Error in signif(trhAssignment, 3)

hummuscience commented 5 years ago

11:24   Step 3. Analyzing the network activity in each individual cell
        Number of regulons to evaluate on cells: 226
Biggest (non-extended) regulons: 
         Etv1 (3407g)
         Atf3 (3171g)
         Egr1 (2197g)
         Srebf2 (2035g)
         Yy1 (942g)
         Esrra (928g)
         Gtf2f1 (766g)
         Etv5 (653g)
         Gabpa (429g)
         Fosb (269g)
Quantiles for the number of genes detected by cell: 
(Non-detected genes are shuffled at the end of the ranking. Keep it in mind when choosing the threshold for calculating the AUC).
    min      1%      5%     10%     50%    100% 
1064.00 1299.37 1630.75 1952.30 3167.50 6254.00 
Using 10 cores.
Using 10 cores.
Error in signif(trhAssignment, 3) : 
  non-numeric argument to mathematical function
In addition: Warning message:
In mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed,  :
  scheduled cores 1, 2, 4 did not deliver results, all values of the jobs will be affected

https://github.com/aertslab/RcisTarget/issues/12#issuecomment-494311765

hummuscience commented 5 years ago

solved by reducing nCores to 10 and increasing RAM to > 50Gb for a 1500 cell dataset

ManarHashemTaha commented 1 month ago

How did you set those parameters , and what did you use first ?

hummuscience commented 1 month ago

Its been a while, but nCores is a parameter you can set in the idividual functions of SCENIC

And for the RAM, I changed to a computer with larger RAM. So you could check out using a cluster for that

aertslab / AUCell

Error in signif(trhAssignment, 3) #6