opain
commented
3 years ago Apologies, I have just seen on another issue that Python 3 is not supported. I have now run using Python 2 and the error no longer persists.
Closed opain closed 3 years ago
opain
commented
3 years ago Apologies, I have just seen on another issue that Python 3 is not supported. I have now run using Python 2 and the error no longer persists.
Hello,
I am receiving the following error when using the test command:
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(base) [k1806347@nodeb21 [rosalind] Software]$ ./popcorn.sh compute -v 2 --bfile1 Popcorn/test/EUR_ref --bfile2 Popcorn/test/EAS_ref --gen_effect Popcorn/test/EUR_EAS_test_ge.cscore Popcorn version 1.0 (C) 2015-2019 Brielin C Brown University of California, Berkeley GNU General Public License v3
Invoking command: python /users/k1806347/brc_scratch/Software/Popcorn/popcorn/main.py compute -v 2 --bfile1 Popcorn/test/EUR_ref --bfile2 Popcorn/test/EAS_ref --gen_effect Popcorn/test/EUR_EAS_test_ge.cscore Beginning analysis at Fri Feb 5 16:26:18 2021 Traceback (most recent call last): File "/users/k1806347/brc_scratch/Software/Popcorn/popcorn/main.py", line 248, in
main()
File "/users/k1806347/brc_scratch/Software/Popcorn/popcorn/main.py", line 234, in main
scores = compute.covariance_scores_2_pop(args)
File "/mnt/lustre/users/k1806347/Software/Popcorn/popcorn/compute.py", line 228, in init
names=['chm','id','pos_mb','pos_bp','a1','a2'])
File "/users/k1806347/.local/lib/python3.7/site-packages/pandas/io/parsers.py", line 765, in read_table
return read_csv(locals())
File "/users/k1806347/.local/lib/python3.7/site-packages/pandas/io/parsers.py", line 686, in read_csv
return _read(filepath_or_buffer, kwds)
File "/users/k1806347/.local/lib/python3.7/site-packages/pandas/io/parsers.py", line 452, in _read
parser = TextFileReader(fp_or_buf, kwds)
File "/users/k1806347/.local/lib/python3.7/site-packages/pandas/io/parsers.py", line 946, in init
self._make_engine(self.engine)
File "/users/k1806347/.local/lib/python3.7/site-packages/pandas/io/parsers.py", line 1178, in _make_engine
self._engine = CParserWrapper(self.f, self.options)
File "/users/k1806347/.local/lib/python3.7/site-packages/pandas/io/parsers.py", line 2008, 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 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: 'Popcorn/test/EUR_ref.bed.bim'
(base) [k1806347@nodeb21 [rosalind] Software]$ cd Popcorn/
(base) [k1806347@nodeb21 [rosalind] Popcorn]$ git pull
Already up-to-date.
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The error suggests it is looking for a file ending .bed.bim, which seems odd.
Do you have any advice on how to resolve this?
Many thanks,
Ollie