Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
0
0
Entering edit mode
17 months 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 • 1.0k views
ADD COMMENT
0
Entering edit mode

so you fixed the problem for your previous question ???? Exec format error

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

if you know that would be great.

ADD REPLY
0
Entering edit mode

check the syntax of the file SRR_adapters.fa

ADD REPLY

Login before adding your answer.

Traffic: 1889 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6