Hi! I'm trying to run trimmomatic, and running into the following error:
My input:
And the output:
How do I fix this????
Thanks in advance!
My input:
java -classpath $BIN/trimmomatic/Trimmomatic-0.20/trimmomatic-0.20.jar org.usadellab.trimmomatic.TrimmomaticPE -phred33 9_1.fastq 9_2.fastq 9_1.fastq_PAIRED_1 9_1.fastq_UNPAIRED_1 9_2.fastq_PAIRED_2 9_2.fastq_UNPAIRED_2 ILLUMINACLIP:contaminants.fa:2:40:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:5:15 MINLEN:36
Exception in thread "main" java.lang.NegativeArraySizeException
at org.usadellab.trimmomatic.fastq.trim.IlluminaClippingTrimmer.packSeq(IlluminaClippingTrimmer.java:578)
at org.usadellab.trimmomatic.fastq.trim.IlluminaClippingTrimmer$IlluminaClippingSeq.<init>(IlluminaClippingTrimmer.java:548)
at org.usadellab.trimmomatic.fastq.trim.IlluminaClippingTrimmer$IlluminaClippingSeq.<init>(IlluminaClippingTrimmer.java:538)
at org.usadellab.trimmomatic.fastq.trim.IlluminaClippingTrimmer.mapClippingSet(IlluminaClippingTrimmer.java:125)
at org.usadellab.trimmomatic.fastq.trim.IlluminaClippingTrimmer.loadSequences(IlluminaClippingTrimmer.java:111)
at org.usadellab.trimmomatic.fastq.trim.IlluminaClippingTrimmer.<init>(IlluminaClippingTrimmer.java:43)
at org.usadellab.trimmomatic.fastq.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:26)
at org.usadellab.trimmomatic.TrimmomaticPE.main(TrimmomaticPE.java:335)
at org.usadellab.trimmomatic.fastq.trim.IlluminaClippingTrimmer.packSeq(IlluminaClippingTrimmer.java:578)
at org.usadellab.trimmomatic.fastq.trim.IlluminaClippingTrimmer$IlluminaClippingSeq.<init>(IlluminaClippingTrimmer.java:548)
at org.usadellab.trimmomatic.fastq.trim.IlluminaClippingTrimmer$IlluminaClippingSeq.<init>(IlluminaClippingTrimmer.java:538)
at org.usadellab.trimmomatic.fastq.trim.IlluminaClippingTrimmer.mapClippingSet(IlluminaClippingTrimmer.java:125)
at org.usadellab.trimmomatic.fastq.trim.IlluminaClippingTrimmer.loadSequences(IlluminaClippingTrimmer.java:111)
at org.usadellab.trimmomatic.fastq.trim.IlluminaClippingTrimmer.<init>(IlluminaClippingTrimmer.java:43)
at org.usadellab.trimmomatic.fastq.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:26)
at org.usadellab.trimmomatic.TrimmomaticPE.main(TrimmomaticPE.java:335)
Thanks in advance!
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