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yanailab / celseq2

Generate the UMI count matrix from CEL-Seq2 sequencing data
https://yanailab.github.io/celseq2/
BSD 3-Clause "New" or "Revised" License
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Re: ParseError #20

Closed mdhe1248 closed 6 years ago

mdhe1248 commented 6 years ago

I ran a command line below, 

celseq2 --config-file test_config.yaml --experiment-table Holy_2606_1/test_experiment_table.txt --output-dir result_dir -j 10

I obtained the error below:

[Fri Apr 20 18:42:59 2018] ParserError in line 28 of /home/donghoon/.local/lib/python3.5/site-packages/celseq2/workflow/celseq2_beta.snakemake:
[Fri Apr 20 18:42:59 2018] Error tokenizing data. C error: Expected 5 fields in line 3, saw 6
[Fri Apr 20 18:42:59 2018] 
[Fri Apr 20 18:42:59 2018]   File "/home/donghoon/.local/lib/python3.5/site-packages/celseq2/workflow/celseq2_beta.snakemake", line 28, in <module>
[Fri Apr 20 18:42:59 2018]   File "/home/donghoon/.local/lib/python3.5/site-packages/celseq2/helper.py", line 128, in cook_sample_sheet
[Fri Apr 20 18:42:59 2018]   File "/home/donghoon/.local/lib/python3.5/site-packages/pandas/io/parsers.py", line 709, in parser_f
[Fri Apr 20 18:42:59 2018]   File "/home/donghoon/.local/lib/python3.5/site-packages/pandas/io/parsers.py", line 455, in _read
[Fri Apr 20 18:42:59 2018]   File "/home/donghoon/.local/lib/python3.5/site-packages/pandas/io/parsers.py", line 1069, in read
[Fri Apr 20 18:42:59 2018]   File "/home/donghoon/.local/lib/python3.5/site-packages/pandas/io/parsers.py", line 1839, in read
[Fri Apr 20 18:42:59 2018]   File "pandas/_libs/parsers.pyx", line 902, in pandas._libs.parsers.TextReader.read
[Fri Apr 20 18:42:59 2018]   File "pandas/_libs/parsers.pyx", line 924, in pandas._libs.parsers.TextReader._read_low_memory
[Fri Apr 20 18:42:59 2018]   File "pandas/_libs/parsers.pyx", line 978, in pandas._libs.parsers.TextReader._read_rows
[Fri Apr 20 18:42:59 2018]   File "pandas/_libs/parsers.pyx", line 965, in pandas._libs.parsers.TextReader._tokenize_rows
[Fri Apr 20 18:42:59 2018]   File "pandas/_libs/parsers.pyx", line 2208, in pandas._libs.parsers.raise_parser_error

I may be wrong, but I think the error is related to python version. Python version control is not being well maintained in our server. Multiple python versions have been installed. Also, python has been installed locally too. Does anyone have any insight?

mdhe1248 commented 6 years ago

Okay, I found my mistakes. I used an old config file. Generating new config file using new-configuration-file solved the problem.