Still having trouble with batch processing

cellprofiler

#1

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!


#2

Can you share your pipeline? Thanks!


#4

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)


#5

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!