ERROR in reading reference index.

[Knnnk]

Hi there,
When I am using octopus v0.7.4 to call germline SV from 1 bam file without forest model and seq_error_model, it throws an error:

[2024-04-11 17:06:33] <INFO> ------------------------------------------------------------------------
[2024-04-11 17:06:33] <INFO> octopus v0.7.4
[2024-04-11 17:06:33] <INFO> Copyright (c) 2015-2021 University of Oxford
[2024-04-11 17:06:33] <INFO> ------------------------------------------------------------------------
[2024-04-11 17:06:36] <EROR> A user error has occurred:
[2024-04-11 17:06:36] <EROR> 
[2024-04-11 17:06:36] <EROR>     The region Chr1:0-76456565 is after Chr19:0-51544995 in reference
[2024-04-11 17:06:36] <EROR>     index.
[2024-04-11 17:06:36] <EROR> 
[2024-04-11 17:06:36] <EROR> To help resolve this error ensure the region range format is <lhs> to
[2024-04-11 17:06:36] <EROR> <rhs> where lhs occurs before rhs in the reference index.
[2024-04-11 17:06:36] <INFO> ------------------------------------------------------------------------

octopus --version says

octopus version 0.7.4
Target: x86_64 Linux 5.11.0-1028-azure
SIMD extension: AVX512
Compiler: GNU 10.3.0
Boost: 1_74

what I knew is I am using a non-human genome, and the seq names aren't sorted, my command is as follows:

octopus -R /mnt/caller/ref/genome.fasta -I /mnt/caller/rgbam/230.bam -T Chr1 to Chr19 --threads 1 -o 230.vcf.gz

[Knnnk]

my chromosome names are

Chr2    Chr7    Chr13   Chr11   Chr19   Chr15   Chr18   Chr1    Chr4    Chr6    Chr8    Chr9    Chr5    Chr3    Chr10    Chr12   Chr14   Chr16   Chr17

[jelber2]

Seems like you just need to remove -T Chr1 to Chr19 (which, I assume is that you want all 19 chromosomes to be variant-called?)