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PapenfussLab / gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite
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Blacklist errror #642

Closed uretaj closed 1 year ago

uretaj commented 1 year ago

Hi,

I'm using hs37d5 as my reference and ENCFF001TDO.bed that I downloaded from here (https://github.com/PapenfussLab/gridss/tree/master/example) but I'm getting this error IntervalBed Error loading record 268 of ENCFF001TDO.bed: 'M' not found in reference genome. Exception in thread "main" java.lang.IllegalArgumentException: Error loading record 268 of ENCFF001TDO.bed: 'M' not found in reference genome.

d-cameron commented 1 year ago

That will be a chromosome naming convention difference between your reference and the blacklist - specifically that error is the mitochondrial chromosome name. Make sure the .bed and .fa reference you use have matching chromosome names.

On Thu, 5 Oct 2023, 5:41 pm Jennifer Ureta, @.***> wrote:

Hi,

I'm using hs37d5 as my reference and ENCFF001TDO.bed that I downloaded from here (https://github.com/PapenfussLab/gridss/tree/master/example) but I'm getting this error IntervalBed Error loading record 268 of ENCFF001TDO.bed: 'M' not found in reference genome. Exception in thread "main" java.lang.IllegalArgumentException: Error loading record 268 of ENCFF001TDO.bed: 'M' not found in reference genome.

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