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ILLUMINACLIP: Unknown Trimmer #57

Closed RankAma closed 11 months ago

RankAma commented 11 months ago

I've installed Trimmomatic from Bioconda and I'm encountering problems while attempting to trim my .fastq sequences. When I run the following command:

trimmomatic PE -threads 4 -phred33 SRR25943901_1.fastq SRR25943901_2.fastq \
SRR25943901_1.trimmed.fastq SRR25943901_1un.trimmed.fastq \
SRR25943901_2.trimmed.fq.gz SRR25943901_2un.trimmed.fq.gz \
ILLUMINACLIP:SRR25943901_adapter.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

I receive the error message:

Exception in thread "main" java.lang.RuntimeException: Unknown trimmer:  ILLUMINACLIP
        at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:73)
        at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59)
        at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:552)
        at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

I've read in some forums that removing spaces in the command might resolve the issue. However, doing so hasn't helped and, in fact, appears to assume that the command line doesn't recognise the first command.

muzilalalla commented 2 months ago

Hello! How did you solve the problem ? Please tell me , it is so important for me. Thanks!!!!!