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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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[BUG]Problem with xml file #179

Closed Rainjie-afk closed 1 year ago

Rainjie-afk commented 2 years ago

I am trying to run RGI v5.2.1. and also the database is auto_load. But enter-counting these errors. How can i solve this?

rgi main --input_sequence /home/hyj/desktop/test/B_ovtus.fna -o /home/hyj/desktop/test/B_ovtus -t contig -a blast -n 6 --clean

Error: NCBI C++ Exception: T0 "/opt/conda/conda-bld/blast_1594418791377/work/blast/c++/src/corelib/ncbistr.cpp", line 6543: Error: ncbi::CUtf8::SymbolToChar() - Failed to convert symbol to requested encoding (m_Pos = 0) T0 "/opt/conda/conda-bld/blast_1594418791377/work/blast/c++/src/serial/objostrxml.cpp", line 1507: Error: ncbi::CObjectOStreamXml::WriteClassMember() - Frame type= eFrameClassMember, Member name= db (m_Pos = 0) T0 "/opt/conda/conda-bld/blast_1594418791377/work/blast/c++/src/serial/objostrxml.cpp", line 1488: Error: ncbi::CObjectOStreamXml::WriteClass() - Frame type= eFrameClass, Object type= BlastOutput (m_Pos = 0) T0 "/opt/conda/conda-bld/blast_1594418791377/work/blast/c++/src/serial/objostr.cpp", line 610: Error: ncbi::CObjectOStream::Write() - Frame type= eFrameNamed, Object type= BlastOutput (m_Pos = 0)

Process Process-1:4: Traceback (most recent call last): File "/home/hyj/miniconda3/envs/rgi5.2.1/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/hyj/miniconda3/envs/rgi5.2.1/lib/python3.8/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/hyj/miniconda3/envs/rgi5.2.1/lib/python3.8/site-packages/app/Filter.py", line 121, in process_rrna res = rrna_obj.run() File "/home/hyj/miniconda3/envs/rgi5.2.1/lib/python3.8/site-packages/app/RrnaModel.py", line 38, in run for blast_record in blast_records: File "/home/hyj/miniconda3/envs/rgi5.2.1/lib/python3.8/site-packages/Bio/Blast/NCBIXML.py", line 800, in parse raise ValueError("Your XML file was empty") ValueError: Your XML file was empty**

Maybe it's not the same problem like https://github.com/arpcard/rgi/issues/31? I'm not sure. Can someone help me deal with it? Many thanks!

raphenya commented 2 years ago

@Rainjie-afk this looks like there are some non-ASCII characters in your input or your input fasta is not formatted correctly.

raphenya commented 1 year ago

@Rainjie-afk Please re-open if you are still experiencing the same issue. Cheers.