Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
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9 weeks ago
sam • 0
$ java -jar /path/to/trimmomatic-0.39.jar PE -threads 4 SRR_1056_1.fastq SRR_1056_2.fastq  \
              SRR_1056_1.trimmed.fastq SRR_1056_1un.trimmed.fastq \
              SRR_1056_2.trimmed.fastq SRR_1056_2un.trimmed.fastq \
              ILLUMINACLIP:SRR_adapters.fa SLIDINGWINDOW:4:20
TrimmomaticPE: Started with arguments:
 -threads 4 SRR_1056_1.fastq SRR_1056_2.fastq SRR_1056_1.trimmed.fastq SRR_1056_1un.trimmed.fastq SRR_1056_2.trimmed.fastq SRR_1056_2un.trimmed.fastq ILLUMINACLIP:SRR_adapters.fa SLIDINGWINDOW:4:20
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
    at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:54)
    at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32)
    at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59)
    at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:552)
    at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)
next-gen RNA-seq • 433 views
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so you fixed the problem for your previous question ???? Exec format error

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I am indecisive about where to run the command(whether in the input directory or in the directory trimmomatic is in). When I run in different directories, I get different errors.

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if you know that would be great.

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check the syntax of the file SRR_adapters.fa

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