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Hi,
When I tried to download the map file of nt database, it said that there is no this file in this link wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz
Did some one also meet this…
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**Snakemake version**
7.21.0
**Describe the bug**
Snakemake rule to create a kaiju database (https://github.com/bioinformatics-centre/kaiju) ends with error. The same command run successfully…
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Hi,
In the example above I can see proteins FASTA file of GCF_009025895.1_virus_proteins.faa. I want to calculate the gene abundance with virus gene sequence.Can we output the corresponding nucleo…
wfgui updated
2 weeks ago
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Hi, I'm curious as to why the name of the genome is added to the results generated by gtdb_to_taxdump.py? Is it possible to add a parameter that prevents the results from containing the genome name?
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Hi,
could you please help me with basta taxonomy problem?
The taxdump.tar.gz gets downloaded but the md5 sum does not match so the file is re-downloaded... resulting in a never-ending loop of re-do…
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When running krakenuniq-download I get the error below. I've also included my arguments for context. It seems like I'm getting more from NCBI than the program expects.
```
krakenuniq-download …
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Hi [jnarayan81](https://github.com/jnarayan81),
I installed alienomics with conda (as described in the wiki), and I tried to download the databases, but it doesn't work:
$ alienomics_v0.3.2 -d…
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PyCogent provided this [support](https://github.com/pycogent/pycogent/blob/master/cogent/parse/ncbi_taxonomy.py), and is useful for getting NCBI Taxon ID and rank information. The files consumed are p…
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Hi Shenwei,
We are exploring building a database where we can include bacteria and archaea (from GTDB) and viral database from NCBI, while using NCBI style taxonomy but grafting the GTDB taxonomy …
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Hi,
I am having trouble with downloading database using this code
`> prepareDatabase('accessionTaxa.sql',types='prot')`
The error message is as follows:
```
Downloading names and nodes with g…