gtdb_to_taxdump

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Question about ncbi-gtdb_map.py

3

Hi! Thank you for this amazing tool! I am using ncbi-gtdb_map.py for the first time, and everything worked perfectly. However, I have a conceptual question. In some cases, the script...

andressamv

lineage2taxid error (module 'gtdb_to_taxdump' has no attribute 'Dmp')

1

Hi Nick. Thanks for developing this tool. I'm trying to get the taxid using the GTDB-tk lineage output for the MAGs I recovered. No matter what I try in my...

emaxortiz

Unclassified sequences TAXID

3

In the NCBI taxonomy, there is on particulary useful TAXID: [12908](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=12908&lvl=3&lin=f&keep=1&srchmode=1&unlock) for *unclassified sequences*. Would it be possible to preserve 12908 for unclassified sequences in `gtdb_to_taxump` or to add an...

maxibor

Preserve IDs

6

Hi Nick, Thanks for this tool. Is there any way to preserve the original GTDB taxids in the dmp files produced? There is no kraken2 GTDB 16S database. However there...

andrewjmc

Using different starting NCBI taxonomy gives different results

8

Hey @shenwei356 and @nick-youngblut Thank you so much for writing the python scripts to convert taxonomy between NCBI and GTDB. It will save so much time as compared to redoing...

Jigyasa3

KeyError: 'Cannot find GCA003697015.1 accession in names.dmp'

3

Hi @nick-youngblut, when I try to build the gtdb database using r207, I get: ``` gtdb_to_diamond.py -o gtdb gtdb_proteins_aa_reps_r207.tar.gz taxdump/names.dmp taxdump/nodes.dmp 2023-08-23 13:53:35,547 - Read nodes.dmp file: taxdump/nodes.dmp 2023-08-23 13:53:35,813...

bheimbu

Remove the name of the genome from the results generated by gtdb_to_taxdump.py

1

Hi, I'm curious as to why the name of the genome is added to the results generated by gtdb_to_taxdump.py? Is it possible to add a parameter that prevents the results...

wqssf102

ngsLCA: ngsLCA.cpp:60: void mod_db(int*, int*, int2int&, int2char&, int2char&): Assertion `parent.count(out[i])==1'

1

I used sequencing data to align with Bowtie2 to the GTDB database, and then I used the gtdb_to_taxdump.py and acc2gtdb_tax.py scripts to generate name, nodes, and acc2tax files. However, I...

itpcas-zcb