Exit after reading test dataset

kingsfordgroup / armatus

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Exit after reading test dataset #14

Open hgu0717 opened 5 years ago

hgu0717 commented 5 years ago

Hey,

I've tried to run with tested Rao's dataset, but the run was abandoned due to the following issues:

Reading input from GM12878_combined/1kb_resolution_intrachromosomal/chr1/MAPQGE30/chr1_1kb. Building matrix for chromosome 1 at resolution 1000bp with 249233 rows. Reading KR normalization counts Initializing matrix to zero elements terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted

nsauerwald commented 5 years ago

It looks like you might not have enough memory for such a large matrix. Does the same command work for chromosome 22 for example (GM12878_combined/1kb_resolution_intrachromosomal/chr22/MAPQGE30/chr22_1kb)? Or at a lower resolution (GM12878_combined/100kb_resolution_intrachromosomal/chr1/MAPQGE30/chr1_100kb)?