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## Short description of the problem
The recently introduced `--prodigal-single-mode` flag from https://github.com/merenlab/anvio/commit/f1291f755c859d55f8152321942f5a62b384676b causes workflows to …
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): v1.2.9
- OS name and version (`lsb_release -ds`): Red Hat Enterprise Linux release 8.5 (Ootpa)
**To Reproduce**
Exact bcbio comma…
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## Short description of the problem
Hello there,
anvi-setup-pfams fail with Config Error
```
anvi-setup-pfams --pfam-data-dir $SCRATCH/pfam
* No Pfam version specified. Using current release.
…
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Hello I am new in programming and I wanted to test lumpy on my Arabodopsis data
When I run lumpyexpress I get this error
$lumpyexpress -B file.sorte.bam -S file.splitters.sorted.bam -D file.disco…
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Hi!
I am trying to binning by SprayNPray, and my command is
`spray-and-pray.py -g /flash/HusnikU/Cong/assembly/ACAB_assembly.fna -bam /flash/HusnikU/Cong/bam/ACAB.bam -out ACAB -t 32 -ref /apps…
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## The need
To annotate pan-genome genes, the user is encouraged to export from an existing pan-genome database via `anvi-get-sequences-for-gene-calls -g` and then annotate the genes via their own …
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## The need
[dbCAN3](https://bcb.unl.edu/dbCAN2/) contains [dbCAN_sub](https://bcb.unl.edu/dbCAN_sub/) which enables substrate annotation for CAZymes. This upgrade will help catalyze CAZyme-related…
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**This is the main issue for adding metagenomics content to the workshop material**
The plan is that we have most of the material first in this repo and then we fork it for the GHPP SGS course end …
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## Short description of the problem
The `--min-alignment-fraction` parameter of `anvi-dereplicate-genomes` is not working as expected.
## anvi'o version
I'm using the master version as of thi…
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## Short description of the problem
Hello again. I found a rather bizarre case in my testing and I'm a bit stuck now. I'm trying to run `anvi-cluster-contigs` with MaxBin2, and it's failing due to …