--pcatype cis crashing

[wkc1986]

This step keeps crashing:

Performing Z transformation: complete!
Performing block wise correlation calculation        Error: upper value must be greater than lower value

Can you offer any advice? Thank you.

[ay-lab]

It can crash if you have non-standard chromosomes like chrY/chrM and others. Please try to remove those instances from the bed file and give it another shot. Let me know how it goes.

[wkc1986]

Yes, this was due to leftover files from a failed run from which chrX had not been omitted. Thanks.