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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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Error while running RGI for loose hit, without nudging #171

Closed absartalat closed 1 year ago

absartalat commented 3 years ago

When I run RGI with the parameter LOOSE hit, I get an error. I have used both nucleotide fasta file as well as protein fasta file. Both give error.

Input $ rgi main --input_sequence Sample_2.fasta --output_file Sample_1rgi_loose --input_type contig --local --include_loose --clean

Error log Process Process-2: Traceback (most recent call last): File "/home/s2/anaconda3/envs/rgi/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/s2/anaconda3/envs/rgi/lib/python3.8/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/s2/anaconda3/envs/rgi/lib/python3.8/site-packages/app/Filter.py", line 92, in prepare_output obj.combine_jsons() File "/home/s2/anaconda3/envs/rgi/lib/python3.8/site-packages/app/ConvertRGIJsonToTSV.py", line 39, in combine_jsons homolog = json.load(hf) File "/home/s2/anaconda3/envs/rgi/lib/python3.8/json/init.py", line 293, in load return loads(fp.read(), File "/home/s2/anaconda3/envs/rgi/lib/python3.8/json/init.py", line 357, in loads return _default_decoder.decode(s) File "/home/s2/anaconda3/envs/rgi/lib/python3.8/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/home/s2/anaconda3/envs/rgi/lib/python3.8/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

CARD Version card_database_v3.1.1

RGI version 5.2.0

Expected behavior I expect it to give an output file of all the resistome having loose hits in eference to CARD

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raphenya commented 1 year ago

@absartalat This looks like there was an issue with the JSON file as it was empty. It will help if you have a sample input file so we can try debugging. Please re-open the issue if you still need help on this. Cheers.