I am attempting to user the 1.0.5811 version of Cell Profiler, after using the 1.0.4553 successfully for more than a year. I’m having a problem generating batch files.
I am attempting to compute a small, 6 cycle test case in preparation for a large run. This test case appears to run fine with my pipeline so long as I don’t create batch files.
However when I add CreateBatchFiles to the end of the pipeline, the first cycle appears to run fine, and the CreateBatchFiles module claims to have output the batch files. However, when I look in the output directory, I only see these two files:
The individual batch file(s) don’t appear. I would expect to see one, named Batch_2_6.mat
(As an aside, in the older versions of CreateBatchFiles, there was an option to specify the number of cycles per batch file. This option doesn’t appear in the 1.0.5811 version. How do I specify this?)
For background, I’m running this on 64 bit Redhat system, using the developers version of CellProfiler running inside matlab 7.4.0. (since a compiled version for Linux isn’t yet available)
[rdb9@c076 TEST092408]$ uname -a
Linux c076 2.6.9-55.0.9.EL_lustre.184.108.40.206smp #1 SMP Wed Jan 16 19:52:57 EST 2008 x86_64 x86_64 x86_64 GNU/Linux