Methylation Classifiers hanging on Promethion install of Robin 1.0.3

[ggrimes]

I am having issues runing robin (v1.0.3) on my Promethion desktop machine.

The Robin application hangs, (stop on processing step on 14 Bam), on following classifier steps

Sturgeon, NanoDX and PanNanoDX classification.

Here is the command I use for running robin

robin \
--port 54321 \
--threads 64 \
-r /data/references/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
-b src/robin/resources/panel_11092024_5kb_pad.bed \
--log-file robin-promethion-0.1.3.log   \
--log-level DEBUG  \
-w ../ROBIN_test_set_A/test_data_set/ robin2-res

The output log file is here

robin-promethion-0.1.3.log

and here is the partially completed report.

NA12878_05_NB4_06_22Rv1_07_run_report-2.pdf

I have exported the conda environment used here if it is any help.

robin-promethion-0.1.3.env.yml.txt

Is there anything I can try to get those steps running.

Thanks,

Graeme

[mattloose]

I shall have a look for you - could you run again with the extra option --showerrors in the meantime and share that log here.

Thanks

[mattloose]

Just to check the obvious... when you installed, you did run:

git clone https://github.com/LooseLab/robin/
cd ROBIN
git lfs install
git lfs pull
git submodule update --init --recursive

Very specifically the git lfs pull command?

You are getting an error accessing the models which might have been triggered by this.

[ggrimes]

I believe so , but will double check this afternoon when I re-run using the show errors option

From: mattloose @.> Date: Thursday, 7 November 2024 at 10:09 To: LooseLab/ROBIN @.> Cc: Graeme Grimes @.>, Author @.> Subject: Re: [LooseLab/ROBIN] Methylation Classifiers hanging on Promethion install of Robin 1.0.3 (Issue #69) This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe.

Just to check the obvious... when you installed, you did run:

git clone https://github.com/LooseLab/robin/

cd ROBIN

git lfs install

git lfs pull

git submodule update --init --recursive

Very specifically the git lfs pull command?

You are getting an error accessing the models which might have been triggered by this.

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[ggrimes]

Thank you, it was the git-lfs that wasn't working, I reinstalled it and now the classfiers work.

Thanks again for your help and patience in getting this working.

[mattloose]

No problem - thank you for using it! I will add a check when ROBIN runs to make sure that git-lfs has been run and is working correctly as well as giving a more informative error message.