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 (
https://local.ugene.unipro.ru/tracker/browse/UGENE-5308).
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:
https://ugene.net/wiki/display/UUOUM23/Logging.
You need "TRACE" and "DETAILS" log categories.
After categories enabling, find a message in the log like:
Quote:[DETAILS][17:15] Launching ClustalO tool: /Applications/U-1.22.0.app/Contents/MacOS/tools/clustalo-1.2.1/clustalo -v --infile=/var/folders/c1/vql5jmsj3rd03xlwyd_gzxzw0000gn/T/ugene_tmp/p15498/clust
alo/ClustalO_338_21.06.2016_17.15.36.425_15498/tmp.aln --outfmt=clu --outfile=/var/folders/c1/vql5jmsj3rd03xlwyd_gzxzw0000gn/T/ugene_tmp/p15498/clus
talo/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.
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