Trimmomatic non-conventional adaptors and error
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.
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Devon Ryan
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valopes •
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valopes •
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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.
But the index won't create a problem when assembling?
It won't/shouldn't be used by the assembler (it's usually not even given to end users, since it just creates confusion).
Can you post an example of an actual fastq read header?
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?
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?