GTDBTk - align step error in hmm file
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Entering edit mode
5 months ago
seok1213neo ▴ 20

i am currently working on one of the gtdbtk first steps; align steps (identify, align and classify)

the following is the message i get (for doing 15 archaea genomes)

Traceback (most recent call last):
  File "/home/yschoi/anaconda3/envs/gtdbtk/lib/python3.8/site-packages/gtdbtk/__main__.py", line 509, in main
    gt_parser.parse_options(args)
  File "/home/yschoi/anaconda3/envs/gtdbtk/lib/python3.8/site-packages/gtdbtk/main.py", line 758, in parse_options
    self.align(options)
  File "/home/yschoi/anaconda3/envs/gtdbtk/lib/python3.8/site-packages/gtdbtk/main.py", line 334, in align
    markers.align(options.identify_dir,
  File "/home/yschoi/anaconda3/envs/gtdbtk/lib/python3.8/site-packages/gtdbtk/markers.py", line 405, in align
    self._write_marker_info(Config.AR122_MARKERS, ar122_marker_info_file)
  File "/home/yschoi/anaconda3/envs/gtdbtk/lib/python3.8/site-packages/gtdbtk/markers.py", line 353, in _write_marker_info
    with open(marker_path) as fp:
FileNotFoundError: [Errno 2] No such file or directory: '/disk7/08.youngseok/hgt/c.GTDB-TK/GTDBTk-master/release202/markers/pfam/individual_hmms/PF01092.14.hmm'

and it seems like PF01092.14.hmm is an older version, which in my reference data

there is PF01092.20.hmm already.

i checked my config file, and the list of the files surely indicates PF01092.20.hmm to be used.

please help me with getting through this.

Thank you!

align hmm GTDBTK • 124 views
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