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czbiohub-sf / MIDAS

Metagenomic Intra-Species Diversity Analysis (MIDAS)
MIT License
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midasv3 chunk size error with midas2 database init #136

Closed uel3 closed 4 months ago

uel3 commented 4 months ago

I am having trouble with the $midas2 database --init --midasdb_name uhgg --midasdb_dir my_midasdb_uhgg with the latest midasv3 update.

conda list midas2 packages in environment at ~/.conda/envs/midasv3:

Name Version Build Channel midas2 2.0.0.rc3 py_0 zhaoc1

However older midas2 conda environments work

conda list midas2 packages in environment at ~/.conda/envs/midas2.0:

Name Version Build Channel midas2 1.0.2 pypi_0 pypi

Here is how I installed midasv3 mamba create -n midasv3 -c zhaoc1 -c conda-forge -c bioconda -c anaconda -c defaults midas2

conda activate midasv3 Running in ~/MIDAS2/tests initiating midas2 db midas2 database --init --midasdb_name uhgg --midasdb_dir my_midasdb_uhgg

Output

1714143353.0: Initate MIDASDB uhgg to my_midasdb_uhgg::start 1714144132.0: Initate MIDASDB uhgg to my_midasdb_uhgg::finish 1714144132.0: Download chunks for MIDASDB uhgg to my_midasdb_uhgg::start Traceback (most recent call last): File "/.conda/envs/midasv3/bin/midas2", line 10, in sys.exit(main()) File "/.conda/envs/midasv3/lib/python3.9/site-packages/midas2/main.py", line 25, in main return subcommand_main(subcommand_args) File "/.conda/envs/midasv3/lib/python3.9/site-packages/midas2/subcommands/database.py", line 146, in main init_midasdb(args) File "/.conda/envs/midasv3/lib/python3.9/site-packages/midas2/subcommands/database.py", line 29, in init_midasdb midasdb.fetch_files("chunks") File "/.conda/envs/midasv3/lib/python3.9/site-packages/midas2/models/midasdb.py", line 190, in fetch_files return self.fetch_tarball(filename, list_of_species) File "/.conda/envs/midasv3/lib/python3.9/site-packages/midas2/models/midasdb.py", line 252, in fetch_tarball md5_fetched = file_md5sum(_fetched_file) File "/.conda/envs/midasv3/lib/python3.9/site-packages/midas2/models/midasdb.py", line 364, in file_md5sum return md5(open(local_file, "rb").read()).hexdigest() FileNotFoundError: [Errno 2] No such file or directory: '~/MIDAS2/tests/my_midasdb_uhgg/chunks/sites/run/chunksize.50000/100001/GUT_GENOME000001.json'

Any help would be appreciated with this matter. Thank you.

zhaoc1 commented 4 months ago

Hi,

MIDAS2 is currently under updates to version 3, with significant changes to the pangenome structure. I haven't finished the publishing of the new MIDASDB yet. Please use the Release version (https://github.com/czbiohub-sf/MIDAS2/releases/tag/v1.0.9) for now. Thanks for the understanding. Hopefully I can publish the new db within the next month.

Thank you Chunyu

uel3 commented 4 months ago

Thank you for getting back to me. I will use release 1.0.9 in the meantime. Looking forward to the update.

Candace