alhafidzhamdan
commented
11 months ago Hi @jackieduckie , any chance you've got this solved? I'm encountering the exact same issue. My sample is aligned using Isaac aligner.
Open jackieduckie opened 1 year ago
alhafidzhamdan
commented
11 months ago Hi @jackieduckie , any chance you've got this solved? I'm encountering the exact same issue. My sample is aligned using Isaac aligner.
Hi Daniel,
GRIDSS failed on one sample with many PositionalAssembler errors. The error message below is one of them. GRIDSS couldn't produce a VCF on this sample.
5659 │ ERROR 2022-10-03 06:10:10 PositionalAssembler Error assembling 1. Please raise an issue at https://github.c │ om/PapenfussLab/gridss/issues. If your data can be shared publicly, please also include a minimal data set fo │ r reproducing the problem by attaching /data/output/gridss_minimal_reproduction_data_for_error_1.zip.. Attemp │ ting recovery by resuming assembly at 1:25099882 5660 │ java.lang.RuntimeException: Sanity check failure: found path with no support (1:24992975) 5661 │ at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.callContig(NonReferenceContigAssemble │ r.java:670) 5662 │ at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.flushCallsOutsideRetainWindow(NonRefe │ renceContigAssembler.java:230) 5663 │ at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.ensureCalledContig(NonReferenceContig │ Assembler.java:260) 5664 │ at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.hasNext(NonReferenceContigAssembler.j │ ava:194) 5665 │ at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.flushIfRequired(PositionalAssembler.java:79) 5666 │ at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.ensureAssembler(PositionalAssembler.java:292) 5667 │ at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.ensureAssembler(PositionalAssembler.java:106) 5668 │ at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.hasNext(PositionalAssembler.java:64) 5669 │ at au.edu.wehi.idsv.AssemblyEvidenceSource.assembleChunk(AssemblyEvidenceSource.java:240) 5670 │ at au.edu.wehi.idsv.AssemblyEvidenceSource.assembleChunk(AssemblyEvidenceSource.java:197) 5671 │ at au.edu.wehi.idsv.AssemblyEvidenceSource.lambda$assembleBreakends$2(AssemblyEvidenceSource.java:100) 5672 │ at java.util.concurrent.FutureTask.run(FutureTask.java:266) 5673 │ at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) 5674 │ at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) 5675 │ at java.lang.Thread.run(Thread.java:748)
The reproduction zip file of this error is attached. gridss_minimal_reproduction_data_for_error_1.zip