python: can't open file '/app/mc-ilastik.py'

[PranavMotarwar]

Hey Team,

I am a new MCMICRO user. I have a MacBook with an M3 chip.

When I was trying to run the MCMICRO, I was getting this error: Process registration:ashlar (1) terminated with an error exit status (125). I resolved it by running the docker pull: Process registration:ashlar (1) terminated with an error exit status (125)

But now I am getting this error: python: can't open file '/app/mc-ilastik.py': [Errno 2] No such file or directory. This is the command that I was running: nextflow run labsyspharm/mcmicro --in exemplar-001 --segmentation ‘ilastik’

I tried pulling the docker pull for ilastik: docker pull labsyspharm/mcmicro-ilastik:1.6 but I am still getting the same error.

How can I check if my MCMICRO docker image is correctly set.

[ArtemSokolov]

Hi @PranavMotarwar,

For some reason, your nextflow installation is not using Docker (which is the default in MCMICRO). It's trying to run commands directly on your machine instead of inside the containers, which is why it's complaining about files not existing.

Can you try telling it explicitly to use the standard config:

nextflow run labsyspharm/mcmicro --in exemplar-001 --segmentation ilastik -profile standard