Error printing whole nanocomp report

[NikoLichi]

Hi Wouter,

I used nanocomp to compare different runs on technical samples. It runs well before printing the whole report. Please see the errors below. This may be related to the issue #41 I will give a try to the create_feather script and see how it goes...

Thanks for any other help, Niko

2024-03-20 19:02:08,621 Writing html report.
2024-03-20 19:02:08,794 Error tokenizing data. C error: Expected 2 fields in line 21, saw 53
Traceback (most recent call last):
  File "/home/itg/niko/miniconda3/envs/nanopack/lib/python3.9/site-packages/nanocomp/NanoComp.py", line 85, in main
    make_report(plots, settings["path"], stats_df=stats_df)
  File "/home/itg/niko/miniconda3/envs/nanopack/lib/python3.9/site-packages/nanocomp/NanoComp.py", line 410, in make_report
    html_content.append(utils.stats2html(path + "NanoStats.txt"))
  File "/home/itg/niko/miniconda3/envs/nanopack/lib/python3.9/site-packages/nanocomp/utils.py", line 31, in stats2html
    df = pd.read_csv(statsf, sep=":", header=None, names=["feature", "value"])
  File "/home/itg/niko/miniconda3/envs/nanopack/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/home/itg/niko/miniconda3/envs/nanopack/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 626, in _read
    return parser.read(nrows)
  File "/home/itg/niko/miniconda3/envs/nanopack/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1923, in read
    ) = self._engine.read(  # type: ignore[attr-defined]
  File "/home/itg/niko/miniconda3/envs/nanopack/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read
    chunks = self._reader.read_low_memory(nrows)
  File "parsers.pyx", line 838, in pandas._libs.parsers.TextReader.read_low_memory
  File "parsers.pyx", line 905, in pandas._libs.parsers.TextReader._read_rows
  File "parsers.pyx", line 874, in pandas._libs.parsers.TextReader._tokenize_rows
  File "parsers.pyx", line 891, in pandas._libs.parsers.TextReader._check_tokenize_status
  File "parsers.pyx", line 2061, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 2 fields in line 21, saw 53

Traceback (most recent call last):
  File "/home/itg/niko/miniconda3/envs/nanopack/bin/NanoComp", line 10, in <module>
    sys.exit(main())
  File "/home/itg/niko/miniconda3/envs/nanopack/lib/python3.9/site-packages/nanocomp/NanoComp.py", line 85, in main
    make_report(plots, settings["path"], stats_df=stats_df)
  File "/home/itg/niko/miniconda3/envs/nanopack/lib/python3.9/site-packages/nanocomp/NanoComp.py", line 410, in make_report
    html_content.append(utils.stats2html(path + "NanoStats.txt"))
  File "/home/itg/niko/miniconda3/envs/nanopack/lib/python3.9/site-packages/nanocomp/utils.py", line 31, in stats2html
    df = pd.read_csv(statsf, sep=":", header=None, names=["feature", "value"])
  File "/home/itg/niko/miniconda3/envs/nanopack/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/home/itg/niko/miniconda3/envs/nanopack/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 626, in _read
    return parser.read(nrows)
  File "/home/itg/niko/miniconda3/envs/nanopack/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1923, in read
    ) = self._engine.read(  # type: ignore[attr-defined]
  File "/home/itg/niko/miniconda3/envs/nanopack/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read
    chunks = self._reader.read_low_memory(nrows)
  File "parsers.pyx", line 838, in pandas._libs.parsers.TextReader.read_low_memory
  File "parsers.pyx", line 905, in pandas._libs.parsers.TextReader._read_rows
  File "parsers.pyx", line 874, in pandas._libs.parsers.TextReader._tokenize_rows
  File "parsers.pyx", line 891, in pandas._libs.parsers.TextReader._check_tokenize_status
  File "parsers.pyx", line 2061, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 2 fields in line 21, saw 53

[NikoLichi]

Hi Wouter,

I gave it a try again with the feather files and have exactly the same errors. All the other files are produced but not the final compiled file.

How this can be solved?

This is the code I am using after feather:

NanoComp -t 32 --verbose -f pdf --feather $FILEIN -p NovoVsGeneC -o NovoVsGenC/qualCont/nanopack --names $PREFIX

Thanks and all the best, Niko

[wdecoster]

Hi Niko,

That is quite remarkable. Could you share the NanoStats.txt file?

Thanks, Wouter

[NikoLichi]

Hi Wouter,

If you mean the .log file after the Nanocomp run, it is enclosed below. Otherwise, please let me know which file you refer to.

All the best, Niko NovoVsGeneC_5don5TimPYFNanoComp_20240322_1426.log

[wdecoster]

Was there no NanoStats.txt file? That should also be generated in /NovoVsGenC/qualCont/nanopack/

[NikoLichi]

I completely missed the file across all the other files, sorry. Here it is.

NovoVsGeneC_5don5TimPYFNanoStats.txt

[wdecoster]

Aha now I see! I see the read identifiers on line 21 are like "141:329|2a491583-c20d-48e9-8ccc-49afe630be59". Is this a duplex run?

[NikoLichi]

Oh... interesting No duplex run. This is cDNAseq from an RNA isolation protocol.

This is the output after trimming and finding directionality using Pychopper. They add those identifiers (e.g.,"141:329|") before the actual read identifier.

But... nanocomp is able to process all the metrics with those headers in separate files (HTML and PDF), but the consensus globall output (HTML) fails.

[wdecoster]

Yes, most of the time it doesn't care about that :, but it is used when generating the HTML report of the NanoStats file. Let me see if I can come up with an easy fix.

[wdecoster]

As a workaround, could you see if running with --tsv_stats fixes things?

[NikoLichi]

Yes! It worked! Thanks!

I ran the command for two data sets already, and it works fine! I'll keep this command trick in mind when using pychopper sequences.

All the best, Niko

[wdecoster]

Thanks for the feedback!