Fatal exception while parsing HMM profile metadata

[galtoledano]

Hi, I'm running the following command: microbeannotator -i ../data/pch.fasta -o pch_light_microbannotator -d ~/MicrobeAnnotator_DB_less -m blast

and getting this fatal exception at the 'Parsing HMM profile metadata' step. do you have any idea why that happened?

2022-05-03 10:37:10,466 [INFO]: ---- This is MicrobeAnnotator v2.0.4 ---- 2022-05-03 10:37:10,466 [INFO]: Validating user inputs 2022-05-03 10:37:10,467 [INFO]: Passed 2022-05-03 10:37:10,467 [INFO]: Processing 1 files. I will run 1 files in parallel with 1 threads per file. 2022-05-03 10:37:10,480 [INFO]: Searching proteins against KOfam profiles 2022-05-03 10:37:10,480 [INFO]: Parsing HMM profile metadata Fatal exception (source file p7_pipeline.c, line 697): Target sequence length > 100K, over comparison pipeline limit. (Did you mean to use nhmmer/nhmmscan?) Fatal exception (source file p7_pipeline.c, line 697): Target sequence length > 100K, over comparison pipeline limit. (Did you mean to use nhmmer/nhmmscan?) Fatal exception (source file p7_pipeline.c, line 697): Target sequence length > 100K, over comparison pipeline limit. (Did you mean to use nhmmer/nhmmscan?) Fatal exception (source file p7_pipeline.c, line 697): Target sequence length > 100K, over comparison pipeline limit. (Did you mean to use nhmmer/nhmmscan?) multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/galtol/miniconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, *kwds)) File "/home/galtol/miniconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar return list(map(args)) File "/home/galtol/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/pipeline/hmmsearch.py", line 57, in hmmer_search output=temporal_result) File "/home/galtol/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/hmmer/hmmer.py", line 250, in search return self._match(hmmsearch, target, opts) File "/home/galtol/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/hmmer/hmmer.py", line 267, in _match check_call(cmd_match) File "/home/galtol/miniconda3/envs/microbeannotator/lib/python3.7/subprocess.py", line 363, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/home/galtol/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/hmmer/bin/v3.3.2/hmmsearch_manylinux2010_x86_64', '-o', '/tmp/tmp9m2uxzxxZ8VF22E6JI17RVTRGG1I', '--tblout', '/tmp/tmphx3ra39v/tbl.txt', '--domtblout', '/tmp/tmphx3ra39v/domtbl.txt', '/home/galtol/MicrobeAnnotator_DB_less/kofam_data/profiles/common_1.model', '/home/galtol/lab/genomic_evo/analysis_results/seq_results_dec2021/annotators_check/../data/pch.fasta']' died with <Signals.SIGABRT: 6>. """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/galtol/miniconda3/envs/microbeannotator/bin/microbeannotator", line 981, in main() File "/home/galtol/miniconda3/envs/microbeannotator/bin/microbeannotator", line 367, in main processes=processes, threads=threads) File "/home/galtol/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/pipeline/hmmsearch.py", line 192, in hmmsearch_launcher hmmer_search, protein_model_list) File "/home/galtol/miniconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 268, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/home/galtol/miniconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 657, in get raise self._value subprocess.CalledProcessError: Command '['/home/galtol/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/hmmer/bin/v3.3.2/hmmsearch_manylinux2010_x86_64', '-o', '/tmp/tmp9m2uxzxxZ8VF22E6JI17RVTRGG1I', '--tblout', '/tmp/tmphx3ra39v/tbl.txt', '--domtblout', '/tmp/tmphx3ra39v/domtbl.txt', '/home/galtol/MicrobeAnnotator_DB_less/kofam_data/profiles/common_1.model', '/home/galtol/lab/genomic_evo/analysis_results/seq_results_dec2021/annotators_check/../data/pch.fasta']' died with <Signals.SIGABRT: 6>.

Thanks.

[Sam-J-1]

Hi, I'm having the same issue. Did you manage to fix it?

[galtoledano]

No, I used a different tool.

[Sam-J-1]

I managed to work out what the problem was for me. You need to use a file containing protein sequences for your genome, as the tool does not have a CDS identification function.