running trimmomatic 0.35

Question

[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 "main" java.lang.RuntimeException: Unknown trimmer: SP_200_R2_unpaired_trimmo.fastq

I used the following command

java \
  -jar /home/bw14/doquispe/Trimmomatic-0.35/trimmomatic-0.35.jar \
  PE \
  -phred33 \
  /home/bw14/doquispe/IlluminaSequences \
  SP_200_R1.fastq SP_200_R2.fastq \
  SP_200_R1_paired_trimmo.fastq SP_200_R1_unpaired_trimmo.fastq SP_200_R2_paired_trimmo.fastq \
  SP_200_R2_unpaired_trimmo.fastq \
  ILLUMINACLIP: /home/bw14/doquispe/Trimmomatic-0.35/adapters/adapters.fas :2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Could you help me to solve this problem?

Answer 1

[trausch]

I think, there is no path argument "/home/bw14/doquispe/IlluminaSequences" for trimmomatic. You need to specify relative or absolute path for every file.