Error with HMM - Githubissues

Greetings! I'm excited to test out MicrobeAnnotator. After getting DBs installed, my first test on annotating a genome (a metagenomic bin draft genome) yielded the following output:

Starting sbatch script myscript.sh at:Sat Jul 1 07:04:53 EDT 2023 running host: node304 assigned nodes: node304 partition used: bigmem jobid: 11015109 2023-07-01 07:04:58,486 [INFO]: ---- This is MicrobeAnnotator v2.0.5 ---- 2023-07-01 07:04:58,487 [INFO]: Validating user inputs 2023-07-01 07:04:58,488 [INFO]: Passed 2023-07-01 07:04:58,488 [INFO]: Processing 1 files. I will run 1 files in parallel with 32 threads per file. 2023-07-01 07:04:58,514 [INFO]: Searching proteins against KOfam profiles 2023-07-01 07:04:58,514 [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?) 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?) 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?) 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?) 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?) 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?)

Fatal exception (source file p7_pipeline.c, line 697): Fatal exception (source file p7_pipeline.c, line 697): Target sequence length > 100K, over comparison pipeline limit. (Did you mean to use nhmmer/nhmmscan?)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 "/users/m/s/mscarbor/anaconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, *kwds)) File "/users/m/s/mscarbor/anaconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar return list(map(args)) File "/users/m/s/mscarbor/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/pipeline/hmmsearch.py", line 57, in hmmer_search output=temporal_result) File "/users/m/s/mscarbor/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/hmmer/hmmer.py", line 250, in search return self._match(hmmsearch, target, opts) File "/users/m/s/mscarbor/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/hmmer/hmmer.py", line 267, in _match check_call(cmd_match) File "/users/m/s/mscarbor/anaconda3/envs/microbeannotator/lib/python3.7/subprocess.py", line 363, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/users/m/s/mscarbor/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/hmmer/bin/v3.3.2/hmmsearch_manylinux2010_x86_64', '-o', '/tmp/tmpv8m9ya3_DPN8S767RNI60NXKTSMG', '--tblout', '/tmp/tmp_0ls2099/tbl.txt', '--domtblout', '/tmp/tmp_0ls2099/domtbl.txt', '/users/m/s/mscarbor/MicrobeAnnotator_DB/kofam_data/profiles/common_6.model', '/gpfs1/home/m/s/mscarbor/MaxBin_Polished/MaxBin_Output_IlluminaMapping_Obj1J1.001.fasta']' died with <Signals.SIGABRT: 6>. """

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

Traceback (most recent call last): File "/users/m/s/mscarbor/anaconda3/envs/microbeannotator/bin/microbeannotator", line 981, in main() File "/users/m/s/mscarbor/anaconda3/envs/microbeannotator/bin/microbeannotator", line 367, in main processes=processes, threads=threads) File "/users/m/s/mscarbor/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/pipeline/hmmsearch.py", line 192, in hmmsearch_launcher hmmer_search, protein_model_list) File "/users/m/s/mscarbor/anaconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 268, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/users/m/s/mscarbor/anaconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 657, in get raise self._value subprocess.CalledProcessError: Command '['/users/m/s/mscarbor/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/hmmer/bin/v3.3.2/hmmsearch_manylinux2010_x86_64', '-o', '/tmp/tmpv8m9ya3_DPN8S767RNI60NXKTSMG', '--tblout', '/tmp/tmp_0ls2099/tbl.txt', '--domtblout', '/tmp/tmp_0ls2099/domtbl.txt', '/users/m/s/mscarbor/MicrobeAnnotator_DB/kofam_data/profiles/common_6.model', '/gpfs1/home/m/s/mscarbor/MaxBin_Polished/MaxBin_Output_IlluminaMapping_Obj1J1.001.fasta']' died with <Signals.SIGABRT: 6>.

I'm at a bit of a loss here. Any guidance would be greatly appreciated.

Thanks!

Matt

cruizperez / MicrobeAnnotator

Error with HMM #82