Hello,
I'm trying to multi-thread CopywriteR on a slurm cluster using openmpi. My jobs seem to be launching properly and run for about 10m, but then they die prematurely.
The final message in my slurm output file looks like this:
Error in `[<-.data.frame`(`*tmp*`, , "total.properreads", value = list( :
replacement element 18 has 2 rows, need 17
Calls: CopywriteR -> [<- -> [<-.data.frame
Execution halted
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[40568,1],0]
Exit code: 1
Any ideas?
ETA:
For clarification, it seems to stop after all the *properreads.bam.bai files have been generated.
Ok, I am interested to see whether you will manage to get the parallel analysis using CopywriteR working.
As to your question: it should not matter whether you run CopywriteR a number of times on single bams, or on the combined set, as long as the provided controls are the same in both analyses (internally the samples are analyzed completely independently even if multiple samples are analyzed together). Did you check whether the input for CGHcall (the 2 .igv files) were identical? I am not quite sure where things went wrong; if you provide me with the exact code you run I might be able to help you out.
Thomas