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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