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java.lang.IndexOutOfBoundsException
I am running Kourami on several samples and ran into the following error with just one sample:
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.rangeCheck(ArrayList.java:659)
at java.util.ArrayList.get(ArrayList.java:435)
at HLAGraph.pathAlign(HLAGraph.java:1296)
at HLAGraph.pathAlign(HLAGraph.java:1249)
at HLAGraph.processBubbles(HLAGraph.java:1043)
at HLAGraph.countBubblesAndMerge(HLAGraph.java:890)
at HLA.countBubblesAndMerge(HLA.java:357)
at HLA.main(HLA.java:585)
This is the only sample out of 39 with this issue. here is my script:
bwa mem -t 2 kourami/db/All_FINAL_with_Decoy.fa.gz sample.hla.1.fastq sample.hla.2.fastq | samtools view -Sb - > mysample.kourami.bam
java -jar /opt/kourami-0.9.6/target/Kourami.jar -d kourami/db/ -o mysample mysample.kourami.bam