error in Trimmomatic command

[Sharmi]

Hello,

I am running Trimmomatic command for ChIP-seq data

/home/bsharmi6/ChIPseqTools/Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred33 /home/bsharmi6/data/Egr1_rep1.ChIP-Seq.R1.fastq /home/bsharmi6/data/Egr1_rep1.ChIP-Seq.R1.output.fastq ILLUMINACLIP:/home/bsharmi6/ChIPseqTools/Trimmomatic-0.36/adapters/TruSeq3-SE.fa:2:30:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:36

and getting the following error-

/home/bsharmi6/ChIPseqTools/Trimmomatic-0.36/trimmomatic-0.36.jar: line 1: $'PK\003\004': command not found
/home/bsharmi6/ChIPseqTools/Trimmomatic-0.36/trimmomatic-0.36.jar: line 2: $'\bi\203uH': command not found
/home/bsharmi6/ChIPseqTools/Trimmomatic-0.36/trimmomatic-0.36.jar: line 3: syntax error near unexpected token `$'\a\217\245\234D\312\017\265\026\234\311{\234T\315.\204\024\266ת\353\2179\343\354\003PK\003\004''
/home/bsharmi6/ChIPseqTools/Trimmomatic-0.36/trimmomatic-0.36.jar: line 3:h?uH??\??META-INF/MANIFEST.MFM?=? w???GSS?V;7.ƕ?ҧ?h??{????F??N???R< ???>??~A?$??-U?ِ+???????i?}M??i@?F???;?????zC?K?X]?L?=g#?(???D????{?T?.??ת?9??PK'

Can someone please help me?

Thank you

[GenoMax]

Are you adding "java -jar" in front of the command above. Take a look at the example command line here.

[Sharmi]

Thank you for the reply. I have tried that as well. With that I get the error

-bash: java: command not found

[GenoMax]

Do you have java installed? If you do then provide full path to java program in the command instead of just java. You could also set $JAVA_HOME variable.