Running prep and post sepparatly

[adi8897]

Hi
I had almost 1800 bam files of mutant
And 800 of control
I created b1.txt and b2.txt includes all the pathes for the bam files.
Because it was very large run. I divided
And ran the prep stage on 10 bam files at a time.
Then I moved all the .rmats files to one directory
( the control and the mutant)
I renamed the files before mv them to the common directory but did not changed them at all .

Now when I'm trying to run the post stage
I inputed the initial b1.txt and b2.txt containing all the patches for the bam files
And in the tmp I wrote the directory with all the .rmats files.
It runs for alote of time but the output directory is empty include the top directory inside
I'm trying to understand what I did wrong along the way? Ther is no log to see if it's processing anything.

[EricKutschera]

The post step will detect splicing events and then it will count reads supporting the events. If there is no output then it may still be working on the event detection

Since you have a lot of samples the post step could take a while. There are supplementary figures showing run time and memory usage from this paper: https://www.nature.com/articles/s41596-023-00944-2

Based on those plots, if you are using --novelSS with that many samples then the post step may not be able to finish in a reasonable amount of time