Comments (5)
Is that 6 minutes to variant call a human ??
from octopus.
Hi Jared,
Thanks for reporting this. Although I can't reproduce the issue on my machine, I think I know what's going on. Basically octopus will try to generate an index for compressed VCF (or BCF) output. This happens on destruction of the handle to the file. When the handle gets moved around early in the run (before anything has been written) the 'moved from' handle gets destroyed. I think the old handle remains in a valid state in your setup and therefore attempts to build an index on the empty file, which triggers this warning.
This shouldn't have any adverse affects downstream, but I've added some additional checks to stop the index being generated on empty handles. Would you mind checking out the develop branch and seeing if the warning is still being generated?
Many thanks,
Dan
from octopus.
Is that 6 minutes to variant call a human ??
@iqbal-lab Alas no, this is on a ~100MB test .bam. Still, we are seeing running times of ~75mins with --fast
enabled on WGS 30x data on a 20-core node
@dancooke checking develop now
from octopus.
Wow.
from octopus.
I can confirm that I no longer see the warning message in the develop branch. Thanks for the fast response.
from octopus.
Related Issues (20)
- can not download the forest files HOT 1
- Remove depreciated inheritance of std::unary_function
- Call in high heterozygotes
- VCF file is empty
- info on UL nanpore reads HOT 2
- Forest file is still not available for donwloading "std::bad_alloc Error" HOT 9
- Population-level variant calling using accessions with complex ploidy level
- Will octopus add a mode using paired information to compose a linked debruijn graph?
- Can octopus add a feature to add supported read query names of the variants in the INFO field of the output VCF file? HOT 1
- Position of maternal or paternal haplotypes in Octopus after performing TRIO analyses HOT 1
- Models for NovaseqX?
- Encountered an exception during calling 'std::bad_alloc' HOT 2
- training data & regions of the genome used for somatic random forest model
- Build failures on `gcc-13`: `option_collation.cpp:1298: error: redundant move in initialization`
- Build fails, is there a singularity? HOT 1
- ERROR in reading reference index. HOT 2
- Starting Call Set Refinement (CSR) filtering provokes RAM overload HOT 2
- Use with Nanopore long reads HOT 2
- After recompiling from source get error 'Phred: negative error [2024-07-15 12:55:12] <EROR> probability -0.000000' HOT 2
- Binaries compiled for AVX-512 cores do not process the whole genome. HOT 2
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