ERROR:parser:File taxadb/nucl_gb.accession2taxid.gz does not exist

[jorvis]

Using the latest version (on Ubuntu, installed from pip3) and I get an error:

jorvis@ref-db-build:/dbs$ taxadb download -o taxadb --type taxa
INFO:taxadb.download:Downloading taxdump.tar.gz
 95%|████████████████████████████████████████████████████████████████████████████▎   | 49.1k/51.4k [00:00<00:00, 15.6kKb/s]/usr/local/lib/python3.8/dist-packages/tqdm/std.py:480: TqdmWarning: clamping frac to range [0, 1]
  full_bar = Bar(
100%|████████████████████████████████████████████████████████████████████████████████| 51.4k/51.4k [00:00<00:00, 61.1kKb/s]
INFO:taxadb.download:Downloading taxdump.tar.gz.md5
1.00Kb [00:00, 821Kb/s]                                                                                                    
INFO:taxadb.util:Checking md5 of taxdump.tar.gz
INFO:taxadb.util:Checking md5 of taxdump.tar.gz: OK
INFO:taxadb.download:Unpacking taxdump.tar.gz


jorvis@ref-db-build:/dbs$ taxadb create -i taxadb --fast --dbname taxadb.sqlite
INFO:taxadb.app:Creating table taxa
INFO:taxadb.app:Parsing files
INFO:taxadb.parser.TaxaDumpParser:Parsed nodes.dmp
INFO:taxadb.parser.TaxaDumpParser:Parsed names.dmp
INFO:taxadb.app:Inserting taxonomy data
INFO:taxadb.app: 4523 chunks [01:05, 68.84 chunks/s]
INFO:taxadb.app:Table Taxa completed
INFO:taxadb.app:Parsing nucl_gb.accession2taxid.gz
**INFO:taxadb.app: 0 chunks [00:00, ? chunks/s]ERROR:parser:File taxadb/nucl_gb.accession2taxid.gz does not exist**
INFO:taxadb.app: 0 chunks [00:06, ? chunks/s]

[danieldjewell]

I'm 99% sure the issue is that by specifying --type taxa you are not downloading the accession nucl_gb file.

You can get the file from:

• ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/
• https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/

The taxdump.tar.gz file is in the parent directory of the above, should you need it.