Pangenome tutorial issue
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Thomas Hanson
Aug 18, 2021, 1:10:46 PM8/18/21
to Anvi'o
Hive mind,
My lab has been working through the Pangenome tutorial for *reasons* this summer and we hit a snag that we have not been able to solve. Working from https://merenlab.org/2016/11/08/pangenomics-v2/ specifically the Creating a quick pangenome with functions section, this code block:
anvi-import-collection -p PROCHLORO-functions-manual-profile.db \
-C default \
PROCHLORO-functions-collection.txt \
--bins-info PROCHLORO-functions-collection-info.txt
produces this error:
WARNING
===============================================
You did not provide a contigs database. Fine. So be it. But know this: anvi'o
has no way to check the consistency of names you provide in the input file. So
if you made a mistake while generating this collection, it probably will cause
issues later on.
Item names in input ..........................: 879
Num bins in input ............................: 1
WARNING
===============================================
Since you are working with a blank proifle, anvi'o is not going to check whether
the names item names in your collections file matches to the item names in other
databases of yours. It is all fine for now, but this requires you to be even
extra careful with your downstream analyses in case stuff hits the fan later.
Items in profile database ....................: 879
Item names shared between input and db .......: 879
Config Error: Bins in the collection dict do not match to the ones in the bins info dict. They
do not have to be identical, but for each bin id, there must be a unique entry
in the bins informaiton dict. There is something wrong with your input :/
You did not provide a contigs database. Fine. So be it. But know this: anvi'o
has no way to check the consistency of names you provide in the input file. So
if you made a mistake while generating this collection, it probably will cause
issues later on.
Item names in input ..........................: 879
Num bins in input ............................: 1
WARNING
===============================================
Since you are working with a blank proifle, anvi'o is not going to check whether
the names item names in your collections file matches to the item names in other
databases of yours. It is all fine for now, but this requires you to be even
extra careful with your downstream analyses in case stuff hits the fan later.
Items in profile database ....................: 879
Item names shared between input and db .......: 879
Config Error: Bins in the collection dict do not match to the ones in the bins info dict. They
do not have to be identical, but for each bin id, there must be a unique entry
in the bins informaiton dict. There is something wrong with your input :/
But the contigs database and profile database were provided in the original tarball, no? We can't get past this. Help?!
Tom
A. Murat Eren
Aug 24, 2021, 10:02:23 AM8/24/21
to Anvi'o
Hi Tom,
Apologies for the late response. Almost the entire team has been traveling.
I am sorry that the tutorial is not working. I will try to get to it soon as a part of our anvi'o v7.1 release.
We have a brand new way of exploring pangenomes of functions via anvi-display-functions, which is currently available only in our active development branch.
Best wishes,
--
--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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