Question: error when running trimmomatic
1
gravatar for F
3.5 years ago by
F3.4k
Iran
F3.4k wrote:

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 • 3.1k views
ADD COMMENTlink modified 3.5 years ago by genomax65k • written 3.5 years ago by F3.4k
2
gravatar for genomax
3.5 years ago by
genomax65k
United States
genomax65k wrote:

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?

ADD COMMENTlink written 3.5 years ago by genomax65k

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

??

ADD REPLYlink written 3.5 years ago by F3.4k
1

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
ADD REPLYlink written 3.5 years ago by genomax65k
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