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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