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PositionalAssembler - Fatal error #55

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warthmann opened this issue Feb 6, 2017 · 1 comment
Closed

PositionalAssembler - Fatal error #55

warthmann opened this issue Feb 6, 2017 · 1 comment

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@warthmann
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Hello,
I have encountered another issue and the error message tells me to raise an issue. I have again used and adapted somatic.sh to compare 2 bam files.

best
Norman

INFO    2017-02-06 12:45:02     SplitReadRealigner      Merging split read alignments for /g/data1/xe2/genomics-vm/norman/Peter_WGS_brachypodium/gridss_runs/./WT_2_S13.bam.gridss.working/gridss.tmp.splitreads.WT_2_S13.bam.sv.bam
INFO    2017-02-06 12:45:26     ExternalProcessFastqAligner     Invoking external aligner
INFO    2017-02-06 12:45:26     ExternalProcessFastqAligner     bwa mem -t 16 /home/norman/Analysis/reference_genomes/brachpodium/Bdistachyon_314_v3.0.softmasked_and_chloropl.fa /g/data1/xe2/genomics-vm/norman/Peter_WGS_brachypodium/gridss_runs/./M150_2_S14.bam.gridss.working/M150_2_S14.bam.realign.1.fq
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2306 sequences (150748 bp)...
[M::mem_process_seqs] Processed 2306 reads in 0.128 CPU sec, 0.076 real sec
[main] Version: 0.7.13-r1134-dirty
[main] CMD: bwa mem -t 16 /home/norman/Analysis/reference_genomes/brachpodium/Bdistachyon_314_v3.0.softmasked_and_chloropl.fa /g/data1/xe2/genomics-vm/norman/Peter_WGS_brachypodium/gridss_runs/./M150_2_S14.bam.gridss.working/M150_2_S14.bam.realign.1.fq
[main] Real time: 0.327 sec; CPU: 0.488 sec
INFO    2017-02-06 12:45:30     SplitReadRealigner      Merging split read alignments for /g/data1/xe2/genomics-vm/norman/Peter_WGS_brachypodium/gridss_runs/./M150_2_S14.bam.gridss.working/gridss.tmp.splitreads.M150_2_S14.bam.sv.bam
INFO    2017-02-06 12:49:41     SAMFileUtil     /g/data1/xe2/genomics-vm/norman/Peter_WGS_brachypodium/gridss_runs/./WT_2_S13.bam.gridss.working/gridss.tmp.SplitReadAligner.sa.gridss.tmp.splitreads.WT_2_S13.bam.sv.bam already sorted by queryname
INFO    2017-02-06 12:50:40     SAMFileUtil     /g/data1/xe2/genomics-vm/norman/Peter_WGS_brachypodium/gridss_runs/./M150_2_S14.bam.gridss.working/gridss.tmp.SplitReadAligner.sa.gridss.tmp.splitreads.M150_2_S14.bam.sv.bam already sorted by queryname
[Mon Feb 06 12:54:43 AEDT 2017] gridss.SoftClipsToSplitReads done. Elapsed time: 17.13 minutes.
Runtime.totalMemory()=13392412672
INFO    2017-02-06 12:54:43     SAMFileUtil     Sorting ./WT_2_S13.bam.gridss.working/gridss.tmp.splitreads.WT_2_S13.bam.sv.bam
[Mon Feb 06 12:56:17 AEDT 2017] gridss.SoftClipsToSplitReads done. Elapsed time: 18.42 minutes.
Runtime.totalMemory()=12895387648
INFO    2017-02-06 12:56:17     SAMFileUtil     Sorting ./M150_2_S14.bam.gridss.working/gridss.tmp.splitreads.M150_2_S14.bam.sv.bam
INFO    2017-02-06 13:07:35     CallVariants    Evidence extraction complete.
INFO    2017-02-06 13:07:35     AssemblyEvidenceSource  Starting assembly on interval Bd1:1-1000000
INFO    2017-02-06 13:07:35     AssemblyEvidenceSource  Starting assembly on interval Bd1:1000001-2000000
INFO    2017-02-06 13:07:35     AssemblyEvidenceSource  Starting assembly on interval Bd1:2000001-3000000
INFO    2017-02-06 13:07:35     AssemblyEvidenceSource  Starting assembly on interval Bd1:3000001-4000000
INFO    2017-02-06 13:07:35     AssemblyEvidenceSource  Starting assembly on interval Bd1:4000001-5000000
INFO    2017-02-06 13:07:35     AssemblyEvidenceSource  Starting assembly on interval Bd1:5000001-6000000
INFO    2017-02-06 13:07:35     AssemblyEvidenceSource  Starting assembly on interval Bd1:6000001-7000000
INFO    2017-02-06 13:07:35     AssemblyEvidenceSource  Starting assembly on interval Bd1:7000001-8000000
INFO    2017-02-06 13:07:35     AssemblyEvidenceSource  Starting assembly on interval Bd1:8000001-9000000
INFO    2017-02-06 13:07:35     AssemblyEvidenceSource  Starting assembly on interval Bd1:9000001-10000000
INFO    2017-02-06 13:07:35     AssemblyEvidenceSource  Starting assembly on interval Bd1:10000001-11000000
INFO    2017-02-06 13:07:36     AssemblyEvidenceSource  Starting assembly on interval Bd1:11000001-12000000
INFO    2017-02-06 13:07:36     AssemblyEvidenceSource  Starting assembly on interval Bd1:12000001-13000000
INFO    2017-02-06 13:07:36     AssemblyEvidenceSource  Starting assembly on interval Bd1:13000001-14000000
INFO    2017-02-06 13:07:36     AssemblyEvidenceSource  Starting assembly on interval Bd1:14000001-15000000
INFO    2017-02-06 13:07:36     AssemblyEvidenceSource  Starting assembly on interval Bd1:15000001-16000000
ERROR   2017-02-06 13:07:43     PositionalAssembler     Fatal error assembling Bd1. This should not happen. Please raise an issue at https://github.com/PapenfussLab/gridss/issues. Attempting recovery by resuming assembly at Bd1:3081384
java.lang.AssertionError
