error when running trimmomatic

Question

[zizigolu]

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

Answer 1

[GenoMax]

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?

[zizigolu]

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

??

[GenoMax]

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