Question: Tool failure that reports: AttributeError: 'module' object has no attribute 'ICM'
2
gravatar for Mickael Di
9 months ago by
Mickael Di30
Belgium
Mickael Di30 wrote:

Hi,

I want to run Tuxedo2 workflow associating cufflinks with a gtf annotation file. TopHat seems to be OK but after I get this error with cufflinks:

Fatal error: Matched on ERROR ERROR:galaxy.datatypes.registry:Error calling method ICM from class Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 425, in load_datatype_sniffers aclass = getattr(module, datatype_class_name)() AttributeError: 'module' object has no attribute 'ICM'

Does anybody can help me with this error?

Thank you

Mickael

ADD COMMENTlink modified 9 months ago by ellascottgm0 • written 9 months ago by Mickael Di30
1

Thanks for your answer Jennifer. I am waiting for your feedback.

This error appears and I can read there is an error with this data. I can open the datafile and is my GTF. Do you think my GTF is wrong? In my GTF the chromosomes loci are annoted as 1:3905738-3986215 for example and not chrs1:3905738-398621. Do you think is a problem for cufflinks?

Thanks you.

Mickael

ADD REPLYlink written 9 months ago by Mickael Di30

Hello, We saw a few jobs end with the error yesterday and are following up. More feedback soon. Jen, Galaxy team

ADD REPLYlink written 9 months ago by Jennifer Hillman Jackson25k
1
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Tool errors can sometimes involve multiple issues that need to be resolved.

This error was determined to be a code bug, tagged as a problem, and fixed. It needs to be applied to the server.

We will be updating Galaxy Main (https://usegalaxy.org) soon. Possibly today, more likely Monday (we generally do not do server updates on a Friday). Track when that is done here: https://github.com/galaxyproject/usegalaxy-playbook/issues/66

For anyone else that runs into this problem on their a local Galaxy running release version 17.09 the solution is to update your instance. How-to: https://getgalaxy.org

And yes, the mismatched chromosome identifiers between the reference genome and reference annotation will be a problem even after the above bug is fixed. It can also impact analysis when using other tools. Some tools will error because of this type of mismatch (different than the one above). Other tools will output results with content issues.

Details explained:

Thanks for reporting the problem! Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson25k
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