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a2iEditing / RNAEditingIndexer

A tool for the calculation of RNA-editing index for RNA seq data
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No files found to run #20

Open drupani opened 4 years ago

drupani commented 4 years ago

Hello, I have been trying to run the tool through docker and it gives the following error. [2020-05-15 21:55:23,124] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove 15-05-2020-21.cnf

[2020-05-15 21:55:23,124] A2IEditingIndex WARNING No Samples Were Found To Run On! Exiting...

[2020-05-15 21:55:41,902] general_functions WARNING

I was able to add the hard drive where I have the samples, to the docker app. It still won't run. Can you please help.

Juke34 commented 3 years ago

Same error here

fardellas commented 3 years ago

Same error here. Did you manage to fix it ?

Juke34 commented 3 years ago

I think my problem was related to the slash at the end of the folder path I provided. The tool does not deal with paths without slash at the end

AMChalkie commented 2 years ago

Same here. the / at the end of the folder path didn't fix it. Changing the -l -o and -os directories seems to fix it as a temporary solution.

But this could also be running the program incorrectly - selecting a single .bam instead of a directory with many .bams all with the same suffix as defined by -f. I personally find it a slightly unusual use of -f and a better error message might tell people when -f matches a single filename, vs a pattern. I.e. a.sorted.bam matches a single file, vs .sorted.bam which matches 1-many.

Overall this is a useful tool and these are just minor comments.