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xihaoli / STAARpipeline-Tutorial

The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary
GNU General Public License v3.0
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Dynamic Window dim(X) error #55

Closed GACGAMA closed 2 months ago

GACGAMA commented 3 months ago

Hello Xihao!

At the Dynamic Window step, i'm getting the following error on some jobs (53 for example):

Attaching package: ‘SCANG’

The following object is masked from ‘package:STAAR’:

    example

Error in apply(emthr_SCANG_O, 2, max) : 
  dim(X) must have a positive length
Calls: Dynamic_Window_SCANG -> apply
Execution halted

This results in no _53.Rdata output for example. And then, when summarizing, I get the error that this slice is missing, but the files are NOT created. Im not sure if this error is innocuous

In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file '/scratch4/STAAR/stepB/7/Disease_Controls_Dynamic_Window_53.Rdata', probabl  e reason 'No such file or directory'
xihaoli commented 2 months ago

Hi @GACGAMA,

I am not sure if this is caused by the fact that you have a small sample size. See [#40] for an example.

Best, Xihao

GACGAMA commented 2 months ago

Running with double the samples worked