These are chat archives for cboursnell/transfuse

May 2018
Stuart Willis
May 07 2018 18:37

@cboursnell do you know of a reason offhand why transfuse would fail on certain (Transabyss) assemblies but not others (Binpacker, Trinity) because of what seems like a memory leak during the salmon stage? e.g.

processed 8000000 reads in current roundterminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc

/var/lib/gems/2.3.0/gems/transrate-1.0.1/lib/transrate/salmon.rb:27:in `run': Salmon failed (Transrate::SalmonError)

If I watch htop the RAM usage climbs to several times a normal run (>75Gb) and then dies. Same assemblies fail with transrate 1.0.1 separately at the same stage too. I previously had this happen on certain Transabyss assemblies from a different dataset but was able to remake the assembly but never identified the specific error.

Stuart Willis
May 07 2018 19:35
I can reproduce the error running salmon 0.4.2 directly on the bam created by snap, and transrate 1.0.3/salmon 0.6.0 work fine on the same assemblies.