Problem with star 2nd pass, Process exceeded running time limit - CIRCexplorer2 about circrna

[csittz]

thank you. i changed the config file and it seems to get pass that error.
will close this.

[nictru]

Hey,
the problem here is not the Could not find any nv files on this host!. This only suggests that you are trying to use nvidia configuration but there is no GPU available on the host. The execution won't stop because of this and this process would not utilize GPU even if it would be correctly provided.

The problem here is Process exceeded running time limit (16h). This indicates that the process did not finish within the per-process time limit of the pipeline. Please take a look at #116 for guidance.

[csittz]

@nictru Thanks for info. The problem is that i don't have GPU.
I'm not sure why STAR use GPU for second pass while in first pass it used CPU and can run without problem.
Is there anyway to specify not too use GPU in config file?

[nictru]

Again, there is no GPU-related problem here. You will also find the same message in the logs of the first STAR pass and all the other pipeline tasks. This does not lead to failure and does not have any effect on the speed or success of the processing.
The only way to fix your problem is to increase the process-specific time limit as described in #116.

If you really want to remove this message

The pipeline would not print these messages if you did not explicitly request a GPU somewhere (thus, you can only disable the behavior by removing this request). A request could look something like this:

apptainer.runOptions = "--nv"

And probably similar for other containerization engines. This could be located in any configuration file.