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
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