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cryoem / eman2

A scientific image processing software suite with a focus on CryoEM and CryoET
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RuntimeError: Exception at /home/eman2/etc.../emutil.cpp:943: 'The mode size was 0?' caught #573

Open GiampaoloMart opened 2 weeks ago

GiampaoloMart commented 2 weeks ago

Hi,

I’m encountering an issue using RELION 5 and EMAN 2.91. During execution, I receive the following error: RuntimeError: Exception at /home/eman2/miniconda3/conda-bld/eman2_1615224802990/work/libEM/emutil.cpp:943: 'The mode size was 0?' caught Details:

repo : https://github.com/moores-lab/MiRPv2 RELION Version: 5 EMAN Version: 2.91 Input File Type: .star Command Executed: (generate segment averages -i ./External/mirp pf sorting/14pf data.star - o ./Extract/segmentAverages) I have verified that the .star file and associated image files are correctly formatted and should be valid. Despite this, the issue persists. It seems to be related to the mode_size calculation, which is resulting in a value of 0.

Could this be a compatibility issue or a potential bug in the code? Any guidance on resolving this problem would be greatly appreciated.

Thank you in advance for your help!

sludtke42 commented 2 weeks ago

The command you executed:

generate segment averages -i ./External/mirp pf sorting/14pf data.star - o ./Extract/segmentAverages

is not an EMAN2 command. Looking at the MIRPv2 library you're pointing to, the documentation points to an EMAN2 version making use of Python 2, which EMAN has not depended on for quite a few years (we switched to Python 3). You really need to contact the developer of MIRP, not EMAN/RELION in this case

Steven Ludtke, Ph.D. @.***> Baylor College of Medicine Charles C. Bell Jr., Professor of Structural Biology Dept. of Biochemistry Deputy Director, Advanced Technology Cores and Molecular Pharmacology Academic Director, CryoEM Core Co-Director CIBR Center

On Aug 30, 2024, at 9:17 AM, Giampaolo Martiniello @.***> wrote:

Hi,

I’m encountering an issue using RELION 5 and EMAN 2.91. During execution, I receive the following error: RuntimeError: Exception at /home/eman2/miniconda3/conda-bld/eman2_1615224802990/work/libEM/emutil.cpp:943: 'The mode size was 0?' caught Details:

repo : https://github.com/moores-lab/MiRPv2 RELION Version: 5 EMAN Version: 2.91 Input File Type: .star Command Executed: (generate segment averages -i ./External/mirp pf sorting/14pf data.star - o ./Extract/segmentAverages) I have verified that the .star file and associated image files are correctly formatted and should be valid. Despite this, the issue persists. It seems to be related to the mode_size calculation, which is resulting in a value of 0.

Could this be a compatibility issue or a potential bug in the code? Any guidance on resolving this problem would be greatly appreciated.

Thank you in advance for your help!

— Reply to this email directly, view it on GitHubhttps://github.com/cryoem/eman2/issues/573, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACPKF2VRBAKKXRCW65NVZA3ZUB5IPAVCNFSM6AAAAABNMSNNDOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4TOMZWHEYDENA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

GiampaoloMart commented 1 week ago

Thank you for your prompt response and for clarifying the situation. As you suggested, it seems likely that the issue could be related to version compatibility, particularly since the version of MIRP I'm using might depend on an older version of EMAN2 that utilizes Python 2. Thank you again for your help.