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error when running trimmomatic

Hi friends,

I was going to adapter trimming by trimmomatic then I did so but

[izadi@lbox161 ~]$ cd /usr/data/nfs6/izadi/Trimmomatic-0.33/
[izadi@lbox161 Trimmomatic-0.33]$ java -jar trimmomatic-0.30.jar SE -phred33 SRR1944913.fastq output.fq ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Error: Unable to access jarfile trimmomatic-0.30.jar

Do you know what happened?

Thank you

adapter trimmomatic
• 6,818 views • link
updated by Ram Ram • written by zizigolu zizigolu

1 answer

Going to guess that since you are in directory for Trimmomatic-0.33 you should be using "java -jar trimmomatic-0.33.jar" instead of trimmomatic-0.30.jar?

• 0 views • link
written by GenoMax GenoMax

sorry you means I should used 

trimmomatic-0.30.jar SE -phred33 SRR1944913.fastq output.fq ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

instead of

java -jar trimmomatic-0.30.jar SE -phred33 SRR1944913.fastq output.fq ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

??

• 0 views • link
updated by Ram Ram • written by zizigolu zizigolu

Jar file has the same number as the version of the program. You appear to be in v.0.33 directory but are trying to run v.0.30 jar.

trimmomatic-0.33.jar SE -phred33 SRR1944913.fastq output.fq ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
• 0 views • link
updated by Ram Ram • written by GenoMax GenoMax

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