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When running `build_kraken`, the `add_existing` process fails with messages such as
```
rsync_from_ncbi.pl: unexpected FTP path (new server?) for https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/7…
cschu updated
5 months ago
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Hi,
I always encounter this issue " Download failed! have a look at valid domains at ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq . ", when I run this script
`# download all bacterial genomes from…
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I keep getting the following when attempting to download all the gff and cds-fasta files for Pantoea from NCBI:
"ERROR: Download from NCBI failed: ConnectionError(MaxRetryError('HTTPSConnectionPool…
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## Expected Behavior
I ran this script with mmseqs2 part shown below and had a prefilter died error. What should I do?
#!/bin/bash
\## specify allocation - we want normal since we don't want to use…
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## Description
Models of the different types of bacteria if there is time to add more
- [x] "Pylori/Tails" Bacteria
- [x] "Ball Spiky" Bacteria
- [x] "Pyogenes/Cluster" Bacteria
- [x] "Snake C…
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Hi,
I am trying to use the function taxa.compare.
I got a data.frame with 2 factors : chimio : Pre, Post and the number of the patients.
Here the structure of the data.frame df:
chimi…
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**./collectInfo.sh -i /path/to/BACTERIA/COLLECTED_INFO/VALID**
-- COLLECTING INFO --
INFO: organism type flag -V not specified. O(thers) assumed (default option).
- PROCESSING DETAILS
…
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Hi:)
I ran kraken2.1.2 for my mice gut microbiome shotgun metagenomic analysis. I built a custom db by using the following command
```
kraken2-build --download-taxonomy --db refseq
kraken2-build …
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Found on qa site today.
logs:
```
2024-05-07 11:19:03.310991 Base plot.data object created.
Error in validObject(.Object) :
invalid class “TwoByTwoTable” object: 1: Specified column r…
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Hello! I am getting this issue when installing the databases using this command:
command: /home/delaney/miniconda3/bin/krakenuniq-download --db DBDIR --threads 10 --dust refseq/bacteria refseq/ar…