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Hello, I am trying to demultiplex some samples with 14 bp Barcode + 14 bp UMI. I have trimmed the reads to 28 bp and verified they are all at that length. When I run BRB-seqTools I get the following error:
java -jar ~/tools/BRBseqTools-1.6.1.jar Demultiplex -r1 R1.trimmed.fastq.gz -r2 R2.fastq.gz -c barcodes_brbtools.txt -o ./BRB-seq -UMI 14
BRBSeqTools 1.6.1 [Demultiplex]
No barcode pattern specified (with '-p' option). Barcode pattern is set as default: 'BU'
Config: Barcode Pattern = BU
Config: Nb Allowed Diff = 1
Config: B1 contains 18 barcodes: [ ACAATAGGTGGTCC AACCATCGCATCCA CAGTCTAGTGCGCA CCGCAAGAGGTTGG TAACACCTCCAACG CAGACATGATAGAG AACAACCGAAGTAA AACTAGTATCCGGA ACGCAGCGAGCAGA TACGTTATTCCGAA AACAGGATAACTCC ACTCAGGCACCTCC ACGAGCAGATGCAG TTCAATCTCCTTAG CTCGGTTCGAATGC TACACTATAGCTAG CAAGTATAAGGAAC CTGATATGCAGCGA ]
Config: B1 length [#nucleotides] = 14
Analyzing barcode Pattern...
According to barcode pattern, reads of R1 FastQ file should contain 28 characters.
Starting demultiplexing...
Exception in thread "main" java.lang.StringIndexOutOfBoundsException: Range [1, -1) out of bounds for length 31
at java.base/jdk.internal.util.Preconditions$1.apply(Preconditions.java:55)
at java.base/jdk.internal.util.Preconditions$1.apply(Preconditions.java:52)
at java.base/jdk.internal.util.Preconditions$4.apply(Preconditions.java:213)
at java.base/jdk.internal.util.Preconditions$4.apply(Preconditions.java:210)
at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:98)
at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckFromToIndex(Preconditions.java:112)
at java.base/jdk.internal.util.Preconditions.checkFromToIndex(Preconditions.java:349)
at java.base/java.lang.String.checkBoundsBeginEnd(String.java:4865)
at java.base/java.lang.String.substring(String.java:2834)
at tools.Utils.nextDataRead(Utils.java:181)
at DemultiplexingManager.demultiplex(DemultiplexingManager.java:39)
at BRBseqTools.main(BRBseqTools.java:87)
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