some error about get_pwy_abundance_v1.py

[weiguanyue]

this is my code : get_pwy_abundance_v1.py -i func.filtered.out -s /hl/weiguanyue/databases/funomic/FunOMIC.P.v1 -o1 pwy_abundance.csv -o2 pwyClass_abundance.csv -o3 pwyType_abundance.csv -o4 full_annotation.csv .
when I run ,the error is :
get_pwy_abundance_v1.py:68: DtypeWarning: Columns (3) have mixed types. Specify dtype option on import or set low_memory=False.
jgi_ann=pd.read_csv(ann_path,delimiter='\t',names=column_names,index_col=False)
get_pwy_abundance_v1.py:70: DtypeWarning: Columns (1) have mixed types. Specify dtype option on import or set low_memory=False.
rid_to_uniprot_species=pd.read_csv(uniprot_catalog,delimiter='\t',names=["rid","uniprotId","speciesID"],dtype={'first_column': 'str'},index_col=False)
Traceback (most recent call last):
File "get_pwy_abundance_v1.py", line 71, in
taxa=pd.read_csv(taxa_path, delimiter="\t",names=["speciesID","taxa"],index_col=False)
File "/miniconda3/lib/python3.9/site-packages/pandas/util/_decorators.py", line 211, in wrapper
return func(*args, **kwargs)
File "/miniconda3/lib/python3.9/site-packages/pandas/util/_decorators.py", line 331, in wrapper
return func(*args, **kwargs)
File "/miniconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 950, in read_csv
return _read(filepath_or_buffer, kwds)
File "/miniconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 611, in _read
return parser.read(nrows)
File "/miniconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1778, in read
) = self._engine.read( # type: ignore[attr-defined]
File "/miniconda3/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 230, in read
chunks = self._reader.read_low_memory(nrows)
File "pandas/_libs/parsers.pyx", line 808, in pandas._libs.parsers.TextReader.read_low_memory
File "pandas/_libs/parsers.pyx", line 866, in pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 852, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 1973, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 2 fields in line 1937, saw 6
I have check many times about the input file ,there are nothing wrong about the file ,so could you help me solve the problem?

[ilarioferrocino]

same error here:
Start removing bacterial reads for FP1
sys:1: DtypeWarning: Columns (3) have mixed types. Specify dtype option on import or set low_memory=False.
Traceback (most recent call last):
File "/home/administrator/programmi/FunOMIC/get_pwy_abundance_v1.py", line 69, in
blastx_out=pd.read_csv(sample_to_process,index_col=False,delimiter='\t',names=["qid","rid","id","lenght","mismatch","gapopne","qstart","qend","sstart","send","evalue","bscore"])
File "/home/administrator/miniconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 685, in parser_f
return _read(filepath_or_buffer, kwds)
File "/home/administrator/miniconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 457, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/administrator/miniconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 895, in init
self._make_engine(self.engine)
File "/home/administrator/miniconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 1135, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/administrator/miniconda3/lib/python3.7/site-packages/pandas/io/parsers.py", line 1917, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 689, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] File b'output_folder_FP/functional_profiling/FP1.func.filtered.out' does not exist: b'output_folder_FP/functional_profiling/FP1.func.filtered.out'

someone can solve it?

[Justinwright973]

I am observing the same error when attempting to run this step/command, was anyone able to troubleshoot this issue so the python script can successfully run? I am stock at this step:

/home/wright2/funOMIC/get_pwy_abundance_v1.py:68: DtypeWarning: Columns (3) have mixed types. Specify dtype option on import or set low_memory=False. jgi_ann=pd.read_csv(ann_path,delimiter='\t',names=column_names,index_col=False,dtype={'fourth_column': 'str'}) /home/wright2/funOMIC/get_pwy_abundance_v1.py:70: DtypeWarning: Columns (1) have mixed types. Specify dtype option on import or set low_memory=False. rid_to_uniprot_species=pd.read_csv(uniprot_catalog,delimiter='\t',names=["rid","uniprotId","speciesID"],dtype={'first_column': 'str', 'second_column': 'str'},index_col=False) Traceback (most recent call last): File "/home/wright2/funOMIC/get_pwy_abundance_v1.py", line 71, in <module> taxa=pd.read_csv(taxa_path, delimiter="\t",names=["speciesID","taxa"],index_col=False) File "/home/wright2/miniconda3/envs/funomic/lib/python3.10/site-packages/pandas/util/_decorators.py", line 211, in wrapper return func(*args, **kwargs) File "/home/wright2/miniconda3/envs/funomic/lib/python3.10/site-packages/pandas/util/_decorators.py", line 331, in wrapper return func(*args, **kwargs) File "/home/wright2/miniconda3/envs/funomic/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 950, in read_csv return _read(filepath_or_buffer, kwds) File "/home/wright2/miniconda3/envs/funomic/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 611, in _read return parser.read(nrows) File "/home/wright2/miniconda3/envs/funomic/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1778, in read ) = self._engine.read( # type: ignore[attr-defined] File "/home/wright2/miniconda3/envs/funomic/lib/python3.10/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 230, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 808, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 866, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 852, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1973, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 2 fields in line 1937, saw 6

[zixuanxie]

Hi @ilarioferrocino , sorry for the late reply, this message was probably because there was no reads mapped to the functional db.

[ManichanhLab]

Hi @weiguanyue and @Justinwright973 , this error was caused by some extra tabs in the annotation file, we have uploaded the FunOMIC-P db with corrected annotation file, could you please download and try again?

[Justinwright973]

Ok thank you!

I am attempting to access this new database, but the site will not load? (https://manichanh.vhir.org/funomic/) perhaps the DB is still updating there? I was able to access it previously. Thank you!

[ManichanhLab]

Hi @Justinwright973 ,

Due to an issue with the server, the website was down for a couple of hours, now it should be working again.
Sorry for the inconvenience!