Closed esebesty closed 3 years ago
Hi There,
This certainly seems like it is caused by a memory error, especially as a 40kb matrix is the pretty large. Can you run the R script (using the printed command) standalone? You could also try adding memory to the chr1 job.
Looks like everything is ok on a larger memory node! Memory usage peaked around 37Gb, and this failed on a 32Gb node.
I'm trying to run dcHiC chromosome-by-chromosome (after removing chrY), and most of the chromosomes seem to be ok, all of the differential compartment, etc files are there, but it fails on chr1, with the following:
FileNotFoundError
``` [1] "Hierarchy" [[1]] [1] 5602 5602 5602 5602 5602 5602 [[2]] [1] 1 1 1 1 1 1 DEBUG:Blank space skipped. No worries. DEBUG:Blank space skipped. No worries. DEBUG:Blank space skipped. No worries. DEBUG:Blank space skipped. No worries. DEBUG:Blank space skipped. No worries. DEBUG:Blank space skipped. No worries. Positions Not Shared Across All Data Sets, Chromosome 1: None 5602 Rscript --vanilla /home/user2031/work/repos/bcro/bit-bio/dcHiC/dchic/Hier.R BalancedChrMatrix_exp_N2P.D0.txt BalancedChrMatrix_exp_N2P.D14.txt BalancedChrMatrix_exp_N2P.D7. R OUTPUT: Traceback (most recent call last): File "/home/user2031/work/repos/bcro/bit-bio/dcHiC/dchic/run.py", line 323, inThis is a 40k matrix from HiC-Pro. Is it possible that the R script failed due to some error (memory limitation, etc)?