Centrifuge-build reports error when building reference index

[ArnieBerg]

I have used the follow command sequence to build the reference index for archaea, bacteria and viral genomes:


centrifuge-download -o taxonomy taxonomy
centrifuge-download -o library -m -d "archaea,bacteria,viral" refseq > seqid2taxid.map
cat library/*/*.fna > input-sequences.fna
centrifuge-build -p 4 --conversion-table seqid2taxid.map --taxonomy-tree taxonomy/nodes.dmp --name-table taxonomy/names.dmp input-sequences.fna abv


On the final step, it reports 'Warning: Taxonomy ID 227859 is not in the provided taxonomy tree (taxonomy/nodes.dmp)' and hangs up.

If I remove this ID from seqid2taxid.map and run again, it reports 'Warning: Taxonomy ID 227859 is not in the provided taxonomy tree (taxonomy/nodes.dmp)' and hangs up. This is the accession number for ID 227859, which at this point no longer exists in seqid2taxid.map.

How do I diagnose and resolve this issue?

[toogoodtobesue]

Any chance you solved this problem? Keeps happening to my nt database index.

[ArnieBerg]

Still waiting for an answer.

[gastonviarengo]

Hello ArnieBerg,

Are you still dealing with this? I have the same problem, although didn't know if the script was hanging up or hadn't enought time to complete the job.

Anyway, I believe this could be solved by removing the sequences that lead to an error in your library/*/ folder and concatenating again to the input-sequences.fna file.

I'll try this approach and let you know how it works, please let me know if you have already solved it or if you try it before me.

Bests,

[ArnieBerg]

No, have not been able to resolve this.

[MarcoAmara]

Once tried this but could not solve.Was told I was doing it wrong.