Trimmomatic Error

Question

[Patricia]

Hello, everyone, I am trying to trim sequences from RNA seq data with Trimmomatic. For reference, I am using a Mac, and I have trimmomatic-0.39.jar in the trimmomatic folder in the Applications. My data is on a folder on the desktop and I have set this folder as my working directory in the terminal. I am putting in the following code.

java -jar Applications/Trimmomatic-0.39/trimmomatic-0.39.jar PE -threads 3 -phred33 raw_data/CON1/CON1_1.fq.gz raw_data/CON1/CON1_2.fq.gz trimmed/CON1_1.tp.fq.gz CON1_1.up.fq.gz/ CON1_2.tp.fq.gz/ CON1_2.up.fq.gz/ SLIDINGWINDOW:5:28 MINLEN:60

However, I continued to get an error saying:

Error: Unable to access jarfile Applications/trimmomatic-0.39/trimmomatic-0.39.jar

I am unsure why this is happening. I am basically learning how to do these kinds of analysis for the first time and have basically no experience, so if someone could point me in the right direction it would be very appreciated.

[GenoMax]

I think you have a $PATH problem.

java -jar Applications/Trimmomatic-0.39/trimmomatic-0.39.jar

should be (note ~ before that refers to your home directory

java -jar ~/Applications/Trimmomatic-0.39/trimmomatic-0.39.jar

See if that works.

[Patricia]

Hi, I tried it this way it didn't work. In addition, when I move the trimmomatic-0.39.jar program into my workin directory and try to run it this way I get an error saying invalid or corrupt file.

(base) Patricias-MBP:~ patriciaablanedomorales$ cd Desktop/RNAseq_fibros_1st_round/
(base) Patricias-MBP:RNAseq_fibros_1st_round patriciaablanedomorales$ ls
RNAseq analysis notes.docx  rnaseq_fibros_script.R
RNAseq_fibros.Rproj     sample info form .pdf
commands for trimmomatic.txt    trimmed
fastQC results          trimmomatic codes .docx
hg38.2bit           trimmomatic-0.39.jar
raw_data            ~$Aseq analysis notes.docx
rna seq data            ~$immomatic codes .docx
(base) Patricias-MBP:RNAseq_fibros_1st_round patriciaablanedomorales$ java -jar trimmomatic-0.39.jar PE -threads 3 -phred33 raw_data/CON1/CON1_1.fq.gz raw_data/CON1/CON1_2.fq.gz trimmed/CON1_1.tp.fq.gz CON1_1.up.fq.gz/ CON1_2.tp.fq.gz/ CON1_2.up.fq.gz/ SLIDINGWINDOW:5:28 MINLEN:60
Error: Invalid or corrupt jarfile trimmomatic-0.39.jar

[GenoMax]

Error: Invalid or corrupt jarfile trimmomatic-0.39.jar

Now you have a different problem. Looks like your copy of this Jar file may be corrupt.

I tried it this way it didn't work.

What was the problem?

[Patricia]

Would you happen to know why it is corrupt? I already downloaded it twice and even dowloaded an earlier version and it does not work