Question: Trimmomatic jar file
0
gravatar for akashgari19
7 months ago by
akashgari190 wrote:

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 .

rna-seq • 329 views
ADD COMMENTlink modified 7 months ago by genomax90k • written 7 months ago by akashgari190
1
gravatar for genomax
7 months ago by
genomax90k
United States
genomax90k wrote:

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
ADD COMMENTlink written 7 months ago by genomax90k
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