CellProfiler Analyst error when opening .properties files

I experience an error when I try to open a properties file using CellProfiler Analyst.
I select a properties file, then the error occurs.

“CellProfiler Analyst Error”

I’m given the option to open the console or terminate.
The console gives me a few errors:

I’m not quite sure what to make of this, so I would appreciate any help.
Thanks!

1 Like

There’s an example properties file at the bottom of this page.
Maybe you could download and try and open it just to exclude an installation issue.

If that opens okay, I think you’ll need to upload the pipeline you use to create the properties file and an example image to run it on.

Laura

Thank you for the reply. I have been testing with the CellProfiler Analyst example .properties file.

After some more digging it looks like the problem is originating with javabridge and the Java VM

ERROR:javabridge.locate:Could not find Java JRE compatible with x86_64 architecture

I think I have the correct JRE.

java -version
java version "1.8.0_211"
Java(TM) SE Runtime Environment (build 1.8.0_211-b12)
Java HotSpot(TM) 64-Bit Server VM (build 25.211-b12, mixed mode)

It turns out that the only way to get this to run on my machine is to launch it from the terminal.
If anyone has insight about this, please let me know.

Hi, I have exactly the same issue, did you manage to find a solution ?

Hi,

What version of MacOS are you using? I’m afraid CPA only supports up to 10.13 for now. We hope to be able to fix that sometime later this year or early next year!

Hi,

Many thanks for you reply. I have the same issue on my both Mac laptops: one is MacOS 10.14 but the other is MacOS 10.11 and I have the same error message. Is there something I can do to fix it ?

What is the output of java -version on the 10.11 system?

Hi,

Here what it says when I ask for the java version:

java version “1.6.0_65”
Java™ SE Runtime Environment (build 1.6.0_65-b14-468-11M4833)
Java HotSpot™ 64-Bit Server VM (build 20.65-b04-468, mixed mode)

Could it come from here?

Yup, you need to have Java8.

I uninstalled java and JDK and setup the last versions for both.
What I have now:
java version “13.0.1” 2019-10-15
Java™ SE Runtime Environment (build 13.0.1+9)
Java HotSpot™ 64-Bit Server VM (build 13.0.1+9, mixed mode, sharing)

Then I installed CPA again and I still have the same error message after selecting the properties files… Can it come from something else ?

