Question: Unable to access jarfile trimmomatic-0.35
0
gravatar for ambika.pokhrel53
12 days ago by
United States/Auburn/Auburn University
ambika.pokhrel530 wrote:

Hi everyone,

I was trying to do the adaptor trimming for my paired end RNA-seq data and I am using trimmomatic. I gave the following commands:

java -jar trimmomatic-0.35.jar PE -phred33 SL264821_1.fastq.gz SL264821_2.fastq.gz SL264821_1_paired.fastaq.gz SL264821_1_unpaired.fastaq.gz SL264821_2_paired.fastaq.gz SL264821_2_unpaired.fastaq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

but it gives me the error Unable to access jarfile trimmomatic-0.35 . Could you please help me with this because I am super new to all of this analysing stuff and kind of lost in this process.

Thank you, Ambika

ADD COMMENTlink modified 12 days ago • written 12 days ago by ambika.pokhrel530

This is a general error message, indicating that the binary is not found. You sure that the jar is in your current working directory?

ADD REPLYlink written 12 days ago by ATPoint1.1k

No jar is not in my working directory. How can I make one. any suggestions?

ADD REPLYlink written 12 days ago by ambika.pokhrel530
1

You need to download the JAR file to a directory, then move ('cd') to that directory, and from there you can run it.

Please be aware also of full/absolute and relative paths.

In linux, get into the habit of always using full/absolute paths. If you save the JAR file to /home/ambika/Desktop/, then the command would be:

java -jar /home/ambika/Desktop/trimmomatic-0.35.jar
ADD REPLYlink written 12 days ago by Kevin Blighe1.1k

Thank you so much for the explaination, it helped me a lot

ADD REPLYlink written 11 days ago by ambika.pokhrel530
0
gravatar for Chris Miller
12 days ago by
Chris Miller18k
Washington University in St. Louis, MO
Chris Miller18k wrote:

Is there a file in your current directory named "trimmomatic-0.35.jar"? If not, then you need to provide the full path to that file.

ADD COMMENTlink written 12 days ago by Chris Miller18k

No I dont have any file like that. So I have to make jar file first and then specify the path.

ADD REPLYlink written 12 days ago by ambika.pokhrel530

You don't have to make it, you need to download it from the trimmomatic site. If you have already downloaded it, you need to provide the path to that file.

ADD REPLYlink written 12 days ago by Chris Miller18k

Thank you for the information, its really helpful for me.

ADD REPLYlink written 11 days ago by ambika.pokhrel530
0
gravatar for ambika.pokhrel53
12 days ago by
United States/Auburn/Auburn University
ambika.pokhrel530 wrote:

No I dont have any files in that directory. So, you mean that I need to provide path to that directory not just the name?

ADD COMMENTlink written 12 days ago by ambika.pokhrel530
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