trimmomatic && ScriptSeq-v2 RNA-Seq Library

[mslider]

--Hi,

i try to use trimmomatic to clean my paired-end reads, i used ScriptSeq-v2 RNA-Seq Library Preparation Kit.
my adaptors file is formated as:

>PrefixPE/1
CAAGCAGAAGACGGCATACGAGAT
>PrefixPE/2
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
>PE/1
CAAGCAGAAGACGGCATACGAGAT
>PE/1_rc
ATCTCGTATGCCGTCTTCTGCTTG
>PE/2
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
>PE/2_rc
AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC

and when i run:

java -jar trimmomatic-0.32.jar PE -threads 2 -phred33 -trimlog r.log 1.fastq 2.fastq Out_paired_1.fastq Out_unpaired_1.fastq Out_paired_2.fastq Out_unpaired_2.fastq ILLUMINACLIP:adapters.fa:2:30:27 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50

my sequences are not cleaned.

the input files i use:

1.fastq
@HWI-D00562:33:C67RBANXX:7:1101:12177:2410 1:N:0:ACAGTG
GACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGAACTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTGAAAAAA
+
BBBCCGGGGGGGGGGGGEGGGGGGGGGGFGGGGGGGGGGGGGGDEGGGGGGGGGGGGGEGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG@DBFEGGGGGGGGGGGGGGGGGGGGGGGGG

2.fastq
@HWI-D00562:33:C67RBANXX:7:1101:12177:2410 2:N:0:ACAGTG
AGTTCCTCTTAATCATGGCCTCAGTTCCGAAAACCAACAAAATAGAACCGCGGTCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAA
+
CCBCCGGGGDGGGGGGCEGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGDDGGGGGGGGGGGGGGGGGGG89


(in sequence 1.fastq you can see the adaptor: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC ACAGTG ATCTCGTATGCCGTCTTCTGCTTG)

i don't know what's wrong, maybe in adaptors file is bad formated ?