        at au.edu.wehi.idsv.debruijn.positional.PathSimplificationIterator.advance(PathSimplificationIterator.java:217)
        at au.edu.wehi.idsv.debruijn.positional.PathSimplificationIterator.ensureBuffer(PathSimplificationIterator.java:171)
        at au.edu.wehi.idsv.debruijn.positional.PathSimplificationIterator.hasNext(PathSimplificationIterator.java:147)
        at com.google.common.collect.Iterators$PeekingImpl.hasNext(Iterators.java:1171)
        at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.advanceUnderlying(NonReferenceContigAssembler.java:328)
        at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.advanceUnderlying(NonReferenceContigAssembler.java:291)
        at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.ensureCalledContig(NonReferenceContigAssembler.java:220)
        at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.hasNext(NonReferenceContigAssembler.java:163)
        at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.flushIfRequired(PositionalAssembler.java:62)
        at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.ensureAssembler(PositionalAssembler.java:94)
        at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.ensureAssembler(PositionalAssembler.java:75)
        at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.hasNext(PositionalAssembler.java:53)
        at au.edu.wehi.idsv.AssemblyEvidenceSource.assembleChunk(AssemblyEvidenceSource.java:242)
        at au.edu.wehi.idsv.AssemblyEvidenceSource.assembleChunk(AssemblyEvidenceSource.java:208)
        at au.edu.wehi.idsv.AssemblyEvidenceSource.lambda$4(AssemblyEvidenceSource.java:92)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
ERROR   2017-02-06 13:07:43     AssemblyEvidenceSource  Error assembling Bd1:3000001-4000000
au.edu.wehi.idsv.SanityCheckFailureException: Subnode [3077898-3077996][3077898-3078095]R 390w CATACACTGATGCAGTATCAGGCC CTCAATAAGATCATGCTAGCAATTA (26)  reachable from score=536870911 pathlength=16 [3077882-3077980][3077882-3077980]R 240w ATGACCTGTGAGTACATCATACACT GATGCAGTATCAGGC (16)  not memoized. [441 nodes memoized, 60 in frontier, maxVisitedEndPosition=3077993, nextPosition=3078184]
        at au.edu.wehi.idsv.debruijn.positional.MemoizedContigCaller.visit(MemoizedContigCaller.java:212)
        at au.edu.wehi.idsv.debruijn.positional.MemoizedContigCaller.advanceFrontier(MemoizedContigCaller.java:190)
        at au.edu.wehi.idsv.debruijn.positional.MemoizedContigCaller.frontierPath(MemoizedContigCaller.java:374)
        at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.removeMisassembledPartialContig(NonReferenceContigAssembler.java:267)
        at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.ensureCalledContig(NonReferenceContigAssembler.java:223)
        at au.edu.wehi.idsv.debruijn.positional.NonReferenceContigAssembler.hasNext(NonReferenceContigAssembler.java:163)
        at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.flushIfRequired(PositionalAssembler.java:62)
        at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.ensureAssembler(PositionalAssembler.java:94)
        at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.ensureAssembler(PositionalAssembler.java:90)
        at au.edu.wehi.idsv.debruijn.positional.PositionalAssembler.hasNext(PositionalAssembler.java:53)
        at au.edu.wehi.idsv.AssemblyEvidenceSource.assembleChunk(AssemblyEvidenceSource.java:242)
        at au.edu.wehi.idsv.AssemblyEvidenceSource.assembleChunk(AssemblyEvidenceSource.java:208)
        at au.edu.wehi.idsv.AssemblyEvidenceSource.lambda$4(AssemblyEvidenceSource.java:92)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
norman@gvm:~/Analysis/datasets/Peter_WGS_brachypodium/gridss_runs$
d-cameron added a commit that referenced this issue Feb 6, 2017
@d-cameron
Corrected misassembly bounds to prevent removal of contigs truncated …
b32432b 
…to empty #55

Exposing sanitycheck.memoization.alloperations to allow for quick memoization sanity check for bug reporting purposes
@d-cameron
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I've pushed up version 1.2.1 which should fix your fatal error. It turns out my error recovery only recovered from some errors.

https://github.com/PapenfussLab/gridss/releases/tag/v1.2.1

I'm not entirely certain 1.2.1 completely fixes the root cause so you might still get a (non-fatal) version of the same error. If you do, it would be helpful if you could rerun it with java -ea -Dsanitycheck.memoization=true (using a different WORKING_DIR so it actually reruns the offending assembly) and cut/paste the stack trace of any java.lang.AssertionError in the log file (they won't be at the end since the error recovery should be working now) so I can identify the code that causes the issue.

Regardless, it shouldn't meaningfully effect your results as the issue (if it still exists), is with the removal of known misassembled contigs which get thrown out anyway).

Thanks for the report.

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@d-cameron @warthmann