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icbi-lab / luca

Single-cell Lung Cancer Atlas with 1.2M cells

Home Page:https://luca.icbi.at

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Index 0 out of bounds for length 0 error

Mengflz opened this issue · comments

commented

Dear authors,
Thank you very much for your work. I am new to nextflow. After I download related and follow the command you give
"nextflow run main.nf --workflow downstream_analyses -resume -profile icbi_lung --build_atlas_dir ./data/20_build_atlas --outdir ./data/30_downstream_analyses"
WX20231013-122501@2x

This error always occurs. I run this on a server instead of HPC. I don't know why this error occurred. Is it related to the environment I am using?

Here is the error info from log file:
image

commented

I believe I have seen this before and it was related to a newer nextflow version that is incompatible with this workflow for whatever reason.

Could you try to run

export NXF_VER=22.04.5

before nextflow run ...?

If this works, I'll update the README accordingly.

commented

Sorry for my delayed response. It works. Thank you very much!

But I met a different problem after I fix this. The apptainer/Singularity shows they lack the permission of namespace. I have installed it with suid and run it as root. I've searched for relevant information , but it is very limited and I can't resolve the issue.