When using a custom DB, metagen.py -r nt doesn't recognise any NCBI taxa

[Steven-Kemp]

Hi there,

Wonderful tool, I'm really pleased with how it works with a standard db!

When I make a custom database, I have renamed the taxa to xxxx|e. coli for example and the CSV files show the correct taxa. However, when I run the command:

    for i in *.res; do CCMetagen.py -i $i -o graphs_$i -r nt; done

An example of the output is:

Reading file results_230_S28_R1.fastq.gz.res

WARNING: no NCBI's taxid found for accession AVRR01000106.93001.94083 This match will not get taxonomic ranks

WARNING: no NCBI's taxid found for accession OBEP010600675.2.1454 This match will not get taxonomic ranks

WARNING: no NCBI's taxid found for accession Y09571.1.1396 This match will not get taxonomic ranks

WARNING: no NCBI's taxid found for accession JQ293090.1.2254 This match will not get taxonomic ranks

WARNING: no NCBI's taxid found for accession JQ342679.1.700 This match will not get taxonomic ranks

WARNING: no NCBI's taxid found for accession GU905014.1.2189 This match will not get taxonomic ranks

WARNING: no NCBI's taxid found for accession HQ022862.1.2290 This match will not get taxonomic ranks

Is there a way to point CCMetagen to my own taxids?

Thanks!

[vrmarcelino]

Hi,

CCMetagen relies on the NCBI taxids to get a taxonomic rank. Is there an equivalent NCBI taxid to your accession IDs?

[vrmarcelino]

Closing issue due to inactivity. Feel free to open it again if you need help.