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Old 12-05-2017, 04:07 AM   #1
Batstaph
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Location: UK

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Unhappy Trimmomatic adapter file error

I am having a problem getting trimmomatic to find the adapter file. I have tried all the options I can think of for the path, and put the file in the trimmomatic folder but still get a file not found error message. I can't spot any syntax errors, so can anyone help me?

error: java.io.FileNotFoundException: /adapters/Truseq3-PE-2.fa (No such file or directory)


java -jar trimmomatic-0.36.jar PE -phred33 27_4_24_LC_R1.fq 27_4_24_LC_R2.fq 27_4_24_LC_forward_paired.fq 27_4_24_LC_forward_unpaired.fq 27_4_24_LC_reverse_paired.fq 27_4_24_LC_reverse_unpaired.fq ILLUMINACLIP:/adapters/Truseq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

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Old 12-05-2017, 04:18 AM   #2
GenoMax
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Are you able to list the file by doing an ls with full path?
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Old 12-05-2017, 04:13 PM   #3
neavemj
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I think it searches for that file from your current directory (not from the trimmomatic folder). You could put the adapter file in the same folder as your raw reads, then change that part of your command to the following:

ILLUMINACLIP:Truseq3-PE-2.fa:2:30:10

Cheers,

Matt.
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