Pangenome - no functional annotation and no genes

anvi-self-test --version
Anvi'o version ...............................: 2.4.0
Profile DB version ...........................: 20
Contigs DB version ...........................: 8
Pan DB version ...............................: 5
Samples information DB version ...............: 2
Genome data storage version ..................: 1
Auxiliary data storage version ...............: 3
Anvi'server users data storage version .......: 1

Hi,

I am trying to run the pan genome function on linux (Compute Canada server) for some anvi'o bins using external gene calls with the attached bin info file. (I know this anvi'o version is out of date but updates won't install in Compute Canada).

The function runs but I get the below error about not having functional annotations and no genes are pulled from the contigs.db for the bins. I suspect this is because in the new versions of anvi'o the contigs.h5 data is now stored in the contigs.db whereas with our old versions they are still separate.

Is it possible to run pangenome on the older file types or will we need to install the new anvi'o on a different server and migrate the old databases to the new format?

Thanks,

Alex

PH3_Jul20_bins.txt

anvi-gen-genomes-storage --internal-genomes PH3_Jul20_bins.txt -o PH3_Jul20-GENOMES.h5 --gene-caller PH3_Jul20_119749.Anvio.external_gene_calls_2.5K.txt 

WARNING
===============================================
None of your genomes seem to have any functional annotation. No biggie. Things
will continue to work. But then your genomes have no functional annotation. SAD.

[01 Feb 19 14:04:43 Initializing internal genomes] working on Bin_22_4         /home/asauk/projects/rrg-laurahug/asauk/virtual-envs/anvio-2.4.0/lib/python3.5/site-packages/numpy/core/fromnumeric.py:2909: RuntimeWarning: Mean of empty slice.
  out=out, **kwargs)
/home/asauk/projects/rrg-laurahug/asauk/virtual-envs/anvio-2.4.0/lib/python3.5/site-packages/numpy/core/_methods.py:80: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
Internal genomes .............................: 7 have been initialized.        
External genomes .............................: 0 found.                        

* Bin_22_2 is stored with 0 genes (0 of which were partial)
* Bin_22_4 is stored with 0 genes (0 of which were partial)                     
* Bin_25_6 is stored with 0 genes (0 of which were partial)                     
* Bin_31_2 is stored with 0 genes (0 of which were partial)                     
* Bin_35_5 is stored with 0 genes (0 of which were partial)                     
* Bin_42_2 is stored with 0 genes (0 of which were partial)                     
* Bin_42_3 is stored with 0 genes (0 of which were partial)                     

The new genomes storage ......................: PH3_Jul20-GENOMES.h5 (signature: 4bdc2e2c)
Number of genomes ............................: 7 (internal: 7, external: 0)
Number of gene calls .........................: 0
Number of partial gene calls .................: 0

merenlab / anvio

Pangenome - no functional annotation and no genes #1094