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PoonLab / gromstole

Quantifying SARS-CoV-2 VoCs from NGS data of wastewater samples
MIT License
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Summary JSON file did not get generated #89

Closed GopiGugan closed 5 months ago

GopiGugan commented 8 months ago

It looks like when there is a file named "Undetermined" in the runs uploads folder, the Freyja summary JSON file does not get generated (e.g. 20240125_122448)

GopiGugan commented 8 months ago 
Traceback (most recent call last):
  File "process.py", line 630, in <module>
    summarize_run_data(args.barcodes, args.update_barcodes, args.freyja_update, run, args.indir, args.outdir, callback=cb.callback)
  File "process.py", line 291, in summarize_run_data
    if isnan(date.loc[sample, date.columns.tolist()[0]]):
IndexError: list index out of range
ArtPoon commented 8 months ago

We might need to add a screen for this to prevent the run from breaking - ignore files that do not have a match in summary JSON file and proceed with the rest. Send e-mail notification about files that do not match.

ArtPoon commented 5 months ago

@GopiGugan to check if this fix has been committed