trimmomatic 0.36 error

Question

[mahjabeen.khan]

Hi everyone I am doing my analysis m very new to it.. I am trimming my sequence but error comes jar file cannot be accessed. I tried every solution provided before can someone help?

[lakhujanivijay]

I have updated the category from TOOL to QUESTION. can you please add the command you ran, trimmomatic version along with the exact error message ?

[mahjabeen.khan]

Thanks so much vijay the exact error is unable to access jarfile trimmomatic-0.36.jar

the command is

java -jar trimmomatic-0.36.jar PE -phred33 "/home/z5045473/workingdir/PA123_S13_R1_001.fastq.gz" "/home/z5045473/workingdir/PA123_S13_R2_001.fastq.gz" PA123_S13_f_P.fq.gz PA123_S13_f_U.fq.gz PA123_S13_r_P.fq.gz PA123_S13_r_U.fq.gz ILLUMINACLIP:TrueSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Answer 1

[agoel]

Is there a file in your current working directory named "trimmomatic-0.36.jar"? If not, you need to provide the full path to that .jar file.