step2_SPAtests.R: error: Error in getopt(spec = spec, opt = args) : long flag "numLinesOutput" is invalid

[surakshavinod]

Hi, I'm getting the following error when I try to run single variant association test using step2_SPAtests.R:

step2_SPAtests.R: error: Error in getopt(spec = spec, opt = args) : 
 long flag "numLinesOutput" is invalid

Here is the log:

R version 4.2.2 (2022-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS/LAPACK: /home/suraksha/anaconda3/envs/RSAIGE/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=en_IN       LC_NUMERIC=C         LC_TIME=en_IN
 [4] LC_COLLATE=en_IN     LC_MONETARY=en_IN    LC_MESSAGES=en_IN
 [7] LC_PAPER=en_IN       LC_NAME=C            LC_ADDRESS=C
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] data.table_1.14.6      optparse_1.7.3         RhpcBLASctl_0.21-247.1
[4] SAIGE_1.1.6.3

loaded via a namespace (and not attached):
[1] compiler_4.2.2     Matrix_1.5-3       Rcpp_1.0.7         getopt_1.20.3
[5] grid_4.2.2         RcppParallel_5.1.6 lattice_0.20-45
Usage: step2_SPAtests.R [options]

step2_SPAtests.R: error: Error in getopt(spec = spec, opt = args) :
  long flag "numLinesOutput" is invalid

Thanks, Suraksha

[Youpu-Chen]

I have the same issue, did you find out how to solve this?