Trimmomatic - unknown trimmer?

Hi, all I have Double End fastq file and it needs trimming. So, I use trimmomatic software for this purpose.based on trimmomatic tutorial I write below code for my .fq.gz file:

enter image description here

but after run it in my Terminal, I see bellow error; Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: GT1-N1.paired_GT1-N1_FRAS210028605-2r_2.fq.gz

enter image description here I run this command in my data folder. so I appreciate if any body help me. Best, Hongran Liu

rnaseq

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updated 4.8 years ago by Istvan Albert

• written 4.8 years ago by liuhongran •

It is not a good idea to post screenshots of code. Please copy and paste the actual code and errors. Use the 101010 button to highlight and format the code.

You can't pass wild card files to trimmomatic. If you have more than one sample then run the trimming for each set of sample via a for loop.

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written 4.8 years ago by GenoMax

1 answer

You are passing too many files into the tool, it runs out the fields that it considers inputs/outputs and starts treating a file name as a trimming action.

Read up on the tool and adjust your inputs.

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written 4.8 years ago by Istvan Albert