Pigeon make-seurat produces empty output

Question

[TheCatalyst]

I am following the isoseq workflow as described here: https://isoseq.how/classification/workflow.html, but I believe the last command fails, since I am getting empty files in the last step of the workflow. info.csv has the expected information, however, annotated.info.csv and annotated-prefilter.info.csv are empty. What could be the issue? I followed the workflow exactly as described using mouse_GRCm39.fasta and gencode.mouse_GRCm39.sorted.gtf. All the intermediate files looks good to me. So I really don't know where I could start debugging.

[yura.grabovska]

First step is probably getting in touch with the people who manage the pipeline they're probably better suited to answering specific debugging questions: https://github.com/PacificBiosciences/pbbioconda/issues/new?template=bug_report.md