Entering edit mode
2.0 years 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)
so you fixed the problem for your previous question ???? Exec format error
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.
if you know that would be great.
check the syntax of the file SRR_adapters.fa