Hi Maria, This message indicates that an error occurred on the cluster node processing the job. Normally these are not linked to inputs or tools and the general solution is to re-run the job. Please give this a try today - it is possible the error was linked to recent transient server issues. If you continue to have problems after the re-run today, please submit a bug report from the error dataset, leaving inputs and outputs undeleted: http://wiki.galaxyproject.org/Support#Reporting_tool_errors Best, Jen Galaxy team On 9/11/13 12:38 PM, Maria Hoffman wrote:

Hello,

I am fairly new to galaxy and I am trying to use bowtie2 to map my reads against a custom genome (specifically a ribosomal RNA fasta file). I have formatted the file as suggested in the Galaxywiki ect and I am still getting the following message: Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error.

Any help would me much appreciated!

Maria

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