Comments (4)
Thanks for the bug report. The problem is that the operating system maximum open file limit is being exceeded (i.e. ulimit -n
). When calling with multiple threads, Octopus creates a temporary BCF file for each unique contig in the calling region set. Since you're not explicitly specifying any input regions in your command, the default behaviour is it to call all contigs in the reference genome. That's all 3366 contigs in GRCh38_full_analysis_set_plus_decoy_hla.fa
, even though reads are only mapped to chr1
.
A robust solution to this is not going to be simple. However, it's fairly easy for you to avoid this problem by either:
- Increasing the maximum open file limit (e.g. set
ulimit -n 10000
). - Manually specify input regions (e.g. add
-T chr1
to your command).
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For my own information, some ideas to help - but not solve - this problem:
- Only open temporary contig BCFs when the first calls from the contig are in.
- Close temporary contig BCFs once all calls for the contig are written.
- Improve exception handling/reporting when file opening fails.
from octopus.
Thanks; adding -T chr1
does work around the problem.
from octopus.
From 42fa364, Octopus will open and close temporary BCFs as needed, which should reduce the occurrence of this type of error. There is also better error reporting. You should now be able to run your command without the -T chr1
(although I'd still recommend including it if you're only calling chromosome 1).
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Related Issues (20)
- 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
- Build fails - Source code errors encountered
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