ChIPQC BiocParallel errors

Question

[Chevy Xu]

Hi, I try to use ChIPQC to assess my ChIP-seq quality while meet an error, I stuck in ChIPQC() step and something wrong just happened:

could you help me figure this out?

[Chevy Xu]

library("BiocParallel") 
register(DoparParam())
registered() 
bpparam("SerialParam")

Problem solved. Thanks for jared.andrews07's help.

[GenoMax]

Please use instructions included in this guide: How to add images to a Biostars post

It would be best to translate and post error messages in English since that is the primary language used on this forum.

Answer 1

[jared.andrews07]

Can't see the error, but I've also run into many of them with the ChIPQC/DiffBind family of packages related to BiocParallel. They just don't seem to handle the parallelization well (or consistently). After loading the BiocParallel package, try setting it to run in serial, which usually fixes the issue for me:

library("BiocParallel")
register(SerialParam)

You can also try the Bioconductor forum, as the package's authors (usually Tom Carroll) answer pretty quickly there.

Answer 2

[Rory Stark]

I have submitted a fix for ChIPQC to makes the use of BiocParallel more explicit, checking for installed backends and reporting information on how ChIPQC will be executed.

This fix will be in effect from version ChIPQC_1.32.1 in the main Release branch. There are related fixes in DiffBind_3.6.2 so these should be updated together.