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For one html string, I waited 10 hours. Finally found out that the problem is just in 'microformat'. After skipping that format, it takes just 1 second.
No, the error is the same when I run 'docker run google/deepvariant:1.6.1 ...'
Based on what I've read so far, it looks that my processor is a bit outdated (since it doesn't support AVX instruction), so I decided to move the pipeline to...
I have also tried not setting those config parameters and a lot of other things, but the problem is still the same. In no way I can achieve haplotypecaller parallelisation....
Thank you for the response. I meant the first thing, to "to spin up a bunch of independent haplotypecaller jobs", but in htop, I do not see any parallelisation. I...
Yes, I have also tried using no custom nextflow.config at all (so only defaults, and '--max_cpus 23' parameter from CLI), but the same problem - no parallelisation.
Hi Friederike, not yet, but I'm working on it, so I will let you know.
Finally, these parameters work best for me, haplotypecalller is using multiple cores now: withName: 'GATK4_HAPLOTYPECALLER' { cpus = 1 memory = 20.GB time = 30.h ext.args = { "--native-pair-hmm-threads 1...
Cool, I'm using deep variant with custom config. If you could help me how to modify the config, that would be great.
[.nextflow.log](https://github.com/user-attachments/files/16762361/default.nextflow.log)