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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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anvi-summarize error with external binning results in v2.0.2 and earlier versions #380

Closed meren closed 8 years ago

meren commented 8 years ago

Cody Sheik discovers a pesky bug in v2.0.2, and David Needham confirms it:

https://groups.google.com/forum/#!msg/anvio/mjIHW51biGU/QBR6DP92CQAJ

This is a problem with the current implementation of the function that initializes a comprehensive profile for a given collection.

Contigs database has all the contig and split names. However, when a BAM file is profiled with anvi'o, some of those splits may not appear in the resulting profile database depending on the parameters used for profiling (i.e., if --min-contig-length is used, then some of the splits that are in the contigs database my end up being removed). Hence, when the user requests a summary of a collection that is generated by an external binning tool, there may be split names in it that do not appear in the profile database although they do in the contigs database. Anvi'o was not ready for this scenario, and gave the error that can be seen in the referenced discussion.

Fixes to this issue will reference this report.

meren commented 8 years ago

These should fix it, but I will keep this issue open until I hear from Cody and David :)

meren commented 8 years ago

David tells me that they didn't fix it :/

meren commented 8 years ago

This seems to be resolved. Both Cody and David confirmed it's now working for them.