On Nov 19, 2012, at 8:01 AM, Nicholas Tucker wrote:

Dear all, I have mapped some Illumina reads to a reference using Bowtie. I am trying to use Sam Tools to convert Sam to Bam on our local galaxy, but it always fails:

Traceback (most recent call last): File "/export/galaxy/galaxy-central/lib/galaxy/jobs/runners/local.py", line 155, in run_job job_wrapper.finish( stdout, stderr, exit_code ) File "/export/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py", line 396, in finish dataset.datatype.set_meta( dataset, overwrite = False ) #call datatype.set_meta directly for the initial set_meta call during dataset creation File "/export/galaxy/galaxy-central/lib/galaxy/datatypes/binary.py", line 213, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found

Tool execution generated the following error message:

Unable to finish job

The resulting failure always generates a large file, as if it has almost completed……

Anybody got an idea what the error might be and how to solve it please?

Hi Nick, samtools appears to be found when running the tool itself (to convert SAM to BAM), however, during the setting of metadata, samtools cannot be found (to create the BAM index). I'd suggest enabling 'set_metadata_externally' in the Galaxy config file and ensuring that the `samtools` binary is on the Galaxy user's $PATH when the server starts (if running jobs locally). --nate

Thanks in advance, Nick

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