J35P312 / SVDB

structural variant database software
MIT License
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Query is failing with UnicodeDecodeError #28

Closed hassanfa closed 4 years ago

hassanfa commented 4 years ago

I have multiple Manta SV files and build a database already. But now with query it fails with the following error:

Traceback (most recent call last):
  File "xxxxx/bin/svdb", line 11, in <module>
    load_entry_point('svdb', 'console_scripts', 'svdb')()
  File "xxxx/SVDB/svdb/__main__.py", line 37, in main
    query_module.main(args)
  File "xxxxxx/SVDB/svdb/query_module.py", line 96, in main
    for line in f:
  File "xxxxxxxx/lib/python3.6/codecs.py", line 321, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf1 in position 99: invalid continuation byte

Commands that I've used are: svdb --build --files *.vcf --prefix my_svdb

Then followed by: svdb --query --db issue_49_svdb.db --query_vcf data_1.vcf

I'm trying to run it using minimal options to test and make it work but I couldn't figure out from documentation what order or how it should be done. I tried --export as well, but I'm not sure how to follow it properly.

hassanfa commented 4 years ago

@J35P312 Thanks for the help. So the procedure is to --export after build and provide *.vcf from the output to --query