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vinisalazar / metaphor

Metaphor: a general-purpose workflow for assembly and binning of metagenomes
https://metaphor-workflow.readthedocs.io/
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DAS tool issue #80

Open francesco-ricci opened 1 week ago

francesco-ricci commented 1 week ago

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 commented 1 week ago

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 commented 1 week ago

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 commented 1 week ago

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

vinisalazar commented 6 days ago

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