jingydz
commented
3 weeks ago 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
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