Issues in downloading database

Hi,
I am trying to download the database through ./run.sh but it shows following error:
2024-06-12 12:17:35,559 generate_taxonomy.py INFO     Downloading and reading the NCBI taxdump file from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz                                            
2024-06-12 12:20:08,786 generate_taxonomy.py INFO     names.dmp and nodes.dmp succeffully downloaded, extracted, and read                                                                                  
2024-06-12 12:20:08,787 generate_taxonomy.py INFO     Processing the names.dmp file to extract the taxonomic names                                                                                         
2024-06-12 12:20:23,623 generate_taxonomy.py INFO     Finished reading names
2024-06-12 12:20:23,623 generate_taxonomy.py INFO     Loading the taxonomic tree from nodes.dmp
2024-06-12 12:20:49,956 generate_taxonomy.py INFO     Finished reading the initial taxonomic tree
2024-06-12 12:20:49,957 generate_taxonomy.py INFO     Exporting the original unedited NCBI taxonomy to: out/taxonomy.txt
2024-06-12 12:20:54,616 generate_taxonomy.py INFO     out/taxonomy.txt saved.
2024-06-12 12:20:54,617 generate_taxonomy.py INFO     Processing the taxonomy for consistency and a fixed number of taxonomic levels
2024-06-12 12:22:25,952 generate_taxonomy.py INFO     Removing noranks from the taxonomy
2024-06-12 12:22:28,673 generate_taxonomy.py INFO     Adding taxon names to the taxonomy
2024-06-12 12:22:29,794 generate_taxonomy.py INFO     Adding nternal missing taxonomic levels
2024-06-12 12:33:23,275 generate_taxonomy.py INFO     Removing duplicated taxa
2024-06-12 12:33:24,510 generate_taxonomy.py INFO     Finished postprocessing the taxonomy
2024-06-12 12:33:24,510 generate_taxonomy.py INFO     Exporting the edited NCBI taxonomy to: out/taxonomy_reduced.txt
2024-06-12 12:33:28,713 generate_taxonomy.py INFO     out/taxonomy_reduced.txt saved.
2024-06-12 12:33:28,713 generate_taxonomy.py INFO     Pickled taxonomy saved to: out/taxonomy.pkl
2024-06-12 12:36:55,620 generate_taxonomy.py INFO     out/taxonomy.pkl saved.
2024-06-12 12:37:06,353 repophlan_get_microbes.py INFO     Reading the taxonomy from out/taxonomy_reduced.txt... 
2024-06-12 12:37:09,589 repophlan_get_microbes.py INFO     Done.
Traceback (most recent call last):
  File "repophlan_get_microbes.py", line 290, in <module>
    refseq_assemblies = get_assemblies( add_protocol(NCBI_ftp + NCBI_ASREFSEQ_file), par['out_dir'] )
  File "repophlan_get_microbes.py", line 249, in get_assemblies
    if line_d['version_status'] != 'latest': continue
KeyError: 'version_status'
2024-06-12 12:40:16,369 generate_taxonomy_taxid.py INFO     Downloading and reading the NCBI taxdump file from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
2024-06-12 12:41:54,219 generate_taxonomy_taxid.py ERROR    Error in downloading, extracting, or reading ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz: Error -3 while decompressing: invalid distance code
Traceback (most recent call last):
  File "parse_taxonomy.py", line 22, in <module>
    fid = open(Accession2TaxIDFile,"r")
IOError: [Errno 2] No such file or directory: 'out/repophlan_microbes.txt'
sed: can't read out/taxonomy_reduced_taxID.txt: No such file or directory
sed: can't read out/taxonomy_reduced_taxID.txt: No such file or directory
Please help me resolve it, thank you..
dkoslicki / MetaPalette

Issues in downloading database #16
