Description
Hi, I am running shapeit5 and coming across a consistent error while using phase_rare. The command looks like something like this repeated for all the chunks of the chromosomes:
phase_rare \
--input /sandbox/PMBB.notrios.rare_prepared.chr22.bcf \
--input-region chr22:37177554-42325255 \
--scaffold /scaffold/PMBB.notrios.phased.chr22.bcf \
--scaffold-region chr22:36677559-43215583 \
--map /maps/chr22.b38.gmap.gz \
--pbwt-mac 2 \
--pbwt-depth-rare 4 \
--pbwt-modulo 0.1 \
--pbwt-mdr 0.1 \
--effective-size 15000 \
--output /output/PMBB.notrios.phased_5.chr22.bcf \
--log /output/PMBB.notrios.phased_5.chr22.log \
--thread 5
Many of the chromosomes phase fine and ligate fine. Some chunks seem to error out with this consistent error. When inspecting the failing regions, nothing stands out. I am using the chunks provided in the github.
The resulting error is typically:
phase_rare: src/containers/genotype_set/genotype_set_phasing.cpp:63: void genotype_set::phaseLiAndStephens(unsigned int, unsigned int, aligned_vector32&, aligned_vector32&, std::vector&, float): Assertion `GRvar_genotypes[vr][tidx].prob >= 0.0f' failed.
The errors result in a core dump.
I have used both the static binaries and an installation that was functional at another lab that was put into a singularity container. The error is consistent across both approaches.