Comments (4)
thank you. i changed the config file and it seems to get pass that error.
will close this.
from circrna.
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.
from circrna.
@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?
from circrna.
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.
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Related Issues (20)
- Implement JCcirc
- Implement CIRI-full
- Implement circRNAfull
- Implement psirc for isoform detection
- Implement miRNA sponging analysis
- Implement circRNA database annotation functionalities HOT 1
- Implement circbase HOT 1
- Implement circatlas HOT 1
- Implement circbank HOT 1
- Implement circRNADisease HOT 1
- Implement polyA-Benchmarking
- Decide how to proceed with the differential expression subworkflow
- Deprecate the `module` parameter
- Add `psirc quant` output to MulitQC via `kallisto` module
- Problems with empty annotation intersection HOT 12
- GTF entries on sequence which is not present in FASTA HOT 11
- GTF file not found with CIRIquant HOT 4
- SOLUTION: re-run with at least --limitSjdbInsertNsj HOT 11
- FATAL: the requested image was not found HOT 1
- ERROR ~ Invalid method invocation `call` with arguments using DCC HOT 1
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