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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
The text was updated successfully, but these errors were encountered:
Hi!
I'm trying to download database using mdmcleaner makedb, and I've got an error like this:
01a: download GTDB data--
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
The text was updated successfully, but these errors were encountered: