lmc297 / btyper3 Goto Github PK

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
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failed

UnsatisfiableError:

$ btyper3 -i 2218710072.fna -o bytper3
Welcome to BTyper3!
You are initializing this run at 2022-07-19 08:56
You ran the following command:
/phe/tools/miniconda3/envs/btyper3/bin/btyper3 -i 2218710072.fna -o bytper3
Report bugs/concerns to Laura M. Carroll, [email protected]
Using FastANI to assign 2218710072 to a species at 2022-07-19 08:56
fastANI: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/phe/tools/miniconda3/envs/btyper3/bin/btyper3", line 10, in <module>
    sys.exit(main())
  File "/phe/tools/miniconda3/envs/btyper3/lib/python3.10/site-packages/btyper3/__init__.py", line 441, in main
    run_pipeline(args)
  File "/phe/tools/miniconda3/envs/btyper3/lib/python3.10/site-packages/btyper3/__init__.py", line 105, in run_pipeline
    final_species = get_species.run_fastani("species", fastani_path, infile, final_results_directory, prefix)
  File "/phe/tools/miniconda3/envs/btyper3/lib/python3.10/site-packages/btyper3/ani.py", line 60, in run_fastani
    proc.check_returncode()
  File "/phe/tools/miniconda3/envs/btyper3/lib/python3.10/subprocess.py", line 456, in check_returncode
    raise CalledProcessError(self.returncode, self.args, self.stdout,
subprocess.CalledProcessError: Command '['fastANI', '-q', '2218710072.fna', '--rl', '/tmp/tmp69n8g9vktxt', '-o', 'bytper3/btyper3_final_results/species/2218710072_species_fastani.txt']' returned non-zero exit status 127

$ python download_pubmlst_latest.py

Downloading most recent PubMLST datbase at 2021-04-12 14:38
Traceback (most recent call last):
  File "download_pubmlst_latest.py", line 74, in <module>
    main()
  File "download_pubmlst_latest.py", line 67, in main
    download_pubmlst(btyper3_path)
  File "download_pubmlst_latest.py", line 28, in download_pubmlst
    tree=ET.parse(xml)
  File "/home/domeni/anaconda3/lib/python3.7/xml/etree/ElementTree.py", line 1197, in parse
    tree.parse(source, parser)
  File "/home/domeni/anaconda3/lib/python3.7/xml/etree/ElementTree.py", line 598, in parse
    self._root = parser._parse_whole(source)
xml.etree.ElementTree.ParseError: no element found: line 1, column 0