Comments (3)
Hi William,
I am not aware of any of the scripts making actual use of multiple cores. I also don't think that Ensembl VEP makes use of it (at least I did not see anything in its documentation on a brief look). We usually parallelize by splitting up variant lists and running separate CADD instances.
Best,
Martin
from cadd-scripts.
Great, thank you!
from cadd-scripts.
The reason we included the parameter was because the first versions of CADD v1.6 generated the annotations for MMSplice themselves (optionally via multicore) which is replaced now by a precomputed annotation. Further, snakemake nowadays requires setting the --cores
(or jobs) argument.
Thanks for letting us know of the issue.
from cadd-scripts.
Related Issues (20)
- Empty analysis - Temp CSV file is empty - "Encountered uncovered chromosome" HOT 2
- snakemake --create-envs-only error HOT 1
- web services HOT 2
- MissingInputException HOT 3
- Release a 1.6.1 version of scripts? HOT 5
- CADD script fails on empty input HOT 1
- Expansion of annotations in CADD v1.6 HOT 1
- one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode! HOT 2
- Feature request: In-memory annotation with python HOT 3
- Getting both imputation file along with annotation file HOT 2
- empty imputation file when looking into SNVs alone HOT 3
- Only a small percentage of SNVs receiving annotation using offline tool HOT 1
- CADD 1.6: Encountered uncovered chromosome/Possible precedence issue with control flow operator HOT 3
- How to get CADD-splice scores? HOT 1
- Splice-AI NA values HOT 2
- Negative value in SpliceAI scores HOT 1
- Where is unzip CADD.zip? HOT 3
- CADD is reporting SNV as intergenic when it is CDS HOT 1
- Which prescored files are necessary? HOT 5
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