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GenomicsAotearoa / Pangenome-Graphs-Workshop

This repository contains material to construct pangenome graphs for a small bacteria dataset detailing every step in the Nesi environment.
https://genomicsaotearoa.github.io/Pangenome-Graphs-Workshop/
GNU General Public License v2.0
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BUS error ? #2

Closed DininduSenanayake closed 1 year ago

DininduSenanayake commented 1 year ago

@JSBoey Can you confirm which singularity block triggered the BUS error which led the Jupyter session to crash ?

JSBoey commented 1 year ago

@DininduSenanayake It was the one linked here that points here. The singularity pull produced the error.

DininduSenanayake commented 1 year ago

Thanks @JSBoey . Right, given the step immediately after that is to run a slurm job for this, I don't see the reason for running it interactively anyway. I believe that was written to describe the steps involved in executing the application,we can it down to a demo block and remove the bash header,etc.

JSBoey commented 1 year ago

I agree, there are a few code blocks like that which are amenable to be demo blocks (e.g. here). I'll close this thread and open a new issue to make sure I tick the demo blocks off as I go.