xms256m java.lang.RuntimeException: java.io.FileNotFoundException: /cvmfs/main.galaxyproject.org/deps/snpEff/4.0/i

I am running it on a vcf pileup and selecting the genome: Bdellovibrio_bacteriovorus_HD100_uid61595

Manual download of this and selecting "reference genome from your history" stops the above error, but SnpEff download seems to have had a problem with this download and the whole of the file appears to be just the lines: Bacillus_thuringiensis_BMB171_uid49135 SnpEff4.1 So it looks like this has just downloaded the first line in a group of genomes.

Any suggestions very welcome. Thanks, Carey

snpeff snp usegalaxy.org • 678 views
ADD COMMENTlink modified 16 months ago by Jennifer Hillman Jackson25k • written 16 months ago by carey.lambert0

Hello, This might be a true bug. Perhaps with compressed file unpacking. Or possibly some connection issue with the data source. Would you please send in a bug report (green bug icon inside the expanded error dataset)

1) Include a link to this Biostars post in the comments

2) And leave all inputs and outputs undeleted. For this case, it is important that we can access the complete analysis path leading up to this error. Undelete datasets or rerun to produce the error if needed.

We'll often need access to the complete analysis thread to effectively troubleshoot and confirm a software or configuration bug and this is new as far as I know. Once we make a copy for testing, I'll email you back so you can then delete data, if the workspace is needed for other analysis while we investigate. Thanks for taking the time to send in the error and very sorry you ran into problems! Jen, Galaxy team

ADD REPLYlink modified 16 months ago • written 16 months ago by Jennifer Hillman Jackson25k

Thanks for the quick response and sorry for the delay in responding. I've re-run and sent the bug report.

ADD REPLYlink written 16 months ago by carey.lambert0

Thanks for sending this in. I'll review and send feedback soon.

ADD REPLYlink written 16 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
16 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Updated reply

The root problem is with the tool itself. A newer version is available that may resolve the issue. Please follow progress here: https://github.com/galaxyproject/tools-iuc/issues/1354

Thank you, Carey, for following up!

Jen, Galaxy team

ADD COMMENTlink modified 16 months ago • written 16 months ago by Jennifer Hillman Jackson25k

Update: The workaround is to use a Genbank annotation dataset with the tools instead.

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson25k
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