Hello Biostars Community/rMATS Developers,
I am encountering a persistent issue when trying to run rMATS (RNA-Seq-MATS) on a Windows Subsystem for Linux (WSL) environment. Despite following the standard setup and execution procedures, rMATS consistently fails to open the specified BAM files for analysis. I am seeking assistance in troubleshooting and resolving this issue.
Environment Details:
Operating System: Windows 10 with WSL
Linux Distribution in WSL: Ubuntu-20.04
rMATS Version: [Specify the version of rMATS you are using]
Python Version: [Specify the version of Python used]
Problem Description:
When executing the rMATS script with properly formatted input files, it systematically fails to open the BAM files, and the process ends with a Python ValueError. The issue occurs despite confirming that the BAM files are accessible and readable within the WSL environment.
Error Messages:
The primary error messages received are as follows:
Fail to open /mnt/c/Users/u253262/Documents/Output/sample_x_Aligned.sortedByCoord.out.bam
[...similar messages for other BAM files...]
ValueError: invalid literal for int() with base 10: '/mnt/c/Users/u253262/Documents/Output/sample_x_Aligned.sortedByCoord.out.bam'
Steps Taken:
- Confirmed that the BAM files are accessible in WSL by running Python scripts and basic Linux commands (ls, head).
- Ensured that file paths are correctly formatted for WSL, using absolute paths.
- Attempted running rMATS with different subsets of BAM files.
I am looking for insights into what might be causing this issue and how to resolve it. Is this a known problem with rMATS in a WSL environment, or could it be related to how file paths are handled in the script? Any advice or suggestions would be greatly appreciated.
Thank you for your time and assistance.
The term is "alternative splicing", not "alternate splicing". I've removed that tag because it wasn't really relevant.
You've posted this on multiple sites. Do not do that, it is bad etiquette.
At the very least, add links to your cross-posts.
https://github.com/Xinglab/rmats-turbo/issues/351