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I am trying to run the humann3 demo, I have the databases downloaded, the most current versions and as far as I can tell there is no mpa_v30_CHOCOPhlAn_201901b. How do I fix this?
I am actually pretty sure the error is being caused by HUMAnN, particularly because of this line of code in the humann.py:
database_files=os.listdir(config.protein_database)
valid_format_database_files=[]
for file in database_files:
if not config.metaphlan_3p0_db_matching_uniref in file:
sys.exit("\n\nCRITICAL ERROR: The directory provided for the translated database contains files ( “+file+” )"+
" that are not of the expected version. Please install the latest version"+
" of the database: "+config.metaphlan_3p0_db_matching_uniref)
Apologies - you are right about this being caused by HUMAnN. I had missed the 201901b in the URLs you initially provided. That database version is HUMAnN-specific (a HUMAnN-specific extension of the MetaPhlAn 201901 database), and so that’s likely why the download is failing. I will look into this - it’s not something that has come up before.
Can you clarify what command you’re running when you see this error? It looks as though MetaPhlAn is being told to use an index named “201901b” (which does not exist). This should not be happening automatically, but it could happen if (e.g.) someone specified that index name when calling the software or in a configuration file.
You mentioned that this issue arose when running the demo. If you can clarify which demo you were running / adapting when performing this test, that would also be helpful (in case there’s something unclear in our documentation re: specifying databases).
This is the command I was using:
humann --input lib/python3.7/site-packages/humann/tests/data/demo.fastq --output demo_out --nucleotide-database /users/clairmontl/humanndb/ --metaphlan-options “–index mpa_v296_CHOCOPhlAn_201901”
I also got the same error when running my own fasta files with this command:
humann --input sample.fasta --output demo_out --metaphlan-options “–index mpa_v296_CHOCOPhlAn_201901”
You shouldn’t need to manually specify the MetaPhlAn index when running HUMAnN - MetaPhlAn will automatically fetch an appropriate index the first time it runs and then reuse it thereafter. Was there a specific reason for wanting the custom command?
Yes, I added the --index command after the same command without --index returned the error I reported above. I had read in the forums that specifying --index could overcome some metaphlan database issues in earlier program versions.
No it did not. None of the options I tried allowed me to run the program. I did get it to run but I had to make alterations to the humann.py and config.py scripts to do so.