Question: TopHat not working
gravatar for tran_tim
2.6 years ago by
tran_tim10 wrote:

My tophat in galaxy is not working. I try to use it to map to the reference human hg19 genome. But the run failed because there is a red mark check on each datasets from the examples.

tophat • 876 views
ADD COMMENTlink modified 2.2 years ago • written 2.6 years ago by tran_tim10
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Recent server configuration changes at likely caused these jobs to fail. Please re-run them.

If these jobs fail again today, send in a bug report from one of the red error datasets and we can provide more feedback. Leave all input and the error datasets undeleted. Include a link to this Biostars post in the comments.

If you are working at a different Galaxy server - then contacting the administrators of that instance is the path for a solution.

There can be many reasons why a job fails. Input formats, other form settings that are in conflict with the inputs or each other, server or cluster issues. The first two you can review yourself and correct, the latter requires either a re-run or admin assistance.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k
gravatar for tran_tim
2.2 years ago by
tran_tim10 wrote:

I receive the following error while running tophat: Traceback (most recent call last): File "/galaxy-repl/main/jobdir/013/902/13902630/", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/cvmfs/", line 85, in set_metadata datatypes_registry.load_datatypes( root_dir=galaxy_root, config=datatypes_config ) File "/cvmfs/", line 97, in load_datatypes tree = galaxy.util.parse_xml( config ) File "/cvmfs/", line 209, in parse_xml root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) ) File "/cvmfs/", line 647, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: '/galaxy/main/scratch/tmp1ilzMo'

Please help. I already try to rerun it now. I use tophat and my input file is a large fastq files >12 G, and a reference genome hg19.

ADD COMMENTlink written 2.2 years ago by tran_tim10

Hello - would you please move this reply to a brand new post question? The issues are different now. I can let you know that we are looking into this, but let's discuss the whole thing in its own thread. I'll remove this post here after I see that you have created the new one.

Jen, Galaxy team

ADD REPLYlink written 2.2 years ago by Jennifer Hillman Jackson25k
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