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bowmanjeffs / paprica

paprica - PAthway PRediction by phylogenetIC plAcement
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paprica mg, Error: Incompatible database version #39

Closed blancaverag closed 7 years ago

blancaverag commented 7 years ago

I haven't build the regular paprica database due to errors, but as I am interested in metagenome annotation I downloaded the paprica-mg databases and followed the instructions here.

And there is an error stating databases versions are incompatible.

paprica-mg_run.py -i Contigs.fna -o test -ref_dir ref_genome_database -pathways F executing DIAMOND blastx, this might take a while... Error: Incompatible database version Error: function Input_stream::Input_stream(const string&, bool) line 75. Error opening file /home/blanca/test.paprica-mg.nr.daa Traceback (most recent call last): File "/home/programas/paprica/paprica-mg_run.py", line 134, in diamond_df = pd.read_csv(cwd + name + '.paprica-mg.nr.txt', sep = '\t', header = None, index_col = 0) File "/usr/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 465, in parser_f return _read(filepath_or_buffer, kwds) File "/usr/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 241, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/usr/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 557, in init self._make_engine(self.engine) File "/usr/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 694, in _make_engine self._engine = CParserWrapper(self.f, self.options) File "/usr/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 1061, in init self._reader = _parser.TextReader(src, **kwds) File "pandas/parser.pyx", line 350, in pandas.parser.TextReader.cinit (pandas/parser.c:3143) File "pandas/parser.pyx", line 583, in pandas.parser.TextReader._setup_parser_source (pandas/parser.c:5765) IOError: File /home/blanca/test.paprica-mg.nr.txt does not exist

Updating diamond to diamond v0.8.24.86 does not solve the problem.

Which version of diamond was used to build them?

Thank you,

bowmanjeffs commented 7 years ago

Trying to reproduce now...

bowmanjeffs commented 7 years ago

Yep, looks like there is a database incompatibility. I'm re-building now, will take a few. Will comment here when new version is posted.

bowmanjeffs commented 7 years ago

New database up, let me know if there are any issues. Be sure to download the updated paprica-mg.ec.csv.gz as well.

blancaverag commented 7 years ago

It works now, thank you.