CP Beta batch mode

Trying to run CP Beta in Batch mode on a Win 7 64 bit. Getting the following error.

C:\Program Files\CellProfiler>CellProfiler.exe -p E:\Parthiv_chip1\output\Batch_ data.h5 E:\Parthiv_chip1\output -c -r -f 1 -l 1024 Version: 2013-11-13T12:57:00 88ad7ca / 20131113125700 Plugin directory doesn't point to valid folder: C:\Program Files\CellProfiler\pl ugins Pipeline saved with CellProfiler version 20131113125700 Uncaught exception in CellProfiler.py Traceback (most recent call last): File "CellProfiler.py", line 222, in main File "CellProfiler.py", line 705, in run_pipeline_headless File "cellprofiler\pipeline.pyc", line 1563, in run File "cellprofiler\measurements.pyc", line 259, in __init__ File "cellprofiler\utilities\hdf5_dict.pyc", line 177, in __init__ File "h5py\highlevel.pyc", line 793, in __init__ File "h5py\highlevel.pyc", line 833, in _generate_fid File "h5f.pyx", line 87, in h5py.h5f.create (h5py\h5f.c:1414) IOError: Permission denied (Internal error (too specific to document in detail): System error message) stopping worker thread 0 stopping worker thread 1 stopping worker thread 2 stopping worker thread 3 stopping worker thread 4 stopping worker thread 5 stopping worker thread 6 stopping worker thread 7 stopping worker thread 8 stopping worker thread 9 stopping worker thread 10 stopping worker thread 11 stopping worker thread 12 Exiting the JVM monitor thread
Parthiv20140109.cpproj (2.35 MB)

Sorry to ask this, but could you post your pipeline rather than the project file? For some reason (possibly related to this, which has been fixed), the modules aren’t loading.

You can export your pipeline by selecting File > Export > Pipeline, and in the dialog box that comes up, rather than export as “CellProfiler pipeline”, use “CellProfiler pipeline and file list”. This will also preserve the file listing in the Images module (I presume I can use the image files from your easier post to test things out?)
-Mark

Also, I see that you are running with this line:CellProfiler.exe -p E:\Parthiv_chip1\output\Batch_data.h5 E:\Parthiv_chip1\output -c -r -f 1 -l 1024
I’m not sure that syntax is correct. Do you want to run with this: CellProfiler.exe -p E:\Parthiv_chip1\output\Batch_data.h5 -o E:\Parthiv_chip1\output -c -r -f 1 -l 1024to specify the Default Output Folder location, or this:

CellProfiler.exe -p E:\Parthiv_chip1\output\Batch_data.h5 -c -r -f 1 -l 1024 E:\Parthiv_chip1\output.h5to specify the optional filename of the output file of measurements?
-Mark

Dear Mark,

I changed it however a new error now pops up at the end of the pipleline. The data files are saved but they are empty.

Failed to complete post_run processing for module ExportToDatabase. Traceback (most recent call last): File "cellprofiler\pipeline.pyc", line 2118, in post_run File "cellprofiler\modules\exporttodatabase.pyc", line 1938, in post_run File "cellprofiler\modules\exporttodatabase.pyc", line 2706, in write_csv_data File "cellprofiler\measurements.pyc", line 910, in get_measurement File "cellprofiler\utilities\hdf5_dict.pyc", line 347, in __getitem__ File "cellprofiler\utilities\hdf5_dict.pyc", line 351, in __getitem__ AssertionError stopping worker thread 0 stopping worker thread 1 stopping worker thread 2 stopping worker thread 3 stopping worker thread 4 stopping worker thread 5 stopping worker thread 6 stopping worker thread 7 stopping worker thread 8 stopping worker thread 9 stopping worker thread 10 stopping worker thread 11 stopping worker thread 12 Exiting the JVM monitor thread

Sorry forgot to attach the pipeline file. Here it is.
parthiv123.cppipe (17.3 KB)

This is a definite bug. I’ve filed it in our bug tracking system and will post here when it’s fixed.
-Mark

Hi,

I was just looking at the command line and just wanted to ask whether the -l an -f flags are optional ?

with version 2.1 if you are running in command line mode you can indicate the pipeline using -p flag and the input image directory using the -i flag. Is this correct?

I’m trying to run on a cluster a pipeline that works when running from the GUI but doesn’t seem to find any images in command line mode.

Thanks,
Elton

[quote]I was just looking at the command line and just wanted to ask whether the -l an -f flags are optional ?
[/quote]

The ‘-l’ and ‘-f’ are optional. Please see this for (not much) more info.

[quote]with version 2.1 if you are running in command line mode you can indicate the pipeline using -p flag and the input image directory using the -i flag. Is this correct?
[/quote]

Yes. Please try the ‘–get-batch-commands’ switch to see some sample commands for your output.

[quote]I’m trying to run on a cluster a pipeline that works when running from the GUI but doesn’t seem to find any images in command line mode.
[/quote]

Possibly this fix may clear this up. Would you try a new trunk build? github.com/CellProfiler/CellPro … TrunkBuild

Thanks,
David

This issue has been resolved with the 2.1.1 release.
-Mark