trimmomatic error with unknown trimmer

Question

[xuanyuan]

I am running trimmomatic using the following command:

java -jar ~/tools/Trimmomatic-0.32/trimmomatic-0.32.jar PE R1_001.fastq R2_001.fastq pair1.fq unpair1.fq pair2.fq unpair2.fq step 1

and then I got the following wrong messages:

TrimmomaticPE: Started with arguments: R1_001.fastq R2_001.fastq pair1.fq unpair1.fq pair2.fq unpair2.fq step 1
Multiple cores found: Using 12 threads
Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: step
        at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:60)
        at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:495)
        at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:35)

Does anybody know what this means? Is there anything wrong?

Thanks

[iraun]

"step 1" is not a valid argument for trimmomatic. What are you trying to do?

[xuanyuan]

i am try to remove the adaptor from the illumina rna-seq raw data. so should i replace <STEP 1> with <ILLUMINACLIP>? thanks a lot!

[iraun]

Yes. You should write in the following format:

ILLUMINACLIP:<fastaWithAdaptersEtc>:<seed mismatches>:<palindrome clip threshold>:<simple clip threshold>

In <fastaWithAdaptersEtc> field you should specify the path to a fasta file with adapters sequences. For example:

ILLUMINACLIP:/home/dir/adapters.fa:2:30:10

cat adapters.fa:

>adapter1
AACACACAAGAGGA
>adapter2
GGAGGAGGCATTT

[xuanyuan]

get it. thanks a lot!

Answer 1

[Devon Ryan]

You don't literally use "step 1". That's just a placeholder for a step in how you want it to trim things. For example, you might use "LEADING:10" there, to specify trimming leading bases with Phred scores below 10.

[xuanyuan]

thanks a lot!