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?
Thanks in advance,
Nick
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