mkdir: cannot create directory ‘.//SCASA_My_Project_20240627144303/’: File exists

[nick-youngblut]

You can just change system("mkdir $file_variable") to system("mkdir -p $file_variable") in order to avoid this issue.

Also, you are not checking the exit status os system, so if the subprocess fails, the parent process will not fail. I believe that this is true for system in both perl and R. That could be very problematic for the code at

scasa/scasa/SCRIPTS/Xmatrix_Gen/scasa_simulate_xmatrix_step1_v1.0.0.R

Line 100 in b86c4a7

system(paste0("cp ",output_dir_chunk,"/*.fasta ",output_dir))

.