Crawl portion of autopipeline misses CT and RTSTRUCT files

[strixy16]

Running autopipeline /Users/katyscott/Documents/SARC021/images/ /Users/katyscott/Documents/SARC021/med-imageout/ --n_jobs 1 --update --overwrite doesn't find all of the CT and RTSTRUCT files in the images directory.

My images directory contains four directories total - one sample has two directories each. Each sample directory contains subdirectories containing CT and RTSTRUCTs as DICOMs. There are three different CT scans for each sample and RTSTRUCTs associated with most of them.

The output of the crawl only finds one of the three sets of CT and RTSTRUCT combinations for the first sample and two of the three CTs and one RTSTRUCT set for the second sample.

When I call the crawl_one function on its own, it appears to find all of the files. So somewhere between this and the output, the files are getting lost.