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genetics-of-dna-methylation-consortium / godmc_phase2

This repository contains the code to run the analysis pipeline for phase 2 of goDMC released June 2024.
GNU General Public License v3.0
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[Bug]: 9 stops at AD EWAS #61

Open drsora opened 2 weeks ago

drsora commented 2 weeks ago

Contact Details

sonja.rajic@tuni.fi

Scripts

09-PRS_EWAS.sh

What happened?

The script ran smoothly until it got to EWAS for AD. Error is shown below.

How can the bug be reproduced?

No response

R version

4.4.0 (April, 2024)

Python version

None

Relevant log output

Running EWAS for AD

Warning messages:
1: multiple methods tables found for ‘sort’
2: multiple methods tables found for ‘sort’
Loading non genetic methylation PCs
No covariates file present for AD
Loading methylation data
Loading PRS data for AD

Performing EWAS for AD on 882 individuals and 768853 CpGs
Error in La.svd(V) : error code 1 from Lapack routine 'dgesdd'
Calls: main ... add.surrogate.variables -> isva -> isvaFn -> fastICA -> La.svd
Execution halted
msolerartigas commented 2 weeks ago

Hi Sonja,

Thanks for your message!

There is an issue that is now closed ([Bug]: 09 - Error in psoriasisNOHLA EWAS #34) that reports the same error and a posible solution. Can you have a look and see whether that works for you?

Thank you! María