Still having trouble with batch processing

Hello all,

Currently having trouble with two errors using the Cell Painting pipeline. I have all my images and my illumination correction files on the cluster already and when I execute the batch file I generated using the given command:

./python -m cellprofiler -p <Default_Output_Folder_path>/Batch_data.h5 \
-c -r -b \
-f <first_image_set_number> \
-l <last_image_set_number>

I first get this error:

main.py: error: no such option: -b

If I remove the -b I get this error:

Could not load cellprofiler.modules.randomwalkeralgorithm
Traceback (most recent call last):
File “/export/share/apps/CellProfiler-master/cellprofiler/modules/init.py”, line 330, in add_module
m = import(mod, globals(), locals(), [‘all’], 0)
ImportError: No module named randomwalkeralgorithm
could not load these modules: cellprofiler.modules.randomwalkeralgorithm
Failed to load pipeline
Traceback (most recent call last):
File “/export/share/apps/CellProfiler-master/cellprofiler/pipeline.py”, line 1046, in loadtxt
module_name, from_matlab)
File “/export/share/apps/CellProfiler-master/cellprofiler/module.py”, line 176, in set_settings_from_values
from_matlab)
File “/export/share/apps/CellProfiler-master/cellprofiler/modules/identifysecondaryobjects.py”, line 501, in upgrade_settings
threshold_settings_version = int(threshold_setting_values[0])
ValueError: invalid literal for int() with base 10: ‘0.8’
Exception in thread “Thread-0” org.mozilla.javascript.WrappedException: Wrapped org.cellprofiler.imageset.filter.Filter$BadFilterExpressionException: No applicable predicate for token Nucleus (#5)
at org.mozilla.javascript.Context.throwAsScriptRuntimeEx(Context.java:1754)
at org.mozilla.javascript.MemberBox.newInstance(MemberBox.java:167)
at org.mozilla.javascript.NativeJavaClass.constructInternal(NativeJavaClass.java:266)
at org.mozilla.javascript.NativeJavaClass.constructSpecific(NativeJavaClass.java:205)
at org.mozilla.javascript.NativeJavaClass.construct(NativeJavaClass.java:166)
at org.mozilla.javascript.ScriptRuntime.newObject(ScriptRuntime.java:2349)
at org.mozilla.javascript.gen._java_python_bridge__8._c_script_0(:5)
at org.mozilla.javascript.gen._java_python_bridge__8.call()
at org.mozilla.javascript.ContextFactory.doTopCall(ContextFactory.java:394)
at org.mozilla.javascript.ScriptRuntime.doTopCall(ScriptRuntime.java:3091)
at org.mozilla.javascript.gen._java_python_bridge__8.call()
at org.mozilla.javascript.gen._java_python_bridge__8.exec()
at org.mozilla.javascript.Context.evaluateString(Context.java:1079)
Caused by: org.cellprofiler.imageset.filter.Filter$BadFilterExpressionException: No applicable predicate for token Nucleus
at org.cellprofiler.imageset.filter.Filter.get(Filter.java:351)
at org.cellprofiler.imageset.filter.Filter.get(Filter.java:331)
at org.cellprofiler.imageset.filter.Filter.get(Filter.java:323)
at org.cellprofiler.imageset.filter.Filter.parse(Filter.java:384)
at org.cellprofiler.imageset.filter.Filter.parse(Filter.java:365)
at org.cellprofiler.imageset.filter.Filter.(Filter.java:110)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at org.mozilla.javascript.MemberBox.newInstance(MemberBox.java:159)
… 11 more
Failed to prepare run for module NamesAndTypes
Traceback (most recent call last):
File “/export/share/apps/CellProfiler-master/cellprofiler/pipeline.py”, line 2070, in prepare_run
if ((not module.prepare_run(workspace)) or
File “/export/share/apps/CellProfiler-master/cellprofiler/modules/namesandtypes.py”, line 858, in prepare_run
image_sets, channel_map = self.java_make_image_sets(workspace)
File “/export/share/apps/CellProfiler-master/cellprofiler/modules/namesandtypes.py”, line 1078, in java_make_image_sets
self.java_make_image_sets_by_metadata(workspace, ipd_list)
File “/export/share/apps/CellProfiler-master/cellprofiler/modules/namesandtypes.py”, line 1200, in java_make_image_sets_by_metadata
cf = self.make_channel_filter(group, name)
File “/export/share/apps/CellProfiler-master/cellprofiler/modules/namesandtypes.py”, line 1113, in make_channel_filter
script, dict(expr=group.rule_filter.value, name=name, axes=axes))
File “/export/share/compilers/python-2.7.13-gcc/lib/python2.7/site-packages/javabridge/jutil.py”, line 392, in run_script
raise JavaException(call(e.throwable, “unwrap”, “()Ljava/lang/Object;”))
JavaException: No applicable predicate for token Nucleus

Any help will be appreciated!

Can you share your pipeline? Thanks!

Hi again!

Tried the same pipeline again today with no luck, getting the same error. Here it is with an image set and the Batch_data.h5 file I generated to run it. I am using CellProfiler version 3.0.0rc1. Any help would be appreciated :slight_smile:

project.files.zip (11.5 MB)

Hi,

There are a ton of bugs in rc1 we fixed, can you confirm whether running v3.0.0 (or v3.1.5) you have the same problem? Thanks!