LoadSingleImage and cluster file system different from local


#1

This problem seems similar to the first one I wrote about.

On my local machine /home corresponds to /blast on the cluster and I believe I properly so indicated in the CreateBatchFiles module.

We are now using LoadSingleImage in our pipeline. I got the error message below, which seems to indicate that LoadSingleImage does not make use of the information in CreateBatchFiles regarding translating local names to cluster names.

-Ben

Batch Error: LoadSingleImage Error using ==> LoadSingleImage Image processing was canceled in the LoadSingleImage module because the directory “/home/bwittner/celld/output/sub.45” does not exist. Be sure that no spaces or unusual characters exist in your typed entry and that the pathname of the directory begins with / (for Mac/Unix) or \ (for PC).


#2

Hi Ben,

The folders in LoadSingleImage are definitely converted by CreateBatchFiles. I do this type of analysis (PC to Linux Cluster) daily with no problems. Perhaps you could send me your pipeline and some images to look at.

Mike


#3

Hi Mike,

Perhaps you could send me your pipeline and some images to look at.

I’ll send you the images and .mat files and .sh file from a small run by email.
Thanks much.

-Ben