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a2iEditing / RNAEditingIndexer

A tool for the calculation of RNA-editing index for RNA seq data
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No Samples Were Found To Run On #29

Open panos-ver opened 3 years ago

panos-ver commented 3 years ago

Hello, I am using the docker fiile. After I have successfully build the image when I try to run it I get this warning and the application exits.

[2021-02-20 12:00:17,977] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove 20-02-2021-12.cnf [2021-02-20 12:00:17,977] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove 20-02-2021-12.cnf [2021-02-20 12:00:17,978] A2IEditingIndex WARNING No Samples Were Found To Run On! Exiting...

These are different commands I have tried to run all with the same result:

docker run \ -v C:/Repos/RNAEditing/RNAEditingIndexer_Data/input:/data/rna_input:ro\ -v C:/Repos/RNAEditing/RNAEditingIndexer_Data/output/outputs:/data/rna_output:rw\ a2i_editing/a2i_editing_index:0.1 RNAEditingIndex -d /data/rna_input\ -l C:/Repos/RNAEditing/RNAEditingIndexer_Data/output/logs\ -o C:/Repos/RNAEditing/RNAEditingIndexer_Data/output/cmpileups\ -os C:/Repos/RNAEditing/RNAEditingIndexer_Data/output/summary_dir\ -f _sampled_with_0.1.Aligned.sortedByCoord.out.bam.AluChr1Only.bam\ --genome hg38

and the more stripped down version:

docker run \ -v C:/Repos/RNAEditing/RNAEditingIndexer_Data/input/:/data/rna_input/:ro\ -v C:/Repos/RNAEditing/RNAEditingIndexer_Data/output/outputs/:/data/rna_output/:rw\ a2i_editing/a2i_editing_index:0.1 RNAEditingIndex -d /data/rna_input/\ -f "_sampled_with_0.1.Aligned.sortedByCoord.out.bam.AluChr1Only.bam"\ --genome hg38

notes:

  1. I am using windows 10 with docker desktop
  2. I have allowed docker file share with the mentioned folders
  3. I have copied the sample/test bam files in the right directory.

Any ideas or suggestions? Thanks