DAS tool issue

[francesco-ricci]

Hi Vini,

I think the last patch of metaphor may have introduced the following issue:

Analyzing assembly
Skipping gene prediction
using protein fasta file: output/annotation/prodigal/cobinning/cobinning_proteins.faa
Annotating single copy genes using diamond
Dereplicating, aggregating, and scoring bins
Error in [.data.table(bin_tab_contig, , .(binSize = calc_bins_size(contig_id, :
Column 1 of result for group 4 is type 'double' but expecting type 'integer'. Column types must be consistent for each group.
Calls: cherry_pick -> score_bins -> %>% -> setkey -> [ -> [.data.table
In addition: Warning message:
In calc_N50(contig_id, contig_length) :
integer overflow in 'cumsum'; use 'cumsum(as.numeric(.))'
Execution halted****

Thanks
Francesco

[vinisalazar]

Hi @francesco-ricci,

Thank you for reporting this. I'm afraid this is an old issue, unrelated to the patch. See cmks/DAS_Tool#99.

I did realise however that we are still using v1.1.4. I am pushing another patch right now.

Best,
Vini

[francesco-ricci]

Thanks for fixing this Vini!

Unrelated to this but unfortunately there is an old problem persisting even with the new patch:

This is the error I got this morning :

Traceback (most recent call last):
File "/home/fricci/rp24/fra/software/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/config/conda/7330173dd812122e296c11d14202aa4a_/bin/concoct", lin$
import vbgmm
ModuleNotFoundError: No module named 'vbgmm'

[francesco-ricci]

I reinstalled metaphor this morning, mkl v2024.0 does not appear among the dependencies that get installed through conda/mamba.

[vinisalazar]

Hi @francesco-ricci,

Thank you for reporting that. I've been at a conference this week so didn't have much time to work on Metaphor, but I will look into it as soon as possible.

I reinstalled metaphor this morning, mkl v2024.0 does not appear among the dependencies that get installed through conda/mamba.

This is expected. The environment containing Metaphor doesn't have mkl as a dependency. mkl is installed on the environments created by Metaphor to run third party software (the ones that are named with a long code such as 7330173dd812122e296c11d14202aa4a_).

Best,
Vini