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lcalviell / ORFquant

An R package for Splice-aware quantification of translation using Ribo-seq data
GNU General Public License v3.0
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task 17 failed - "'end' must be <= 'length(x)'" in run_ORFquant step #15

Open tsekara opened 2 years ago

tsekara commented 2 years ago

Hi,

I am running the ORFquant as per the instructions mentioned in the manual. While running the "run_ORFquant" it threw me the following error:

run_ORFquant(for_ORFquant_file = "sample_Rep1_for_ORFquant",annotation_file = "gencode.v23.annotation.Rannot",n_cores = 20)`
  Loading annotation and Ribo-seq signal ... Thu Dec  2 15:26:12 2021
  Loading annotation and Ribo-seq signal --- Done! Thu Dec  2 15:26:18 2021
  Summoning ORFquant with 20781 P_sites positions over 2002 genomic regions using 20 processor(s) ... Thu Dec  2 15:26:19 2021
  **Error in { : task 17 failed - "'end' must be <= 'length(x)'"**

Any guidance to resolve the error is highly appreciated. Thanks in advance.

lcalviell commented 2 years ago

Hi tsekara,

Can you re-install ORFquant from the github repository and try again? There were some bugs in populating GRangesList objects in the newer versions of Bioconductor packages, hopefully now it works. However, without data and/or more details about your ORFquant run, I cannot tell you what happened.

Thanks for using ORFquant!

Best, Lorenzo