I don’t know it helps but here’s what I get when I open the console after the error message:
06/11/2019 09:43:29,379 CellProfiler Analyst[790]: WARNING:root:PROPERTIES WARNING: Unrecognized field “series_id” in properties file
06/11/2019 09:43:29,379 CellProfiler Analyst[790]: WARNING:root:PROPERTIES WARNING: Unrecognized field “group_id” in properties file
06/11/2019 09:43:29,379 CellProfiler Analyst[790]: WARNING:root:PROPERTIES WARNING: Unrecognized field “timepoint_id” in properties file
06/11/2019 09:43:29,379 CellProfiler Analyst[790]: WARNING:root:PROPERTIES WARNING (channels_per_image): No value(s) specified. CPA will assume 1 channel per image.
06/11/2019 09:43:29,379 CellProfiler Analyst[790]: INFO:root:PROPERTIES: Using default image_buffer_size=1
06/11/2019 09:43:29,379 CellProfiler Analyst[790]: INFO:root:PROPERTIES: Using default tile_buffer_size=1
06/11/2019 09:43:29,379 CellProfiler Analyst[790]: INFO:root:PROPERTIES: Per-Object classes will be written to table “Phenotype”
06/11/2019 09:43:29,379 CellProfiler Analyst[790]: WARNING:root:PROPERTIES WARNING (plate_id): Field is required for plate map viewer.
06/11/2019 09:43:29,379 CellProfiler Analyst[790]: WARNING:root:PROPERTIES WARNING (well_id): Field is required for plate map viewer.
06/11/2019 09:43:29,379 CellProfiler Analyst[790]: WARNING:root:PROPERTIES WARNING (plate_type): Field is required for plate viewer
06/11/2019 09:43:29,379 CellProfiler Analyst[790]: WARNING:root:PROPERTIES WARNING (well_format): Field was not defined, using default format of “A01”.
06/11/2019 09:43:29,413 CellProfiler Analyst[790]: INFO:root:[MainThread] Connecting to the database…
06/11/2019 09:43:29,413 CellProfiler Analyst[790]: INFO:root:[MainThread] SQLite file: /Users/paulinejeannot/Documents/Labo/Image Analysis/Astrocyte_2nd try/Astrocyte_2ndtry_database.db
06/11/2019 09:43:29,468 CellProfiler Analyst[790]: ERROR:javabridge.locate:Could not find Java JRE compatible with x86_64 architecture
06/11/2019 09:43:29,513 CellProfiler Analyst[790]: ERROR:javabridge.locate:Could not find Java JRE compatible with x86_64 architecture
06/11/2019 09:43:29,516 CellProfiler Analyst[790]: ERROR:javabridge.jutil:Failed to execute “find” when searching for libjvm
06/11/2019 09:43:29,516 CellProfiler Analyst[790]: Traceback (most recent call last):
06/11/2019 09:43:29,516 CellProfiler Analyst[790]: File “/Applications/CellProfiler Analyst.app/Contents/Resources/lib/python2.7/javabridge/jutil.py”, line 115, in _find_mac_lib
06/11/2019 09:43:29,517 CellProfiler Analyst[790]: [“find”, os.path.dirname(jvm_dir), “-name”, library+extension])
06/11/2019 09:43:29,517 CellProfiler Analyst[790]: File “posixpath.pyc”, line 122, in dirname
06/11/2019 09:43:29,517 CellProfiler Analyst[790]: AttributeError: ‘NoneType’ object has no attribute ‘rfind’
06/11/2019 09:43:29,517 CellProfiler Analyst[790]: ERROR:javabridge.jutil:Failed to execute “find” when searching for libjvm
06/11/2019 09:43:29,517 CellProfiler Analyst[790]: Traceback (most recent call last):
06/11/2019 09:43:29,517 CellProfiler Analyst[790]: File “/Applications/CellProfiler Analyst.app/Contents/Resources/lib/python2.7/javabridge/jutil.py”, line 115, in _find_mac_lib
06/11/2019 09:43:29,517 CellProfiler Analyst[790]: [“find”, os.path.dirname(jvm_dir), “-name”, library+extension])
06/11/2019 09:43:29,517 CellProfiler Analyst[790]: File “posixpath.pyc”, line 122, in dirname
06/11/2019 09:43:29,517 CellProfiler Analyst[790]: AttributeError: ‘NoneType’ object has no attribute ‘rfind’
06/11/2019 09:43:29,517 CellProfiler Analyst[790]: ERROR:javabridge.jutil:Failed to find libjvm
06/11/2019 09:43:29,562 CellProfiler Analyst[790]: ERROR:javabridge.locate:Could not find Java JRE compatible with x86_64 architecture
06/11/2019 09:43:29,562 CellProfiler Analyst[790]: ERROR:javabridge.jutil:Failed to execute “find” when searching for libjli
06/11/2019 09:43:29,562 CellProfiler Analyst[790]: Traceback (most recent call last):
06/11/2019 09:43:29,562 CellProfiler Analyst[790]: File “/Applications/CellProfiler Analyst.app/Contents/Resources/lib/python2.7/javabridge/jutil.py”, line 115, in _find_mac_lib
06/11/2019 09:43:29,562 CellProfiler Analyst[790]: [“find”, os.path.dirname(jvm_dir), “-name”, library+extension])
06/11/2019 09:43:29,562 CellProfiler Analyst[790]: File “posixpath.pyc”, line 122, in dirname
06/11/2019 09:43:29,562 CellProfiler Analyst[790]: AttributeError: ‘NoneType’ object has no attribute ‘rfind’
06/11/2019 09:43:29,562 CellProfiler Analyst[790]: ERROR:javabridge.jutil:Failed to execute “find” when searching for libjli
06/11/2019 09:43:29,562 CellProfiler Analyst[790]: Traceback (most recent call last):
06/11/2019 09:43:29,562 CellProfiler Analyst[790]: File “/Applications/CellProfiler Analyst.app/Contents/Resources/lib/python2.7/javabridge/jutil.py”, line 115, in _find_mac_lib
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: [“find”, os.path.dirname(jvm_dir), “-name”, library+extension])
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: File “posixpath.pyc”, line 122, in dirname
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: AttributeError: ‘NoneType’ object has no attribute ‘rfind’
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: ERROR:javabridge.jutil:Failed to find libjli
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: Traceback (most recent call last):
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: File “/Applications/CellProfiler Analyst.app/Contents/Resources/lib/python2.7/javabridge/jutil.py”, line 274, in start_thread
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: raise Exception(“Javabridge failed to find JVM library”)
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: Exception: Javabridge failed to find JVM library
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: ERROR:javabridge.jutil:Failed to create Java VM
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: Traceback (most recent call last):
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: File “/Applications/CellProfiler Analyst.app/Contents/Resources/CellProfiler-Analyst.py”, line 557, in
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: app.Start()
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: File “/Applications/CellProfiler Analyst.app/Contents/Resources/CellProfiler-Analyst.py”, line 473, in Start
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: javabridge.start_vm(class_path=bioformats.JARS, run_headless=True)
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: File “/Applications/CellProfiler Analyst.app/Contents/Resources/lib/python2.7/javabridge/jutil.py”, line 312, in start_vm
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: raise RuntimeError(“Failed to start Java VM”)
06/11/2019 09:43:29,563 CellProfiler Analyst[790]: RuntimeError: Failed to start Java VM
06/11/2019 09:43:29,615 CellProfiler Analyst[790]: CellProfiler Analyst Error
06/11/2019 09:43:29,615 CellProfiler Analyst[790]: 2019-11-06 09:43:29.615 CellProfiler Analyst[790:16870] CellProfiler Analyst Error

Hi,

Do you have any idea about why it doesn’t work? And how I could fix it?
Sorry to insist but I’d really like to use it.