Hi,
Is there support for running this tool on RNA seq datasets. I tried to run it but it failed. I guess support would require input of a gtf/gff file of intron/exon boundaries so that these will not be interpreted as structural variants. Maybe this tool could be made to work as is, but it not clear to me how. I was hoping to just ignore the intron/exon SVs and look at the rest of the variants. Our interest is looking at potential Ribozymes modifications which may appear like SVs. Maybe someone knows of a similar tool that would work?
I get many errors like this:
java.lang.RuntimeException: Sanity check failure: found path with no support (chr1:34275184)
and finally this:
Error assembling chr1. Please raise an issue at https://github.com/PapenfussLab/gridss/issues. If your data can be shared publicly, please also include a minimal data set for reproducing the problem by attaching ./gridss_minimal_reproduction_data_for_error_1.zip.
java.lang.RuntimeException: Sanity check failure: found path with no support (chr1:34275184)
at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.callContig(NonReferenceContigAssembler.java:673)
at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.flushCallsOutsideRetainWindow(NonReferenceContigAssembler.java:233)
at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.ensureCalledContig(NonReferenceContigAssembler.java:263)
at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.hasNext(NonReferenceContigAssembler.java:197)
at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.flushIfRequired(PositionalAssembler.java:77)
at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.ensureAssembler(PositionalAssembler.java:298)
at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.ensureAssembler(PositionalAssembler.java:107)
at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.hasNext(PositionalAssembler.java:62)
at au.edu.wehi.idsv.AssemblyEvidenceSource.assembleChunk(AssemblyEvidenceSource.java:246)
at au.edu.wehi.idsv.AssemblyEvidenceSource.assembleChunk(AssemblyEvidenceSource.java:199)
at au.edu.wehi.idsv.AssemblyEvidenceSource.lambda$assembleBreakends$2(AssemblyEvidenceSource.java:102)
d-cameron
commented
6 months ago
Hi, Is there support for running this tool on RNA seq datasets. I tried to run it but it failed. I guess support would require input of a gtf/gff file of intron/exon boundaries so that these will not be interpreted as structural variants. Maybe this tool could be made to work as is, but it not clear to me how. I was hoping to just ignore the intron/exon SVs and look at the rest of the variants. Our interest is looking at potential Ribozymes modifications which may appear like SVs. Maybe someone knows of a similar tool that would work?
I get many errors like this: java.lang.RuntimeException: Sanity check failure: found path with no support (chr1:34275184)
and finally this:
Error assembling chr1. Please raise an issue at https://github.com/PapenfussLab/gridss/issues. If your data can be shared publicly, please also include a minimal data set for reproducing the problem by attaching ./gridss_minimal_reproduction_data_for_error_1.zip. java.lang.RuntimeException: Sanity check failure: found path with no support (chr1:34275184) at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.callContig(NonReferenceContigAssembler.java:673) at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.flushCallsOutsideRetainWindow(NonReferenceContigAssembler.java:233) at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.ensureCalledContig(NonReferenceContigAssembler.java:263) at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.hasNext(NonReferenceContigAssembler.java:197) at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.flushIfRequired(PositionalAssembler.java:77) at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.ensureAssembler(PositionalAssembler.java:298) at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.ensureAssembler(PositionalAssembler.java:107) at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.hasNext(PositionalAssembler.java:62) at au.edu.wehi.idsv.AssemblyEvidenceSource.assembleChunk(AssemblyEvidenceSource.java:246) at au.edu.wehi.idsv.AssemblyEvidenceSource.assembleChunk(AssemblyEvidenceSource.java:199) at au.edu.wehi.idsv.AssemblyEvidenceSource.lambda$assembleBreakends$2(AssemblyEvidenceSource.java:102)