anvi-rename-bins_ Config Error

[nahbergo]

Hi,

I am having error with the anvi-rename-bins. I don't know why.

Here is the command I used: anvi-rename-bins -p SAMPLES-MERGED/PROFILE.db -c 03_CONTIGS/contigs.db --collection-to-read CONCOCT --collection-to-write selectedMAGs --call-MAGs --prefix M250 --min-completion-for-MAG 40 --max-redundancy-for-MAG 15 --report-file REPORT_rename_mags

And here is the error report:

Config Error: TablesForCollections::append: 143 split names or contig IDs appear more than once in your input for this collection. This part of the code is unable to
predict how you may have ended up here, but check your input file maybe? :/

Could you please, help me?

[meren]

Hey @nahbergo, I just tested your command and it seems to be working fine in anvio-dev. Sorry, I'm not sure how you ended up here.

But I realize there is a problem with filtering based on completion and I'll look into that.

[nahbergo]

Hi @meren, thank you for the reply.

I refined 347 bins. I thought it was the large amount of bins. But I tested the same command for another group of samples with coassembly (249 bins) and got the same error. The command generates the report file with the renamed MAGs but does not filter the MAGs.

I hope you can help me.

rename.txt

[meren]

If you hadn't removed the the issue template and leave all the questions it requested you to respond unanswered, I may have had some suggestions.

[nahbergo]

If you hadn't removed the the issue template and leave all the questions it requested you to respond unanswered, I may have had some suggestions.

Sorry I do not understand. What questions were not answered? Yes, I accept suggestions.

[meren]

Hey @nahbergo, this error does not make any sense to me unfortunately. My only suggestion is to try running the same command in anvio-dev, and we may be able to solve the remaining issues quickly if you run into a problem in avnio-dev (installation instructions for anvio-dev are on anvio.org).