Segmentation fualt (again)

[MichelNivard]

I raised an issue regarding segmentation faults occuring before. THat turned out to be a case of specified paths. I am now again encountering segmentation faults, but at a later stage in the process.

I run the following code: ./PAINTOR -input Data/input.files -out paintor_output/ -in Data/ -Zhead Zscore -LDname ld

Which sems to work becase POAINTOR starts reading files: Reading in files for: ld_out.Ext1 Running PAINTOR in sampling mode. Parameters Used: Seed value: 1495436710 Number of draws for importance sampling: 1000000 Pre-computing functional enrichments considering up to 2 causals per locus Segmentation fault (core dumped)

But again PAINTOR terminates after a segmentation fault.

All LD and input files are created using the python tool provided with PAINTOR. I explicitly am trying to run PAINTOR without annotations, so perhaps that is causing the issue?

Best, Michel

[gkichaev]

Hi Michel,

Since PAINTOR is intended to be used with annotations, it requires an annotation file as input. You can hack this by feeding it a dummy annotation file with all 1's.

However, are you only interested in running PAINTOR without annotations? If so, I would recommend using the FINEMAP tool developed by Christian Benner: http://www.christianbenner.com/#

I say this because you incur a statistical penalty (which could deflate performance) and computational overhead for estimating annotation enrichment parameters.

The inputs and outputs are more or less the same for both PAINTOR and FINEMAP.

[MichelNivard]

Hi,

I prefer to work in PAINTOR because we are still considering the inclusion of annotations (But are still working on a decision rule for including annotations if we decide to do so)

I do however encounter a new error.

When I run paintor for 1 lcus I get output and everything works great. When I then consider 42 loci I get the following error:

PAINTOR: /PAINTOR_V3.0/eigen/Eigen/src/Core/DenseCoeffsBase.h:378: Eigen::DenseCoeffsBase<Derived, 1>::Scalar& Eigen::DenseCoeffsBase<Derived, 1>::operator[](Eigen::DenseCoeffsBase<Derived, 1>::Index) [with Derived = Eigen::Matrix<double, -1, 1>; Eigen::DenseCoeffsBase<Derived, 1>::Scalar = double; Eigen::DenseCoeffsBase<Derived, 1>::Index = long int]: Assertion `index >= 0 && index < size()' failed.

Any syugestions what might be going on?

[MichelNivard]

I solved, it, for future reference this error arises if the dimensions of your annotations are not equal to the dimension of the other input files.