Hi!

I want to pull out Tcell receptors from Tcell WGS data using mitcr and the following command

java -Xmx50g -jar mitcr-1.0.3.jar -pset flex -gene TRB sample.r1.fq.gz sample_r1.txt

i get the following java error:

Initialisation: progress unknown
Individual sequence analysis & clone generation: 0%
Error occurred in the analysis pipeline.

java.lang.RuntimeException: java.lang.ArrayIndexOutOfBoundsException: 1
        at cc.redberry.pipe.blocks.ParallelProcessor.join(ParallelProcessor.java:225)
        at com.milaboratory.mitcr.pipeline.FullPipeline.run(FullPipeline.java:167)
        at com.milaboratory.mitcr.cli.Main.main(Main.java:405)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 1
        at com.milaboratory.util.Bit2Array.get(Bit2Array.java:49)
        at com.milaboratory.core.sequence.nucleotide.NucleotideSequence.codeAt(NucleotideSequence.java:66)
        at com.milaboratory.mitcr.qualitystrategy.IlluminaQualityInterpretationStrategy$1$1.codeAt(IlluminaQualityInterpretationStrategy.java:90)
        at com.milaboratory.mitcr.vdjmapping.trivial.TrivialSegmentMapper.map(TrivialSegmentMapper.java:169)
        at com.milaboratory.mitcr.vdjmapping.trivial.TrivialSegmentMapper.map(TrivialSegmentMapper.java:42)
        at com.milaboratory.mitcr.vdjmapping.VJSegmentsMapperAdapter.map(VJSegmentsMapperAdapter.java:44)
        at com.milaboratory.mitcr.vdjmapping.VDJSegmentsMapper.map(VDJSegmentsMapper.java:74)
        at com.milaboratory.mitcr.cdrextraction.CDR3Extractor._process(CDR3Extractor.java:66)
        at com.milaboratory.mitcr.cdrextraction.CDR3Extractor._process(CDR3Extractor.java:59)
        at com.milaboratory.mitcr.cdrextraction.CDR3ExtractorFromSRead.process(CDR3ExtractorFromSRead.java:71)
        at com.milaboratory.mitcr.cdrextraction.CDR3ExtractorFromSRead.process(CDR3ExtractorFromSRead.java:37)
        at cc.redberry.pipe.blocks.ParallelProcessor$Worker.run(ParallelProcessor.java:305)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:748)

Any ideas?

Thanks in advance!