NameError: name '_LOGGER' is not defined

[atraunbauer]

Hi, when doing a test run with the test1 files provided the script is running until the test1_bamQC.tsv should be created. At this point I am getting an error message:

NameError: name '_LOGGER' is not defined

I attached the PEPATAC_log.txt

Could you please help to solve this? Thank you so much!

PEPATAC_log.txt

[donaldcampbelljr]

Hello,

Just curious, did you use Looper to run your samples? https://github.com/pepkit/looper

I'm wondering if not using Looper would cause this to happen as Looper gets Logger.

[atraunbauer]

Hi,

thanks for getting back to me!

Yes, I used looper (version 1.6.0) to run the test1 samples.

[donaldcampbelljr]

Did you happen to edit the file bamQC.py? Can you confirm that this code is still present? https://github.com/databio/pepatac/blob/ffa7cc23ff9b11483f1ab317670d06bb886d6288/tools/bamQC.py#L243-L257

Specifically: _LOGGER = logmuse.logger_via_cli(args, make_root=True)

[atraunbauer]

Yes _LOGGER = logmuse.logger_via_cli(args, make_root=True) is still there. I didn't edit the bamQC.py file.

parallel processed computation of matrix for each chromosome

if name == "main":

args = parse_args(sys.argv[1:])
_LOGGER = logmuse.logger_via_cli(args, make_root=True)

qc = bamQC(reads_filename=args.infile,
           out_filename=args.outfile,
           n_proc=args.cores,
           verbosity=args.verbosity)

qc.register_files()
good_chromosomes = qc.run()

_LOGGER.debug("Reduce step (merge files)...")
qc.combine(good_chromosomes)