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Dear Tim,
when running the basta commands (from a cloned git in the envs bin folder) I get the following buggy uotpu when downloading the taxdump and databse association files:
Traceback (most rec…
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Hello,
I am trying to use BASTA on some DIAMOND tsv output. When I run basta sequence, however, I get a warning `# [BASTA WARNING] No taxon found for 1346611` and the basta output file contains on…
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Currently `NCBITaxa` uses `https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz` as its data source, however it appears to be semi-incomplete. There is, however, another subdirectory `new_taxdump` whi…
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Everything seems to be fine through `conda activate venv` (though I had to switch to bash to get this to work, as it doesn't work in tcsh - perhaps this should be mentioned in the readme...). Anyway,…
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I'm trying to build a custom database.
Based on your documentation (https://prophyle.github.io/custom_db.html) I succeed to:
1) Download and extract sequences
2) Index sequences with _samtools f…
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Hi,
I am using mmseqs taxonomy, and following the taxonomy assignment workflow, using uniref100 as a target DB.
the entire workflow works great, until the "mmseqs taxonomy" command.
The first…
henav updated
6 years ago
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The clusters.ci_gi.seqs.create function in the run.R script drops the following error:
Counting species for taxon 15123
Number of sequences for taxon 15123 : 541
Will process taxon 15123
eva…
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Hi there,
I'm on MacOS, I used makeDB.sh to download the progenomes and viral protein set, but after this I get the following error message:
(command used was: makeDB.sh -p -v -t 1)
Extracting …
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Using the current master for osf-client:
```
pip install https://github.com/dib-lab/osf-cli/archive/cf525b42de3ef8ddef8cb4a4d4f5c826160f7a35.zip
```
When I try to list the contents of project [`…
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@halexand suggested adding taxonomic breakdowns to sbt signatures and subsequently, gather output. This could facilitate downstream analysis at different taxonomic levels. For example, kraken does ```…