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PapenfussLab / gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite
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error with simple-event-annotation.R script #656

Open shaghayeghsoudi opened 8 months ago

shaghayeghsoudi commented 8 months ago

Hello developers, I started running gridss for our sarcoma cell lines. I had called them and now trying to find the Sv the and SV length. The manual suggests I can use simple-event-annotation.R .

When I run the script I keep getting this error message:

Warning message:
In .breakpointRanges(x, ...) :
  Removing 4 unpaired breakend variants. Use inferMissingBreakends=TRUE to recover with inferred partner breakends. Missing breakends:  gridss112bf_557o, gridss112bf_561o, gridss112bf_562o, gridss276bf_155o
Error in .subassign_columns(x, nsbs, value) : 
  provided 68 variables to replace 67 variables
Calls: [<- ... [<- -> mergeROWS -> mergeROWS -> .subassign_columns
In addition: Warning message:
info fields with no header: SVLEN 
Execution halted

Can you please help to resolve the error? Thank you very much

HuangYihang1222 commented 5 months ago

Have you solved the problem now? The same thing happened to me

HuangYihang1222 commented 5 months ago

maybe this is helpful, https://github.com/PapenfussLab/gridss/issues/561#issuecomment-1049927318