Error : Mat::operator(): index out of bounds & Error in apply(emthr_SCANG_O, 2, max) :

[jingydz]

Is it acceptable for a few samples to exhibit the following error during the Dynamic_window step?

#######-- Dynamic_window Start time is 2024/08/22--16:22 --#######
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 294469 15.8 692257 37 478219 25.6
Vcells 511131 3.9 8388608 64 1925018 14.7
Attaching package: ‘SCANG’
The following object is masked from ‘package:STAAR’:
example
[1] 1879
# of selected samples: xxx
# of selected variants: 9,967
Error : Mat::operator(): index out of bounds
# of selected samples: xxx
# of selected variants: 1,649,378
Error in apply(emthr_SCANG_O, 2, max) :
dim(X) must have a positive length
Calls: Dynamic_Window_SCANG -> apply
Execution halted
#######-- Dynamic_window End Time:2024/08/22--17:31 --#######

According to the operating instructions you provided, I should have obtained 1879 Rdata files in the STAARpipeline_Dynamic_Window.R process.
But I only ended up with 1862 files, and the remaining 17 windows all resulted in the same error after multiple executions.

Can I ignore this error?

> sum(jobs_num$scang_num)
[1] 1879
for i in {1..1879};do Rscript 5STAARpipeline_Dynamic_Window.R ${i};done
ls /xxx/STAARpipeline/association/Dynamic_Window/*.Rdata |wc -l
1862

[jingydz]

Rscript 6.4STAARpipelineSummary_Dynamic_Window.R

It seems I cannot ignore this error.

[1] 79
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: Dynamic_Window_Results_Summary -> get -> load -> readChar
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
cannot open compressed file '/xxx/STAARpipeline/association/Dynamic_Window/xxx_SCANG_79.Rdata', probable reason 'No such file or directory'
Execution halted