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AstraZeneca-NGS / VarDictJava

VarDict Java port
MIT License
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No line found error in the java version, works in the perl version #359

Closed rglusic closed 2 years ago

rglusic commented 2 years ago

Hello, one of the researchers at my institution has been running into an issue when trying to run VarDict. The below error is only present within the Java version of VarDict and does not error out within the perl version. We have tried multiple fasta files and the issue still remains. The problem occurs before teststrandbias.R runs.

VarDict -G human_g1k_v37.fasta -N 1seracare0p1-1hyb68-rep1 -f 0.01 -b 1seracare0p1-1hyb68-rep1_bwa.TP53.sort.bam -c 1 -S 2 -E 3 TP53_Multiplicom.BED -U | teststrandbias.R | var2vcf_valid.pl -N 7CYCOLOEZ100_tumor -E -f 0.01 > 7CYCOLOEZ100_tumor.vcf
Critical exception occurs on region: 17:7572834-7573032, program will be stopped.
java.util.NoSuchElementException: No line found
    at java.util.Scanner.nextLine(Scanner.java:1540)
    at htsjdk.samtools.reference.FastaSequenceIndex.parseIndexFile(FastaSequenceIndex.java:161)
    at htsjdk.samtools.reference.FastaSequenceIndex.<init>(FastaSequenceIndex.java:72)
    at htsjdk.samtools.reference.IndexedFastaSequenceFile.<init>(IndexedFastaSequenceFile.java:71)
    at com.astrazeneca.vardict.data.ReferenceResource.lambda$fetchFasta$0(ReferenceResource.java:34)
    at java.util.HashMap.computeIfAbsent(HashMap.java:1127)
    at com.astrazeneca.vardict.data.ReferenceResource.fetchFasta(ReferenceResource.java:30)
    at com.astrazeneca.vardict.data.ReferenceResource.retrieveSubSeq(ReferenceResource.java:52)
    at com.astrazeneca.vardict.data.ReferenceResource.getReference(ReferenceResource.java:94)
    at com.astrazeneca.vardict.data.ReferenceResource.getReference(ReferenceResource.java:74)
    at com.astrazeneca.vardict.modes.AbstractMode.tryToGetReference(AbstractMode.java:153)
    at com.astrazeneca.vardict.modes.SimpleMode.processBamInPipeline(SimpleMode.java:98)
    at com.astrazeneca.vardict.modes.SimpleMode.notParallel(SimpleMode.java:45)
    at com.astrazeneca.vardict.VarDictLauncher.start(VarDictLauncher.java:65)
    at com.astrazeneca.vardict.Main.main(Main.java:15)
rglusic commented 2 years ago

We discovered that the issue was a corrupted set of .fasta files and their indexes