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BCCDC-PHL / auto-cpo

Automation of Genomic Analyses for Carbapenemase-Producing Organisms (CPOs)
GNU General Public License v3.0
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KeyError while preparing assembly SampleSheet #11

Open dfornika opened 1 year ago

dfornika commented 1 year ago

We've run into an error:

Traceback (most recent call last):
  File "auto-cpo/bin/auto-cpo", line 33, in <module>
    sys.exit(load_entry_point('auto-cpo', 'console_scripts', 'auto-cpo')())
  File "auto-cpo/auto_cpo/__main__.py", line 62, in main
    core.analyze_run(config, run, "short")
  File "auto-cpo/auto_cpo/core.py", line 327, in analyze_run
    writer.writerow(library_fastq_paths[library_id])
KeyError: '<SAMPLE_ID>'

The context is: https://github.com/BCCDC-PHL/auto-cpo/blob/ee7ba4e3cb05862ee51948e3ff697cf8166b4d92/auto_cpo/core.py#L318-L327

This function also relevant: https://github.com/BCCDC-PHL/auto-cpo/blob/ee7ba4e3cb05862ee51948e3ff697cf8166b4d92/auto_cpo/core.py#L118-L143