samtools index did not end, shell script did NOT end!

[houruiyan]

Hello, Thank you for your developing for this tools.

But here I cannot understand the logic behind. You set this judge sentence.

if (!all(file.exists(paste0("./temp/UB.", samples.vector, ".bam.bai")))) { write_log(stage = "samtools index", success = F) stop("samtools index did not end, shell script did NOT end!") }

I do not know why should I always run two times then it can detect the .bam.bai file ? Thanks you

[liaobinhong]

Hello, I meet a similar problem in the previous step.

Warning message:
In system(command = FilterBAM.command, wait = T) : error in running command
Error: FilterBAM did not end, shell script did NOT end!
Execution halted

I don't know the logic behind this error. I wonder if you meet the same problem when you run this code. Thank you!