Error installing GTDB database.

[Ronflatau]

I try to install the GTDB database and I get the following error anyone have an idea how to solve it ?

[07/29/2023 01:22:30 PM DEBUG] autometa.taxonomy.gtdb: Extracting tarball containing GTDB ref genome animo acid data sequences to: /work/kraken1/RonFlatau/Discovery/autometa/GTDBdatabases/protein_faa_reps
[07/29/2023 01:41:35 PM DEBUG] autometa.taxonomy.gtdb: Extraction done.
[07/29/2023 01:43:13 PM DEBUG] autometa.taxonomy.gtdb: Merging 0 faa files.
[07/29/2023 01:43:13 PM DEBUG] autometa.taxonomy.gtdb: Combined GTDB faa file written to /work/kraken1/RonFlatau/Discovery/autometa/GTDBdatabases/gtdb.faa
[07/29/2023 01:43:13 PM DEBUG] autometa.common.external.diamond: diamond makedb --in /work/kraken1/RonFlatau/Discovery/autometa/GTDBdatabases/gtdb.faa --db /work/kraken1/RonFlatau/Discovery/autometa/GTDBdatabases/gtdb.dmnd -p 20
Traceback (most recent call last):
File "/home/r.flatau/.conda/envs/autometa/bin/autometa-setup-gtdb", line 10, in
sys.exit(main())
File "/home/r.flatau/.conda/envs/autometa/lib/python3.9/site-packages/autometa/taxonomy/gtdb.py", line 356, in main
diamond.makedatabase(
File "/home/r.flatau/.conda/envs/autometa/lib/python3.9/site-packages/autometa/common/external/diamond.py", line 51, in makedatabase
subprocess.run(
File "/home/r.flatau/.conda/envs/autometa/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['diamond', 'makedb', '--in', '/work/kraken1/RonFlatau/Discovery/autometa/GTDBdatabases/gtdb.faa', '--db', '/work/kraken1/RonFlatau/Discovery/autometa/GTDBdatabases/gtdb.dmnd', '-p', '20']' returned non-zero exit status 1.

[evanroyrees]

Hi Ron,

Thank you for reaching out. We have a similar issue (#328) that is being resolved in #329. When this PR is merged we will release v2.2.1 which will be available.

In the mean time you can clone the repo and check out the sidd/gtdb-hotfix branch which have the latest fixes from the pull request.

We apologize for the trouble and hope to have this resolved soon! Please do not hesitate to reach out again with any questions or troubles you run in to!

[evanroyrees]

Hi Ron,

We have released v2.2.1 where the GTDB database setup step is fixed. This is currently available in the main branch of the Autometa repo. This is not yet available on bioconda, but should be in less than 24 hours. Happy binning!