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Error running rMATS in ubuntu with conda #369

Closed mlcsmits closed 3 months ago

mlcsmits commented 4 months ago

Hey rMATS team, I was working on ubuntu with conda and trying to run rMATS turbo 4.2.0 when it exited in failure. Here is everything that I know: I ran the following command: python /mnt/studentfiles/2024/2024MBI03/rmats_turbo_v4_2_0/rmats.py --b1 /mnt/studentfiles/2024/2024MBI03/subset/subset_SRR19760417.bam --gtf /mnt/studentfiles/2024/2024MBI03/RefSeq/genomic.gtf -t paired --readLength 100 --nthread 4 --od /mnt/studentfiles/2024/2024MBI03/rmats/ --tmp /mnt/studentfiles/2024/2024MBI03/rmats/ This is the output of the tool: (See figure attached) rMATS error

I have read it but I do not understand what those error means. I've read the manual page for the rMATS tool and I think I'm calling it correctly, I attempted calling with --variable-read-length and we have tried to make the path into a text file, it did not succeed. Could you please help me?

EricKutschera commented 4 months ago

Here's the line for that error: https://github.com/Xinglab/rmats-turbo/blob/v4.2.0/rmats.py#L189

It's trying to read your --b1 file as a text file, but your command gave subset_SRR19760417.bam as --b1

Here's an example of --b1 b1.txt from the README: https://github.com/Xinglab/rmats-turbo/tree/v4.2.0?tab=readme-ov-file#starting-with-bam-files

mlcsmits commented 4 months ago

Thanks for your quick response, but now I have the following error if I run the .txt file instead of the .bam file image The b1.txt is as follows: image

EricKutschera commented 4 months ago

Here's the line for the error: https://github.com/Xinglab/rmats-turbo/blob/v4.2.0/rMATS_pipeline/rmatspipeline/rmatspipeline.pyx#L3737

It's reading all the .rmats files in your --tmp directory and for each file it expects the 1st line to be comma separated bam paths (like from --b1). Then it expects the 2nd line to be the read length. Somehow it found what looks like a line from a .sam file. My guess is that it's reading a .rmats file created from a previous run where --b1 was not being supplied correctly

If you remove your --tmp directory (or use a new empty --tmp directory) and try again then that error might go away

mlcsmits commented 3 months ago

The code worked with a new tmp directory. Thank you