Trimmomatic: invalid FASTQ name line

[alisrpp]

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(FastqParser.java:45)
at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:69)
at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:240)
at org.usadellab.trimmomatic.TrimmomaticPE.main(TrimmomaticPE.java:338)

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

Thanks!

[bob-loblaw]

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

[alisrpp]

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

[JackieBadger]

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.