If the number of individuals is around 150,000, PrediXcan fails with a MemoryError exception.
I've used the DGN model.
./PrediXcan.py --predict --assoc --linear \
--weights ./models/DGN-HapMap-2015/DGN-WB_0.5.db \
--dosages /dir --samples myfile.fam \
--pheno pheno.txt --pheno_name myphenotype \
--output_prefix test
2017-04-06 11:24:08.266724 Preloading weights...
2017-04-06 11:24:10.281721 Processing chr1.txt.gz
Traceback (most recent call last):
File "./PrediXcan.py", line 230, in <module>
main()
File "./PrediXcan.py", line 211, in main
transcription_matrix.update(gene, weight, ref_allele, allele, dosage_row)
File "./PrediXcan.py", line 101, in update
self.D = np.zeros((len(self.gene_list), len(dosage_row))) # Genes x Cases
MemoryError
If the number of individuals is around 150,000, PrediXcan fails with a MemoryError exception.
I've used the DGN model.