ERROR: Index 1 out of bounds for length 1

[berath]

Please report

• version of RNA-Bloom with java -jar RNA-Bloom.jar -version
• version of java with java -version
  openjdk version "11.0.13" 2021-10-19
  OpenJDK Runtime Environment JBR-11.0.13.7-1751.21-jcef (build 11.0.13+7-b1751.21)
  OpenJDK 64-Bit Server VM JBR-11.0.13.7-1751.21-jcef (build 11.0.13+7-b1751.21, mixed mode)
• exact command used to run RNA-Bloom
  java -Xmx100g -jar rnabloom-v2.0.1.jar -t 32 -long barcode05_trimmed.fastq.gz barcode06_trimmed.fastq.gz barcode07_trimmed.fastq.gz barcode08_trimmed.fastq.gz -o sticcoassembled

Hi, I got below error message during de novo assembly of ONT cDNA reads.

Stage 3: Assemble long reads for "rnabloom"
Overlapping sequences...
ERROR: Index 1 out of bounds for length 1
java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
at rnabloom.io.PafRecord.update(PafRecord.java:32)
at rnabloom.io.ExtendedPafRecord.update(ExtendedPafRecord.java:32)
at rnabloom.io.PafReader.next(PafReader.java:63)
at rnabloom.olc.Layout.extractUniqueFromOverlaps(Layout.java:1660)
at rnabloom.olc.OverlapLayoutConsensus.overlapWithMinimapAndExtractUnique(OverlapLayoutConsensus.java:156)
at rnabloom.olc.OverlapLayoutConsensus.uniqueOLC(OverlapLayoutConsensus.java:1159)
at rnabloom.RNABloom.assembleUnclusteredLongReads(RNABloom.java:3314)
at rnabloom.RNABloom.main(RNABloom.java:7430)

Any idea on the cause and a possible solution?
Thanks,
Berat

[kmnip]

Hi,
I think the minimap2 overlap command failed and its PAF output is truncated.
Can you please check the *.log files?