Hi All, I have installed snpEff 3.1 from the galaxy toolshed into my cloud man instance. The tool runs to completion, but I get an empty file. It says as 'no peek' in the history. When I view the details and check the stderr and get the following: WARNING: Chromosome '@PG' not found. File '/mnt/galaxyData/files/000/dataset_58.dat', line 85 java.lang.ArrayIndexOutOfBoundsException: 5 at ca.mcgill.mcb.pcingola.fileIterator.SeqChangeFilePileUp.readNext(SeqChangeFilePileUp.java:69) at ca.mcgill.mcb.pcingola.fileIterator.SeqChangeFilePileUp.readNext(SeqChangeFilePileUp.java:1) at ca.mcgill.mcb.pcingola.fileIterator.FileIterator.hasNext(FileIterator.java:69) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.iterateSeqChange(SnpEffCmdEff.java:139) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.runAnalysis(SnpEffCmdEff.java:750) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:689) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:564) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:276) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:75) I reinstalled the tool and reran the job. Now I get this from the stderr: java.lang.ArrayIndexOutOfBoundsException: 7 at ca.mcgill.mcb.pcingola.fileIterator.SeqChangeFilePileUp.readNext(SeqChangeFilePileUp.java:70) at ca.mcgill.mcb.pcingola.fileIterator.SeqChangeFilePileUp.readNext(SeqChangeFilePileUp.java:1) at ca.mcgill.mcb.pcingola.fileIterator.FileIterator.hasNext(FileIterator.java:69) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.iterateSeqChange(SnpEffCmdEff.java:139) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.runAnalysis(SnpEffCmdEff.java:750) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:689) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:564) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:276) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:75) Any ideas? Thanks, Iry Witham 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.