Error in train.cytonorm

[mayanbriller]

Hello!
While running the workflow for batch correction, I am getting the following:

Training alignment - file (batch) preparation
Training alignment - file (batch) and metacluster splitting
 -- running File '1'
Error in flowCore::write.FCS(file.ff[cellClusterIDs == cluster, ], file = file.path(getwd(),  : 
  Argument 'filename' has to be a character of length 1.
Calls: train.cytonorm
Execution halted

I noticed that no where in the workflow do we define fine.dir , so I defined it as

setwd("Output 2.4 - fine alignment")
fine.dir = getwd()

Could it be the reason for this error?
Thanks
Mayan

[tomashhurst]

Hi @mayanbriller ,

Could I ask what OS you are using? The filename issue is a little weird. Does it run with the demo dataset?

Tom

[mayanbriller]

I am working on Google Cloud.
I was able to reproduce this error with the demo data.

I don't think it's related - but for the purposes of testing the workflow I deleted the parts of the code that produce graphs. Do you think it could be related?

Training alignment - file (batch) preparation
Training alignment - file (batch) and metacluster splitting
 -- running File '1'
Error in flowCore::write.FCS(file.ff[cellClusterIDs == cluster, ], file = file.path(getwd(),  : 
  Argument 'filename' has to be a character of length 1.
Calls: train.cytonorm
Execution halted
sh: 0: getcwd() failed: No such file or directory

Hi @mayanbriller ,

Could I ask what OS you are using? The filename issue is a little weird. Does it run with the demo dataset?

Tom