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Thanks for your work.
I want to use my downloaded GTDB database, it seem work.
But in running Mmseq2, it throw a error
Input taxonomy database "//mmseqs2-GTDB/GTDB" is missing files:
- //mmseq…
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Here:
https://github.com/KosinskiLab/AlphaPulldown/blob/47036047d461f4eae10d09275a24a4f149e72fbe/alphapulldown/objects.py#L245
template_features are always recalculated, even in case of the remote m…
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I am trying to use the taxonomy --majority parameter for taxonomic assignment to metagenomic contigs described in this paper, https://www.biorxiv.org/content/10.1101/2020.11.27.401018v1.full.pdf, but …
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## Expected Behavior
Cluster a fasta input using `easy-cluster` because `linclust` sometimes removes important sequences
## Current Behavior
\> 50% tested fastas die with a result2flat error
`…
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Hello,
I think GeMoMa is overestimating the number of genes in my genomes. I'm working with 3 haploid genome assemblies and using GeMoMa to annotate them. These are a few stats for one of them using …
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Hi I'm trying to use DRAM on our supercomputer which should have enough memory but I keep getting an error with installing the uniref database. Here is the last bit of output from the command `DRAM-se…
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## Expected Behavior
Workflow:
cluster -> alignall -> createtsv
I noticed there are cluster members in my output with very short alignment lengths. I was expecting the aligned length to be at l…
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This is not a bug, but simply a question about how Pfam is implemented in DRAM.
Hello, I'm just trying to understand how DRAM works.
In the Pfam documentation [10.1093/nar/gky995](https://doi.org…
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Hi,
My local installation of colabfold_batch is running fine with the default mmseq2 server. My local mmseq2 server with one example is running fine when accessed in the browser and via curl. However…
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Assumption: Databases not indexed correctly or naming mismatch.
Input /apps/prod/COMPCHEM/colabfold/git/ColabFold/MsaServer/databases/uniref30_2103 does not exist -> ?
Input /apps/prod/COMPCHEM/cola…