I would like to report a critical error when running LJA on my HIFI data. The error cropped up around the 48 hr mark, and appears to have happened due to some violation of FreezeUnpairedVertices().
I have no clue what to do here and figure I can at least make the devs aware of this instance. Has anyone else encountered such an error ? I have attached the stace trace output below and logOutput is attached.
The data in question is a single library of HIFI reads, approx 1.8M reads, with approx 32X coverage on our species genome which is a planarian flat worm which are known to be highly repeat rich, highly heterozygous and with a large AT composition skew of ~70%. I won't be able to share the data as It belongs to our collaborators. The data set of prefiltered (kraken2) reads is ~12Gb total, and the LJA job was ran using 16 cores and 500Gb RAM.
Hi there,
I would like to report a critical error when running LJA on my HIFI data. The error cropped up around the 48 hr mark, and appears to have happened due to some violation of FreezeUnpairedVertices().
I have no clue what to do here and figure I can at least make the devs aware of this instance. Has anyone else encountered such an error ? I have attached the stace trace output below and logOutput is attached.
The data in question is a single library of HIFI reads, approx 1.8M reads, with approx 32X coverage on our species genome which is a planarian flat worm which are known to be highly repeat rich, highly heterozygous and with a large AT composition skew of ~70%. I won't be able to share the data as It belongs to our collaborators. The data set of prefiltered (kraken2) reads is ~12Gb total, and the LJA job was ran using 16 cores and 500Gb RAM.
dbalog.Last1000lines.txt LJA_LogOut.txt
Stack trace output on crashing:
_lja(_Z16print_stacktracev+0x40) [0x46cf10] lja(_ZN17repeat_resolution12MultiplexDBG22FreezeUnpairedVerticesEv+0xe4) [0x57d7b4] lja(_ZN17repeat_resolution12MultiplexDBGC2ERKSt6vectorINS_16SuccinctEdgeInfoESaIS2_EEmPNS_7RRPathsEb+0x77d) [0x58313d] lja(_ZN17repeat_resolution12MultiplexDBGC2ERN3dbg9SparseDBGEPNS_7RRPathsEmR19UniqueClassificator+0x33) [0x5831c3] lja(_ZN17repeat_resolution14RepeatResolver14ResolveRepeatsERN7logging6LoggerEm+0x1ac) [0x48643c] lja() [0x46a90d] lja(_Z9runInForkRKSt8functionIFvvEE+0x20) [0x46da90] lja(_Z9MDBGPhaseRN7logging6LoggerEmmmmmbRKNSt12experimental10filesystem2v17cxx114pathES8_S8_bb+0xfc) [0x46587c] lja(main+0x15bd) [0x462b6d] /lib64/libc.so.6(libc_start_main+0xf3) [0x14efe07607b3] lja(_start+0x2e) [0x463fae] lja: /homes/lcampbell/hps_metazoa_softwares/lcampbell/LJA/src/projects/repeat_resolution/mdbg.cpp:171: void repeat_resolution::MultiplexDBG::FreezeUnpairedVertices(): Assertion `in_edges==outedges' failed.