ERROR: An error was encountered while running hmmsearch.

[J-Weijie98]

[2024-11-18 09:40:19] TASK: Identifying TIGRFAM protein families.

==> Processed 0/79 genomes (0%) | | [?genome/s, ETA ?]Process Process-4:
Traceback (most recent call last):
File "/media/desk16/tly2105/miniconda3/envs/gtdbtk-2.4.0/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/media/desk16/tly2105/miniconda3/envs/gtdbtk-2.4.0/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/media/desk16/tly2105/miniconda3/envs/gtdbtk-2.4.0/lib/python3.8/site-packages/gtdbtk/external/tigrfam_search.py", line 154, in _workerThread
self._topHit(output_hit_file)
File "/media/desk16/tly2105/miniconda3/envs/gtdbtk-2.4.0/lib/python3.8/site-packages/gtdbtk/external/tigrfam_search.py", line 94, in _topHit
hmm_id = line_split[3]
IndexError: list index out of range
[2024-11-18 09:40:27] ERROR: An error was encountered while running hmmsearch.
[2024-11-18 09:40:27] ERROR: Controlled exit resulting from an unrecoverable error or warning.
[2024-11-18 09:40:27] INFO: GTDB-Tk v2.4.0
[2024-11-18 09:40:27] INFO: gtdbtk align --identify_dir /media/desk16/tly2105/Bin_all/gtdbtk_identify
--out_dir /media/desk16/tly2105/Bin_all/gtdbtk_align
[2024-11-18 09:40:27] INFO: Using GTDB-Tk reference data version r220: /media/desk16/tly2105/miniconda3/envs/gtdbtk-2.4.0/share/gtdbtk-2.4.0/db
[2024-11-18 09:40:27] ERROR: Uncontrolled exit resulting from an unexpected error.
GATBDK.zip

[pchaumeil]

Hello,

I am unable to reproduce this error with the 2 genomes you have provided, the process is running without problem.

What are the completeness and contamination of the 79 genomes you are trying to analyse? Can you try to rerun the identify step to another directory (/media/desk16/tly2105/Bin_all/gtdbtk_identify_2 for example)