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 The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.