Trimmomatic jar file

Question

[akashgari19]

Hi everyone,

I am using supercomputer to analyze my RNA seq data and now I am in the step of adapter removal. I am trying to use trimmomatic and I loaded the module using command: i downloaded the program to my home directory then unzipped it. But when I run it it gives error. This is how I typed on my command line.

 java –jar/root/users/my home directory/apps/Trimmomatic-0.39/trimmomatic-0.39.jar PE -phred33 SRR3726664_1.fastq  SRR3726664_2.fastq SRR3726664_1 paired_trim.fastq  SRR3726664_1_unpaired_trim.fastq SRR3726664_2 paired_trim.fastq  SRR3726664_2_unpaired_trim. ILLUMINACLIP:/root/users/my home directory/apps/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Error: Could not find or load main class –jar.root.users.my home directory.apps.Trimmomatic-0.39.trimmomatic-0.39.jar
-bash: ILLUMINACLIP:/root/users/my home directory/apps/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10: No such file or directory.

I obtained my path by typing pwd so every location is actually correct. I am new to RNA-seq and bash terminal. Please Help. Thank you .

[ahmer]

Hello I am using Bash shell in windows and have installed Trimmomatic using

sudo apt install trimmomatic
Reading package lists... Done
Building dependency tree
Reading state information... Done
trimmomatic is already the newest version (0.39+dfsg-1).
0 upgraded, 0 newly installed, 0 to remove and 100 not upgraded.

But when I try to run commands it comes with error

module load trimmomatic or trimmomatic/0.39
module: command not found

java -jar trimmomatic-0.39.jar PE input_PY53_R1.fastq.gz input_PY53_R2.fastq.gz output_PY53_R1_paired.fq.gz output_PY53_R1_unpaired.fq.gz output_PY53_R2_paired.fq.gz output_PY53_R2_unpaired.fq.gz SLIDINGWINDOW:4:20 MINLEN:2
Error: Unable to access jarfile trimmomatic-0.39.jar

Urgent help will be really appreciated.

Best regards

[GenoMax]

Can you clarify if you are using Windows subsystem for Linux (WSL2) or something else?

As was explained in your other question, modules (LINK) is a completely separate software system used for management of software versions. This is typically not installed on individual computers but mainly targeted to clusters/larger servers.

Answer 1

[GenoMax]

You probably need a space between -jar and file name. Try this:

 java –jar /root/users/my home directory/apps/Trimmomatic-0.39/trimmomatic-0.39.jar PE -phred33 SRR3726664_1.fastq  SRR3726664_2.fastq SRR3726664_1 paired_trim.fastq  SRR3726664_1_unpaired_trim.fastq SRR3726664_2 paired_trim.fastq  SRR3726664_2_unpaired_trim. ILLUMINACLIP:/root/users/my home directory/apps/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

[ahmer]

No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 20.04.3 LTS Release: 20.04 Codename: focal

However I have solved the issue. Thanks.