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Trimmomatic: invalid FASTQ name line

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  • Trimmomatic: invalid FASTQ name line

    Hi all,

    I'm trying to trim the adapters of my Illumina PE reads using Trimmomatic.

    java -classpath trimmomatic-0.22/old/Trimmomatic-0.20/trimmomatic-0.20.jar org.usadellab.trimmomatic.TrimmomaticPE -phred33 C1_OCT09_tissue_w_larvae/C1_1_s_1_1_sequence.fa C1_OCT09_tissue_w_larvae/C1_2_s_1_2_sequence.fa C1_OCT09_tissue_w_larvae_forward_paired.fq.gz C1_OCT09_tissue_w_larvae_forward_unpaired.fq.gz C1_OCT09_tissue_w_larvae_reverse_paired.fq.gz C1_OCT09_tissue_w_larvae_reverse_unpaired.fq.gz ILLUMINACLIP:IlluminaPE.fa:2:40:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20

    And i'm having this problem:

    Exception in thread "main" java.lang.RuntimeException: Invalid FASTQ name line: >ILLUMINA-3AB384_0007:1:1:1011:8817#0/1
    at org.usadellab.trimmomatic.fastq.FastqParser.parseOne(
    at org.usadellab.trimmomatic.fastq.FastqParser.parse(
    at org.usadellab.trimmomatic.TrimmomaticPE.process(
    at org.usadellab.trimmomatic.TrimmomaticPE.main(

    I have no idea how to fix it.
    Some advice???


  • #2
    ID lines in fastq files start with an @ symbol, your one starts with an > symbol, like a fasta file.


    • #3
      I have my raw data in .txt, do you know how can i convert them to .fastq?


      • #4
        If you have your fasta and qual file you can convert to fastq using Galaxy.
        If all you have is fasta and no quality info you can just make a dummy quality line as long as your sequence. Obviously if thats the case you can not trim your sequences by quality.