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Metagenomic Intra-Species Diversity Analysis (MIDAS)
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KeyError: 'chunks_centroids' during MIDAS database initialization #141

Closed zfsh closed 2 months ago

zfsh commented 3 months ago

Dear Developer, When I attempt to initialize the MIDAS database using the --init command, I encounter a KeyError: 'chunks_centroids'. Here are the details: (midasv3) lenovo@lenovo-ThinkStation:~/software/MIDAS-3$ midas database --init --midasdb_name uhgg --midasdb_dir my_midasdb_uhgg/ 1720838073.1: Initate MIDASDB uhgg to my_midasdb_uhgg/::start 1720838142.8: Initate MIDASDB uhgg to my_midasdb_uhgg/::finish 1720838142.8: Download chunks for MIDASDB uhgg to my_midasdb_uhgg/::start Traceback (most recent call last): File "/home/lenovo/anaconda3/envs/midasv3/bin/midas", line 10, in sys.exit(main()) File "/home/lenovo/anaconda3/envs/midasv3/lib/python3.9/site-packages/midas/main.py", line 25, in main return subcommand_main(subcommand_args) File "/home/lenovo/anaconda3/envs/midasv3/lib/python3.9/site-packages/midas/subcommands/database.py", line 146, in main init_midasdb(args) File "/home/lenovo/anaconda3/envs/midasv3/lib/python3.9/site-packages/midas/subcommands/database.py", line 29, in init_midasdb midasdb.fetch_files("chunks") File "/home/lenovo/anaconda3/envs/midasv3/lib/python3.9/site-packages/midas/models/midasdb.py", line 190, in fetch_files return self.fetch_tarball(filename, list_of_species) File "/home/lenovo/anaconda3/envs/midasv3/lib/python3.9/site-packages/midas/models/midasdb.py", line 251, in fetch_tarball _fetched_file = self.get_target_layout(ct, False, sid, gid, DEFAULT_CHUNKS[i]) File "/home/lenovo/anaconda3/envs/midasv3/lib/python3.9/site-packages/midas/models/midasdb.py", line 165, in get_target_layout local_path = self.construct_local_path(filename, species_id, genome_id, component) File "/home/lenovo/anaconda3/envs/midasv3/lib/python3.9/site-packages/midas/models/midasdb.py", line 152, in construct_local_path local_path = _get_local_path(get_midasdb_layout(species_id, genome_id, component)[filename], self.db_dir) KeyError: 'chunks_centroids'

I can make sure that my midasv3 environment is installed and I have successfully run _testanalysis.sh and _testdb.sh. According to _testdb.sh, I should have pre-downloaded the midasdb, but when I use the commands in the midas2 User manual to download the database, I always get this problem. How can I solve this problem. Thanks a lot!

zhaoc1 commented 3 months ago

Hi,

test_db.sh is for testing building custom MIDASDB, and it doesn't mean you have downloaded the midasdb.

Despite that, I fixed midas database init and please re-install midas 3.0.1.

Thanks. Chunyu

zfsh commented 2 months ago

Hi Chunyu,

Thank you very much for your help and clarification. I have reinstalled MIDAS 3.0.1 as you suggested, and everything is running smoothly now.

I really appreciate your support. Wishing you all the best in your work!