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**Describe the bug**
I am using the most recent version
```
datasets --version
datasets version: 16.33.0
```
When I down…
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Hello,
I'm trying to generate a new taxonomic tree (described on Generating the taxonomic tree and genome vitals references) to use with gottcha using a specific set of viral genomes.
I generated a .…
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Taxdump.tar.gz is downloaded to a user directory, it contains the names and nodes files.
```
Downloading http://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz to /home/adam/.local/var/lpi/taxdump.…
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Hi,
I got the masked genomes from the eupathDBclean, and built a kraken database on it (kmer = 25). By looking back at the reports, some of the kmers fully mapped to the masked sequences, e.g.
…
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Hi!
I cloned the krakenuniq repository and followed the instruction of the readme but I have an error trying to build the database.
This is th code I used
`krakenuniq-download --db DBDIR refseq/v…
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Hi there, I am trying to use extract_kraken_reads.py to exclude the human reads.
I have kraken output file kraken.report.txt and kneaddata processed fastq file other_kneaddata.fastq as inputs:
…
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and put taxid and ortholog group in output file name
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* NCBI taxdump format
* greengenes tsv format
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Hi,
I'm super new to programming so I believe I'm missing something VERY obvious, so I apologize in advance for this question. In case these are relevant, I'm using a Mac and the PyCharm IDE. I dow…
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`[01-15 14:10:34] [ReferenceDbCreator] Adding taxonomy to fasta
Use of uninitialized value in numeric eq (==) at /NCBI-Taxonomy/lib/NCBI/Taxonomy.pm line 407, line 157.
`
Happens for approx 30 IDs…