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Form of .intervals

I'm running GenomicsDBImport to combine my 100 samples and my command line is

gatk --java-options "-Xmx10240m -Djava.io.tmpdir=./" GenomicsDBImport --genomicsdb-workspace-path my_database -L 1.intervals --sample-name-map map2

The error message is
A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "Contig:scaffold1 start:0 end:416820" is not valid for this input.

So I want to know what the intervals document should be like.

My reference only has thousands of sacffolds in it .
So the .intervals I used is
Contig:scaffold1 start:0 end:416820
Contig:scaffold2 start:0 end:868635
Contig:scaffold3 start:0 end:530760
Contig:scaffold4 start:0 end:723991
Contig:scaffold7 start:0 end:431581
Contig:scaffold8 start:0 end:94119
Contig:scaffold9 start:0 end:1039220
Contig:scaffold10 end:start:0 1039754

Is there anything wrong? How to correct it?

Thanks a lot!


Best Answer


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