Viral new File format?

[mwylerCH]

Dear dev team,
it's possible, that the viral file changed again? Centrifuge is not downloading anything for viral.
Here the files:
assembly_summary.txt
assembly_summary_filtered.txt

[mourisl]

Thank you for sharing the file. I'll look into this. The filtered file is empty, so the issue should be in the summary.txt file.

[mwylerCH]

Yes, probably the columns changed.
Many thanks

[mourisl]

Sorry for the delayed reply. It seems the awk in centrifuge-download can find some rows in the assembly_summary.txt file. What was your running command? Thank you.

[mwylerCH]

No problems. I usually use this:

mkdir DB_centrifuge
centrifuge-download -o DB_centrifuge/taxonomy taxonomy
centrifuge-download -P 100 -o DB_centrifuge/library -m -d "archaea,bacteria,viral,vertebrate_mammalian" refseq > DB_centrifuge/seqid2taxid.map

However, today I had to reproduce the error with ...

centrifuge-download -P 100 -o DB_centrifuge/library -m -d "viral" refseq > DB_centrifuge/seqid2taxid.map

... since today also the bacteria part gives me some challenge. The error log is here:
bacteriDownError.txt
Should I open a new issue for that?

Maybe some helpful informations:

• installation happen with conda with:

git clone https://github.com/DaehwanKimLab/centrifuge
module load Anaconda3/2023.09-0
conda create -n centrifuge
source activate centrifuge
conda install bioconda::centrifuge

• everything runs on a Rocky 9.3 Blue Onyx cluster with slurm scheduler
• centrifuge is version 1.0.4
• all commands are submitted as a wrap with sbatch

Let me knwo if you need further informations.