Trimmomatic String index error

[marlivlok]

I've been using Trimmomatic 0.30 with great success, but today I got an error message for 8 of my 9 libraries and I have no idea how to fix it.

Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: 0
at java.lang.String.charAt(String.java:658)
at org.usadellab.trimmomatic.fastq.FastqParser.parseOne(FastqParser.java:47)
at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:93)
at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:254)
at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:347)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:23)

Any help would be much appreciated.

[GenoMax]

Do you possibly have a blank line somewhere in your fastq files? You could try and validate them: https://github.com/statgen/fastQValidator

[marlivlok]

Awesome, thanks. Yeah for some reason my GBS sequence removal script added blank lines to some of the reverse read files. All running smoothly now