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KIT-IBG-5 / mdmcleaner

MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs
GNU General Public License v3.0
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Error in database downloading #52

Open uzun-masha opened 1 year ago

uzun-masha commented 1 year ago

Hi! I'm trying to download database using mdmcleaner makedb, and I've got an error like this: 01a: download GTDB data--

    Now downloading from gtdb: "gtdb_taxfiles" (attempt 1)...

    Now downloading from gtdb: "gtdb_fastas" (attempt 1)...

    Now downloading from gtdb: "gtdb_vs_ncbi_lookup" (attempt 1)...

Traceback (most recent call last): File "/mnt/storage/lab4/progs/miniconda3/envs/mdmcleaner/bin/mdmcleaner", line 10, in sys.exit(main()) ^^^^^^ File "/mnt/storage/lab4/progs/miniconda3/envs/mdmcleaner/lib/python3.11/site-packages/mdmcleaner/mdmcleaner.py", line 231, in main read_gtdb_taxonomy.main(args, configs) File "/mnt/storage/lab4/progs/miniconda3/envs/mdmcleaner/lib/python3.11/site-packages/mdmcleaner/read_gtdb_taxonomy.py", line 1142, in main getNprepare_dbdata_nonncbi(args.outdir, verbose=args.verbose, settings=configs.settings) File "/mnt/storage/lab4/progs/miniconda3/envs/mdmcleaner/lib/python3.11/site-packages/mdmcleaner/read_gtdb_taxonomy.py", line 1036, in getNprepare_dbdata_nonncbi progressdump = _download_dbdata_nonncbi(targetdir, progressdump, verbose=verbose) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/mnt/storage/lab4/progs/miniconda3/envs/mdmcleaner/lib/python3.11/site-packages/mdmcleaner/read_gtdb_taxonomy.py", line 714, in _download_dbdata_nonncbi progressdump["gtdb_download_dict"], progressdump["gtdb_version"] = download_gtdb_stuff(gtdb_source_dict, targetdir, verbose=verbose) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/mnt/storage/lab4/progs/miniconda3/envs/mdmcleaner/lib/python3.11/site-packages/mdmcleaner/read_gtdb_taxonomy.py", line 316, in download_gtdb_stuff download_dict = get_download_dict(sourcedict, targetfolder) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/mnt/storage/lab4/progs/miniconda3/envs/mdmcleaner/lib/python3.11/site-packages/mdmcleaner/read_gtdb_taxonomy.py", line 300, in get_download_dict okdownloadfilelist, allisfine = check_gtdbmd5file(which_md5filename(targetfolder), targetfolder, sourcedict[x]["pattern"]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/mnt/storage/lab4/progs/miniconda3/envs/mdmcleaner/lib/python3.11/site-packages/mdmcleaner/read_gtdb_taxonomy.py", line 243, in which_md5filename return glob.glob(targetdir + "/" + MD5FILEPATTERN_GTDB)[0] # --> assumes there is only one hit, therefore takes only the first of the list returned by glob.glob(); todo: make sure md5sum file is always deleted after db-setup! otherwise there may be problems if preexisting dbs are updated


IndexError: list index out of range

Can you please help me to solve it?

Regards,
Maria