Error when running cctyper: sed: cannot rename <output filename>/sed78a7GM: Permission denied

[jdcfc]

After running INFO: Running HMMER against Cas profiles , the job will instantly terminate and I receive the following error:

sed: cannot rename <output filename>/sed78a7GM: Permission denied Traceback (most recent call last): File "/opt/miniconda3/envs/cctyper/bin/cctyper", line 83, in <module> hmmeri.main_hmm() File "/opt/miniconda3/envs/cctyper/lib/python3.8/site-packages/cctyper/hmmer.py", line 26, in main_hmm self.load_hmm() File "/opt/miniconda3/envs/cctyper/lib/python3.8/site-packages/cctyper/hmmer.py", line 85, in load_hmm hmm_df = pd.read_csv(self.out+'hmmer.tab', sep='\s+', header=None, File "/opt/miniconda3/envs/cctyper/lib/python3.8/site-packages/pandas/util/_decorators.py", line 211, in wrapper return func(*args, **kwargs) File "/opt/miniconda3/envs/cctyper/lib/python3.8/site-packages/pandas/util/_decorators.py", line 331, in wrapper return func(*args, **kwargs) File "/opt/miniconda3/envs/cctyper/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 950, in read_csv return _read(filepath_or_buffer, kwds) File "/opt/miniconda3/envs/cctyper/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 605, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File "/opt/miniconda3/envs/cctyper/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1442, in __init__ self._engine = self._make_engine(f, self.engine) File "/opt/miniconda3/envs/cctyper/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1735, in _make_engine self.handles = get_handle( File "/opt/miniconda3/envs/cctyper/lib/python3.8/site-packages/pandas/io/common.py", line 856, in get_handle handle = open( FileNotFoundError: [Errno 2] No such file or directory: '<output filename>/hmmer.tab'

I was just wondering if anyone has come across this error and if so, how they resolved it?

Thanks in advance!

[Russel88]

Hi

I think it's because you have no matches to any of the HMMs. Is it a very short sequence? Does it work with other sequences?

[jdcfc]

Hi,

Thank you for your response. And thank you for making such a handy tool!

You're right! I was testing the software with a file that had very short sequences. When using a full genome, it worked just fine. Thanks again.