Sam-J-1
commented
1 year ago Hi, I'm having the same issue. Did you manage to fix it?
Open kdyoung100 opened 1 year ago
Sam-J-1
commented
1 year ago Hi, I'm having the same issue. Did you manage to fix it?
microbeannotator -i /home/kdyoung/1158_Efaecium.fasta -d /data1/tools/MicrobeAnnotator_DB/ -o /home/kdyoung/1158_Efaecium_microbeannotator/ -m blast -t 16 2022-12-02 10:16:36,244 [INFO]: ---- This is MicrobeAnnotator v2.0.5 ---- 2022-12-02 10:16:36,244 [INFO]: Validating user inputs 2022-12-02 10:16:36,245 [INFO]: Passed 2022-12-02 10:16:36,245 [INFO]: Processing 1 files. I will run 1 files in parallel with 16 threads per file. 2022-12-02 10:16:36,252 [INFO]: Searching proteins against KOfam profiles 2022-12-02 10:16:36,252 [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): 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?) 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?) multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/data1/tools/anaconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, *kwds)) File "/data1/tools/anaconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar return list(map(args)) File "/data1/tools/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/pipeline/hmmsearch.py", line 57, in hmmer_search output=temporal_result) File "/data1/tools/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/hmmer/hmmer.py", line 250, in search return self._match(hmmsearch, target, opts) File "/data1/tools/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/hmmer/hmmer.py", line 267, in _match check_call(cmd_match) File "/data1/tools/anaconda3/envs/microbeannotator/lib/python3.7/subprocess.py", line 363, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/data1/tools/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/hmmer/bin/v3.3.2/hmmsearch_manylinux2010_x86_64', '-o', '/tmp/tmpgufeiwtk2CN2VKSY4SF30Q90HTOD', '--tblout', '/tmp/tmp66s4x5b2/tbl.txt', '--domtblout', '/tmp/tmp66s4x5b2/domtbl.txt', '/data1/tools/MicrobeAnnotator_DB/kofam_data/profiles/independent_2.model', '/home/kdyoung/1158_Efaecium.fasta']' died with <Signals.SIGABRT: 6>. """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/data1/tools/anaconda3/envs/microbeannotator/bin/microbeannotator", line 981, in
main()
File "/data1/tools/anaconda3/envs/microbeannotator/bin/microbeannotator", line 367, in main
processes=processes, threads=threads)
File "/data1/tools/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/pipeline/hmmsearch.py", line 192, in hmmsearch_launcher
hmmer_search, protein_model_list)
File "/data1/tools/anaconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/data1/tools/anaconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
subprocess.CalledProcessError: Command '['/data1/tools/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/hmmer/bin/v3.3.2/hmmsearch_manylinux2010_x86_64', '-o', '/tmp/tmpgufeiwtk2CN2VKSY4SF30Q90HTOD', '--tblout', '/tmp/tmp66s4x5b2/tbl.txt', '--domtblout', '/tmp/tmp66s4x5b2/domtbl.txt', '/data1/tools/MicrobeAnnotator_DB/kofam_data/profiles/independent_2.model', '/home/kdyoung/1158_Efaecium.fasta']' died with <Signals.SIGABRT: 6>.