Question: On executing SnpEff n a Galaxy cloud instance we have the error: All frames are zero
gravatar for msprindzhuk
21 months ago by
msprindzhuk50 wrote:

On executing SnpEff we have the following error:

WARNING: All frames are zero! This seems rather odd, please check that 'frame' information in your 'genes' file is accurate. java.lang.RuntimeException: Most Exons do not have sequences! at ca.mcgill.mcb.pcingola.snpEffect.factory.SnpEffPredictorFactoryGff.create( at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdBuild.createSnpEffPredictor( at

How to fix that? Thank you.

snpeff • 540 views
ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson25k • written 21 months ago by msprindzhuk50
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k wrote:


This appears to be a data problem from the error message. Check the content of the reference annotation and correct it to work with this tool.

I also suggest checking the input BAM dataset to ensure expected mapping rates and checking that the reference annotation is a match for the target reference genome. You could also try visualizing (at UCSC, IGV, etc) for a few target genes to help determine what the exact issue is.

Does this mean that the configuration issues for this tool are now resolved? If so, please post back with a comment on this thread and we can close it out. If you want to share what the issue was and how you resolved it, that can be helpful information for others.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson25k
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