MCMICRO: Cellpose Issue

[virlyananda]

Hi all,

I tried to run Cellpose through MCMICRO (O2 based). The log file says it was completed but I couldn't find the segmentation results. I haven't seen much discussion regarding this issue. Looking forward to hearing your advice. Thank you!

Best, Virly

[ArtemSokolov]

Hi @virlyananda,

Can you please share your params.yml, the command you are using to run the pipeline and the output log you are getting?

Another thing to check is the work directory. If you type nextflow log last -f name,workdir in the same directory as where you started the pipeline, it will list the work directory associated with every process. Find the work directory for Cellpose and see if the outputs were generated.

I've heard some users report that files were sometimes not getting property copied on O2 during peak usage hours.

[virlyananda]

Hi @ArtemSokolov,

Thank you for your response.

This is my params.yml based on QC: name: backsub container: ghcr.io/schapirolabor/background_subtraction version: v0.3.3 cmd: |- python3 /background_subtraction/background_sub.py \ -r ${image} -m ${marker} \ -o ${image_id}_backsub.ome.tif -mo markers_bs.csv segmentation:

• name: cellpose container: biocontainers/cellpose version: 2.1.1_cv2 cmd: cellpose --channel_axis 0 --save_tif --savedir . --verbose input: --image_path model: --pretrained_model idxbase: 0 watershed: 'no' watershed: name: s3seg container: labsyspharm/s3segmenter version: 1.5.5 channel: --probMapChan idxbase: 1 quantification: name: mcquant container: labsyspharm/quantification version: 1.5.3 downstream:
• name: scimap container: labsyspharm/scimap version: 0.17.7 cmd: scimap-mcmicro -o . input: '' viz: name: autominerva container: ghcr.io/labsyspharm/mcmicro version: auto-minerva-2023-08-29

This is my error log output:

Best Regards, Virly

[ArtemSokolov]

It looks like it's trying to run the container from your user directory, which the research compute team at HMS doesn't allow. There is a couple of extra caveats to running the pipeline on O2. Take a look at https://mcmicro.org/platforms/run-O2.html

In particular, you will want to make sure you do nextflow run labsyspharm/mcmicro/setup/O2ext.nf to set up the appropriate links to the containers. Then don't forget to include -profile O2ext when actually running the pipeline.