GTDB via Diamond BLASTx to Krona output

[alvizain786]

Hi All,

I hope everyone is well. I am trying to output/convert the Diamond BLASTX results through GTDB protein database to a Krona html output. I regularly convert my Dimaond BLASTx output through NCBI NR database to Krona output with no issues at all. I use the ImportBLAST.pl script in Krona.

Unfortunately, when I used ImportBLAST.pl script on GTBD database. Krona unfortunately cannot find taxonomic database for GTDB and thinks of them as NCBI Ids.

I got the following error:

The following accessions were not found in the local database (if they were recently added to NCBI, use updateAccessions.sh to update the local database): GCF002763455 GCF002276555 etc...

Those GCF# are GTDB ids.

When I even try to do it manually.

Command:

path/to/ImportBLAST.pl -c ./sample.txt -tax /path/to/the/converted/GTDB/taxonomic/database/for/DiamondBLAST/ -o sample.html

I get this error:

/path/to/GTDB/taxonomy/database. Was updateTaxonomy.sh run? at /path/to/KronaTools-2.8/scripts/../lib/KronaTools.pm line 1540.

Sources: https://github.com/nick-youngblut/gtdb_to_taxdump https://gtdb.ecogenomic.org/downloads https://github.com/bbuchfink/diamond