This is a test version of Biostars. For the public version, visit https://www.biostars.org.
trimmomatic: command not found

hello, I'm new here. I was using trimmomatic and I put this commands,

 trimmomatic PE -phred33 testadapt.1.fastq testadapt.2.fastq test_trim_paired.1.fq.gz testes_trim_unpaired.1.fq.gz test_trim_paired.2.fq.gz test_trim_unpaired.2.fq.gz ILLUMINACLIP:/home/lab/Software/Trimmomatic-0.38/adapters/NexteraPE-PE.fa:2:30:10:4 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

but it reminds to me

trimmomatic: command not found

Any helps?

trimming software error
• 6,663 views • link
written by SeaStar • SeaStar

How did you install Trimmomatic? It is a Java program, and according to the manual, it should be used with:

java -jar <path to trimmomatic jar> SE [-threads <threads>] [-phred33 | -phred64] [-trimlog <logFile>] <input> output> <step 1> ...

If you are using Ubuntu / Debian and installed from the distro repository, there are two wrappers: TrimmomaticPE and TrimmomaticSE.

• 0 views • link
written by h.mon h.mon

Program is not installed or is not in system path (your shell path). SeaStar

• 0 views • link
written by cpad0112 cpad0112

0 answers

No answers yet.

Log in to answer this question.

More posts like this
  • Trimmomatic adapter file not found when running using conda environment (Nextflow)
    written by Eliveri • Eliveri
    I have a nextflow script which uses trimmomatic, I am running the script using a conda environment from HPC server. Trimmomatic is able to run …
  • Run trimmomatic with Trinity
    written by YATING • YATING
    I want to run trimmomatic with Trinity, but there's some error that I can't solve. “ILLUMINACLIP:/tempwork173/r09b45015/anaconda3/envs/rnaseq/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:20 TRAILING:3 MINLEN:25” **Error, do not understand options: …
  • Trimmomatic parameters
    written by ronny • ronny
    $java -jar /apps/eb/Trimmomatic/0.39-Java-1.8.0_144/trimmomatic-0.39.jar PE -phred33 seq1_L2_1.fq.gz seq1_L2_2.fq.gz _L2_r1_paired_fq.gz seq1_L2_r1_unpaired.fq.gz seq_L2_r2_paired.fq.gz Seq1_L2_r2_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:5 #what values I should use for following parameters? ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 …
  • Confusion about trimmomatic
    written by szahid • szahid
    Hi All, I'm new to bioinformatics and currently working on some rna seq data. I'm using trimmomatic to remove adaptor contamination. I'm using the following …
  • error en trimmomatic
    written by laurapeaz_21315 • laurapeaz_21315
    Hola soy nueva usando trimmomatic y linnux use la siguiente linea de comando : lau@DESKTOP-1B4G2I6:/mnt/c/Users/acer/Documents/doctorado/Genoma 4IGSN1/4IgSN1$ java -jar /usr/share/java/trimmomatic.jar PE -threads 8 -phred33 1_HIg5N1_S1_L001_R1_001.fastq 2_HIg5N1_S1_L001_R2_001.fastq …
  • Trimmomatic usage error( a little bit weird)
    written by Decen • Decen
    Hi All, I am a newcomer in bioinformatics. recently I use the trimmomatic to train myself. First, I install the trimmomatic by conda(it is really …
  • Trimmomatic execution removes the data from my fastq sequence file. What am I doing wrong?
    written by kristina.mahan kristina.mahan
    I'm trying to use Trimmomatic 0.38 to trim my Illumina fastq sequences. Something must be wrong with my syntax because after execution I get a …
  • quality trimming with trimmomatic
    written by blooming.daisy333 • blooming.daisy333
    I am using trimmomatic for quality trimming of fastq files for my project. im usig default values for paired end reads that trim the sequences …
  • error in execution of Trimmomatic 0.36
    written by F.I.2011 • F.I.2011
    I am new in Linux and Trimmomatic , do after installation i need to run it by any specific command **I am using this command:** …
  • running trimmomatic 0.35
    written by dora.quispe • dora.quispe
    Dear, I am running trimmomatic 0.35 to remove the adapters sequences from my Illumina data but I got the following error message Exception in thread …