When I try to run InSilicoSeq on my multifasta, I am getting the following error:
Additionally, once the program errors out, I am left with hundreds of temporary FASTQs in my directory.
Any help is appreciated!
Thanks.
INFO:iss.app:Generating reads for record: Prevalence_Sequence_ID:107139|ARO_Name:mexM|ARO:3003704|Detection_Model:Protein
INFO:iss.app:Generating reads for record: Prevalence_Sequence_ID:122540|ARO_Name:OpmH|ARO:3003682|Detection_Model:Protein
INFO:iss.app:Generating reads for record: Prevalence_Sequence_ID:190619|ARO_Name:SHV-11|ARO:3001070|Detection_Model:Protein
INFO:iss.app:Generating reads for record: Prevalence_Sequence_ID:196611|ARO_Name:Mycobacterium
joblib.externals.loky.process_executor._RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/panousie/.local/lib/python3.8/site-packages/joblib/externals/loky/process_executor.py", line 436, in _process_worker
r = call_item()
File "/home/panousie/.local/lib/python3.8/site-packages/joblib/externals/loky/process_executor.py", line 288, in __call__
return self.fn(*self.args, **self.kwargs)
File "/home/panousie/.local/lib/python3.8/site-packages/joblib/_parallel_backends.py", line 595, in __call__
return self.func(*args, **kwargs)
File "/home/panousie/.local/lib/python3.8/site-packages/joblib/parallel.py", line 262, in __call__
return [func(*args, **kwargs)
File "/home/panousie/.local/lib/python3.8/site-packages/joblib/parallel.py", line 262, in <listcomp>
return [func(*args, **kwargs)
File "/home/panousie/.local/lib/python3.8/site-packages/iss/generator.py", line 62, in reads
forward, reverse = simulate_read(record, ErrorModel, i, cpu_number)
File "/home/panousie/.local/lib/python3.8/site-packages/iss/generator.py", line 138, in simulate_read
forward.seq = ErrorModel.introduce_indels(
File "/home/panousie/.local/lib/python3.8/site-packages/iss/error_models/__init__.py", line 186, in introduce_indels
if random.random() < deletions[position][mutable_seq[nucl].upper()]:
KeyError: '-'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/panousie/.local/bin/iss", line 8, in <module>
sys.exit(main())
File "/home/panousie/.local/lib/python3.8/site-packages/iss/app.py", line 608, in main
args.func(args)
File "/home/panousie/.local/lib/python3.8/site-packages/iss/app.py", line 306, in generate_reads
record_file_name_list = Parallel(
File "/home/panousie/.local/lib/python3.8/site-packages/joblib/parallel.py", line 1056, in __call__
self.retrieve()
File "/home/panousie/.local/lib/python3.8/site-packages/joblib/parallel.py", line 935, in retrieve
self._output.extend(job.get(timeout=self.timeout))
File "/home/panousie/.local/lib/python3.8/site-packages/joblib/_parallel_backends.py", line 542, in wrap_future_result
return future.result(timeout=timeout)
File "/usr/lib/python3.8/concurrent/futures/_base.py", line 444, in result
return self.__get_result()
File "/usr/lib/python3.8/concurrent/futures/_base.py", line 389, in __get_result
raise self._exception
KeyError: '-'
Hi there!
When I try to run InSilicoSeq on my multifasta, I am getting the following error:
Additionally, once the program errors out, I am left with hundreds of temporary FASTQs in my directory.
Any help is appreciated!
Thanks.