General Category >> Help and How-to >> Clustal Omega error code

Message started by izwan on Jun 20th, 2016 at 2:36pm

Title: Clustal Omega error code
Post by izwan on Jun 20th, 2016 at 2:36pm
Hi guys,

I've been getting some error codes when running Clustal Omega on Ugene. Is there a repository for a list of error codes and their interpretations available anywhere? My attempts at searching for the info via Google haven't been fruitful for a while now.


Title: Re: Clustal Omega error code
Post by Yuliya Algaer on Jun 22nd, 2016 at 12:56pm
We have no list of error codes of the Clustaw Omega tool.

I've quickly checked tool's source code and I suppose that there is no connection between errors and return codes. Clustal Omega returns the error message as plain text.

UGENE should correctly parse these messages and show them to user, a new issue is created in the bug tracker (

To see the error message that Clustal Omega returns to UGENE you can turn on additional log messages displaying. To do it follow the next instructions:

You need "TRACE" and "DETAILS" log categories.

After categories enabling, find a message in the log like:

[DETAILS][17:15] Launching ClustalO tool: /Applications/ -v --infile=/var/folders/c1/vql5jmsj3rd03xlwyd_gzxzw0000gn/T/ugene_tmp/p15498/clustalo/ClustalO_338_21.06.2016_17.15.36.425_15498/tmp.aln --outfmt=clu --outfile=/var/folders/c1/vql5jmsj3rd03xlwyd_gzxzw0000gn/T/ugene_tmp/p15498/clustalo/ClustalO_338_21.06.2016_17.15.36.425_15498/tmp.aln.out.aln --threads=4

There should be Clustal Omega output right after this message.

Title: Re: Clustal Omega error code
Post by izwan on Aug 2nd, 2016 at 10:23am
Thank you for the reply.

I've taken the recommended steps, and generated the error log (included in the attachment).

The error code pops up after the "pairwise distance calculation progress". There isn't much information beyond that, from what I can gather. Is there anything else I can do to troubleshoot this?;file=Ugene_error_logs.log (79 KB | 369 )

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