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zavolanlab / PAQR_KAPAC

scripts, pipelines and documentation to run PAQR and KAPAC; KAPAC allows to infer regulatory sequence motifs implicated in 3’ end processing changes; PAQR enables the quantification of poly(A) site usage from standard RNA-seq data

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Infer relative usage: IndexError: list index out of range

peterkilfeather opened this issue · comments

commented

Hi, I am running the example data through the snakemake pipeline to test it. Part one proceeds successfully, however I get a 'list index out of range' error while it runs the 'deNovo-used-sites-and-usage-inference.single_distal_included.py' script. I have attached the log.

I am using a conda installation, using the 'UPDATED' requirements text file.
I have attached the log from the failing step.

Thanks,
Peter
infer_relative_usage.log

commented

I have since changed the number of cores to below my max (<8) and now get the end_idx error

commented

I tested the script with an input for --processor that is far beyond the available number of cores but could not reproduce the error.
Also since this thread refers now to the end_idx error I close it for now.
Please feel free to reopen it if the problem persists.