[wgs-assembler-users] cgw error

[Ben E. <el...@gm...>]

Hi,

I'm running celera 6.1 inside MaSuRCA and I appear to have a never ending
CGW condition which keeps giving this error:

WARNING: variance difference is negative -- probably trouble with variances
after interleaving
WARNING: variance difference is negative -- probably trouble with variances
after interleaving
WARNING: variance difference is negative -- probably trouble with variances
after interleaving
WARNING: variance difference is negative -- probably trouble with variances
after interleaving
*SOMEBODY IS SCREWING UP SCAFFOLDING -- RecomputeOffsetsInScaffold has a
singularity -- assert skipped!*
*ReomputeOffsetsInScaffold failed (1) for scaffold 898025 in MergeScaffolds*
MergeScaffoldsAggressive()-- iter 312 -- continue because we merged 3
scaffolds. minWeightThreshold = 6.9 maxAllowedIterations = 16
* CleanupScaffolds through scaffold 90000
* CleanupScaffolds through scaffold 120000
* CleanupScaffolds through scaffold 150000
* CleanupScaffolds through scaffold 160000
* CleanupScaffolds through scaffold 170000

I've tried stopping it and starting at a later checkpoint but it still
seems to be stuck. Will this eventually finish or should I intervene?

Cheers,

Ben