Comments (6)
Ignore that - have now reproduced. Will work on a fix!
from octopus.
Thanks for reporting this Greg. The error is raised when Htslib does not successfully load a contig for VCF/BCF streaming. I'll investigate...
from octopus.
Thanks Dan. My open file limit was:
$ ulimit -Sn
16384
Not sure if that could be a factor here or not.
from octopus.
Hi Greg, I'm having trouble reproducing this. Could you check if there are any reads mapped to HLA-A*01:01:01:01
in any of the BAMs please? Also, do you get the error if you just try to call this contig?
from octopus.
This was due to htslib not being able to parse :
s in contig names (see here). Octopus creates temporary .bcf
files - one for each contig - when using multithreading. During the merging of these temporaries after calling, the error was thrown. I've 'fixed' this by using ".vcf" temporary files for contig names with :
(37a3329).
from octopus.
aha...great!...thanks very much Dan
from octopus.
Related Issues (20)
- Remove depreciated inheritance of std::unary_function
- Call in high heterozygotes
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- 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
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- 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
- Build fails - Source code errors encountered
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from octopus.