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.