Trimmomatic non-conventional adaptors and error

Question

[valopes]

Hi everybody,

I am trying to trim an Illumina sequencing with non-conventional adaptors and for that, I am facing an error.

For example, one set of adaptor is:

>G17775-L1_1
TCGCCTTA
>G17775-L1_2
AAGGAGTA

And I am using the command:

java -Xmx4G -jar trimmomatic.jar PE -threads 10 -phred33 \
G17775-L1_S1_L001_R1_001.fastq.gz \ G17775-L1_S1_L001_R2_001.fastq.gz \
Sample1_R1_forward_paired.trim.fastq.gz \
Sample1_R1_forward_unpaired.trim.fastq.gz \
Sample1_R2_forward_paired.trim.fastq.gz \
Sample1_R2_forward_unpaired.trim.fastq.gz \
ILLUMINACLIP:G17775.fa:2:7:2 \ 
LEADING:3 TRAILING:3 \
SLIDINGWINDOW:4:25 \
MINLEN:40

I got the error:

Exception in thread "main" java.lang.RuntimeException: Unknown
trimmer: Sample1

Does anyone know how can I fix this?

Thanks in advance.

[GenoMax]

Those don't look like adapters to me but are likely index/tag sequences (judging by their length). Index reads are never part of the actual sequence in Illumina and do not need to be trimmed.

[valopes]

But the index won't create a problem when assembling?

[Devon Ryan]

It won't/shouldn't be used by the assembler (it's usually not even given to end users, since it just creates confusion).

[GenoMax]

Can you post an example of an actual fastq read header?

[Matteo Schiavinato]

It doesn't look like the adapters are the problem, rather the reads (Trimmer: Sample_1). Or if you use the normal adapters in their directory it works?

[cschu181]

Could you try running that with only single spaces between the arguments, i.e. remove all the backslashes and newlines? It kinda looks as if Trimmomatic mistakes one of the output files as trimming module. Now the question is, why?