Quantification step fails with skimage.morphology.convex_hull ModuleNotFoundError error #565
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What kind of computer and operating system are you running mcmicro on? |
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I re-read your report and I see now you said "HPC" so I figure it's x86_64 machines running Linux, but it would still be good to verify that. |
Yes, you are right. |
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Hi @emir-radkevich, That's a super weird error message. We suspect it may have to do with how the container got converted to Singularity. Do you get this error with every image you try to process or just that one? Also, do you get the error with exemplar-001? |
No, exemplar-001 ran smoothly. |
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Would you be able to share a small image that's giving you issues, so we can try to reproduce the issue on our end? |
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Do you mean slide image or singularity image [work/singularity/labsyspharm-quantification-1.6.0.img]? |
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The slide image, but ideally a small (<1GB) crop from it that still gives you the issue. If you are not getting an issue with exemplar-001, then there is something different about your data that is triggering this error. If we can reproduce the issue on our end, we can help figure out what the problem is. |
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The nextflow output should have mentioned a path within your work directory that ends with a long alphanumeric string. Could you zip up all the files in that directory whose names begin with |
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I cropped the slide to a very small piece (<200 MB). Pipeline starting from segmentation or quantification works. I noticed something weird -- the whole slide is pink when loading in QuPath-0.5.1, the cropped image is also pinkish. See screenshots attached. 
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Could you try starting an interactive job on the HPC system with 48GB of memory and running the following command in it to run the quantification step in Singularity directly? |
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Can you try running that same command one more time? I am wondering if it will show the same exact error, or something different. I can't figure out how you would see different ModuleNotFoundError messages on different runs when the container didn't change. |
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Please re-run mcmicro on the whole slide with The log file will include information on how python is locating files for |
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The log message "INFO: Converting SIF file to temporary sandbox..." indicates that singularity isn't running the .img file directly but rather expanding it into a temporary directory (within /tmp by default) first. This is apparently the mode of operation for certain singularity installations. If there's not enough space in the temporary location, I'm not sure what would happen. I reached out to a colleague at Mount Sinai who has run mcmicro successfully on Minerva, and he said he can only run a couple of modules, then has to remove |
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The logfile.log that you uploaded indicates there are files missing from the |
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I removed images from After that, I got the same error as in this thread's subject. .command.log is attached: |
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Could you share your submit script so I could compare with the one from my MSKCC colleague? Here is the body of his: (I don't think any of the #BSUB option lines would matter so I omitted those) |
Hi.
I am using mcmicro on our lab's image from Orion machine.
I am using your pipeline on HPC starting at segmentation. So far, unmicst and s3seg are working.
I am getting this error during quantification step though:
I tried to look into the error inside the contatiner:
Looks like this module exists.
Do not understand the error.
Could you please help me?
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