Question: Workflow always crashes in same step
gravatar for nermze
3 months ago by
nermze0 wrote:

Hi, im running a local Galaxy server, and using a tried and tested workflow to do some analysis on my data. My problem is that it keeps crashing on the same step in the workflow, even when I use data and workflow provided by the same paper. It starts fine and does step 1 to 4, but than it just stops with the following error:

Traceback (most recent call last):

File "/home/nermze/shed_tools/", line 203, in <module> File "/home/nermze/shed_tools/", line 172, in run self._sortFiles() File "/home/nermze/shed_tools/", line 102, in _sortFiles fs.sort() File "/home/nermze/shed_tools/", line 78, in sort self._batchSort() File "/home/nermze/shed_tools/", line 204, in _batchSort self._merge(self._chunks[chromosome], chromosome, outputHandle) File "/home/nermze/shed_tools/", line 133, in _merge self._mergeParts(chunks, outputHandle) File "/home/nermze/shed_tools/", line 156, in _mergeParts transcript = pickle.load(chunk) ValueError: I/O operation on closed file

Does anyone have any idea whats going on, is there a problem with the data, or some python or ..?`

rna-seq galaxy bam • 136 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by nermze0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:


I would suggest contacting the authors of the publication/workflow. They'll be able to offer more support to determine the problem.

This could be either a data problem (perhaps the prior steps output is empty or malformed?) or there could also be a tool bug or some conflict between the version of Galaxy required by the tools/workflow and the one you are using.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k
gravatar for nermze
3 months ago by
nermze0 wrote:

The guy who wrote it has long abandoned the workflow and his job, as the email provided is not in use anymore. Since I'm unable to replicate his research, and subsequently not able to do my own, i think i will abandon it for now.

Are there are other workflows in galaxy designed to discover new small RNA? That's really all i need, i have already trimmed and assembled all my sequences. I really just cant find any good ways to analyze them to discovered new small RNA.

Any input is appreciated.

ADD COMMENTlink written 3 months ago by nermze0

I understand, not all authors will continue to support published work (unfortunately). Or, you might be able to track them down with a google (perhaps they switched institutions/place of work).

Or, you can move on as planned. Please see the Galaxy tutorials for examples of current RNA-seq tools/workflows. Even if the tutorial does not have a workflow attached yet, one could be created from a history based on the hands-on protocol. From there it can be customized as needed for your own work.

If you do create a workflow that is an exact match for a tutorial that doesn't have one yet, it could be sent in as a contribution to the Galaxy Training Network (GTN). The GTN hosts a "Contribution Co-Fest" every three months. We just had one last Friday. The GTN has a Gitter channel if you run into problems or wish to contribute/get involved:

To learn which public Galaxy servers are known to contain all of the tool/versions included any particular tutorial, review the menu under "Galaxy instances". Newer versions of the tool may be on other public Galaxies, so you'll need to check and then adapt the protocol. Updated tools/forms are often modified to fix bugs and/or include more options and/or work with newer versions of the underlying 3rd party tools.

Some tutorial groups also have a pre-configured Docker image for local use. When available, that is noted on the tutorial group's homepage.

There are also domain-specific Galaxy servers. Some have custom wrapped tools and include even more analysis workflows.

Hope that helps! Jen

ADD REPLYlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson25k
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