Simon Heumos
Simon Heumos
Great idea @jmonlong! Running with `-t 1` GraphAligner behaves deterministic so far. It seems that the multi-threading is the bad guy here @maickrau.
Updated link to data: http://fex.belwue.de/fop/njCHy3QX/issue_GraphAligner_not_deterministic.tar.gz
Ah, that's where it's coming from. In https://github.com/pangenome/pgge I am measuring the reconstruction accuracy of a pangenome graph. I want to find out how well the sequences, we created the...
To give a concrete example: One sequence in the graph is the full chm13 chr8 sequence. When aligning this sequence back to the created pangenome graph, we split the chm13...
@maickrau I could do a PR to allow `--precise-clipping` to not be lower than `0.001` from https://github.com/subwaystation/GraphAligner/tree/precise_clipping_min_0.001 as it was the case in the old GraphAligner version. Not sure if...
Are there any updates here @maickrau ?
Hi @cmonat Is your CMake version up to date? https://stackoverflow.com/questions/47238577/target-requires-the-language-dialect-cxx17-with-compiler-extensions-but-cma states that an older CMake version than 3.8 is not compatible with CXX17. Best, Simon
I am using the same version, so this is not the issue. What gcc and g++ versions do you have?
Whoops, it says right there GNU 4.8.5. This is too old. At least GCC 9.3 is required. Better 10.2.
Hi @cmonat The output of your error message still says that CMake is working with GNU 4.8.5. Please fix this. Then it should compile. Best, Simon