I am trying to resolve an issue with snpEff 3.4 running on a cloudman instance 
of galaxy.  The instance is invoking the following command and failing:

java -Xmx6G -jar $SNPEFF_JAR_PATH/snpEff.jar eff -c 
$SNPEFF_JAR_PATH/snpEff.config -i vcf -o vcf -upDownStreamLen 5000 
-spliceSiteSize 1 -stats /mnt/galaxy/files/000/dataset_364.dat -noLog -download 
GRCh37.68 /mnt/galaxy/files/000/dataset_313.dat > 
/mnt/galaxy/files/000/dataset_363.dat

The error it is reporting is:

Fatal error: Exit code 255 (Error)
java.lang.RuntimeException: java.lang.RuntimeException: File not found on the 
server. Make sure the database name is correct.
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.download(SnpEffCmdDownload.java:159)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:234)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:217)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1001)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)
Caused by: java.lang.RuntimeException: File not found on the server. Make sure 
the database name is correct.
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.download(SnpEffCmdDownload.java:122)
... 8 more
java.lang.RuntimeException: Genome download failed!
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1002)
at 
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)

I have upgraded to java 1.7.0 due to an issue with GATK2.

In addition to this when I try to run snpEff I am unable to select a genome 
source unless I use the "Named on demand" option.  How do I get snpEff genome 
version data configured?  The snpEff_genomes.loc file lists all of the genomes 
I need and many more.  I appreciate the help.

Regards,
Iry

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