Error with gridss_somatic_filter

[Teezi]

Hi,

Any one encounter the following errors when running with gridss_somatic_filter. Any insights will be much appreciated!!

Error in .width_as_unnamed_integer(width, msg = "an end that is greater or equal to its start minus one") : 
  each range must have an end that is greater or equal to its start minus
  one
Calls: gridss_breakend_filter ... .new_IRanges_from_start_end -> .width_as_unnamed_integer
Execution halted

[Mousiekin]

I had this error yesterday when I was playing with GRIDSS for the first time. I found that hmf_dna_pipeline_resources.38_v5.34.tar.gz (sgl_pon.38.bed) was quite different to the two preceding versions 32 and 33 (which are identical to each other). These older versions work well.

[Teezi]

I had this error yesterday when I was playing with GRIDSS for the first time. I found that hmf_dna_pipeline_resources.38_v5.34.tar.gz (sgl_pon.38.bed) was quite different to the two preceding versions 32 and 33 (which are identical to each other). These older versions work well.

Thanks, this is very helpful. Another question, which blacklist do you use to run gridss? i.e., ENCFF356LFX.bed file (for hg38) or gridss_blacklist.38.bed.gz (in the hmf_dna_pipeline_resources.38_v5.33/sv)?