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Cellranger-arc

Hi,

Running cellranger-arc on some multiome datasets and I was wondering if anyone had experience with approximate processing time as it seems to be taking more than 24 hours for a single dataset. I know of course its slightly different case by case, but was just curious about the experience of others. Thanks.

cellranger cellranger-arc scrna-seq 10x
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written by LacquerHed • LacquerHed

How many cores are you using? Is the data from NovaSeq? It does take a long time for the processing to complete. So this sounds about normal.

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written by GenoMax GenoMax

This data is from NovaSeq and I am using only one core (long, 40 task), could probably have split it amongst several but followed the instructions on 10x site as to easiest implementation of cellranger-arc count. My concern is that this node has a 48 hour job timelimit so hoping it doesn't surpass that.

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written by LacquerHed • LacquerHed

I hope you meant 1 node with 40 cores because with 1 core this job will not complete in 48 h.

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written by GenoMax GenoMax

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