Trimmomatic problem

Question

[sehriban.buyukkilic]

hi everyone, Is anyone can help me with trimmomatic problem?* I'm trying to run it but it's giving error like that:

-bash-4.2$ java -jar /truba/home/sbuyukkilic/trimmomatic/Trimmomatic-0.39/trimmomatic-0.39.jar PE SRR12182130_1_fastqc.zip SRR12182130_1_fastqc.zip SRR12182130_1_paired_fastqc.zip SRR12182130_1_unpaired_fastqc.zip SRR12182130_2_paired_fastqc.zip  SRR12182130_1_paired_fastqc.zip ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:3
TrimmomaticPE: Started with arguments:
 SRR12182130_1_fastqc.zip SRR12182130_1_fastqc.zip SRR12182130_1_paired_fastqc.zip SRR12182130_1_unpaired_fastqc.zip SRR12182130_2_paired_fastqc.zip SRR12182130_1_paired_fastqc.zip ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:3
java.io.FileNotFoundException: /truba/home/sbuyukkilic/fastqc_tool/TruSeq3-PE.fa (No such file or directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at org.usadellab.trimmomatic.fasta.FastaParser.parse(FastaParser.java:54)
    at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.loadSequences(IlluminaClippingTrimmer.java:110)
    at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:71)
    at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32)
    at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59)
    at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:552)
    at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)
Error: Unable to detect quality encoding

[barslmn]

Why are you trying to trim fastqc reports?

[Fatemeh Nabizadeh]

Check these parameters: LEADING:3 TRAILING:3 MINLEN:3

Are you sure you're using the right numbers?

Also, TruSeq3-PE.fa is not found. Make sure to do something like this:

cp -r Trimmomatic-0.39/adapters /usr/local/share/adapters

Additionally, you are using the same file for PE:

repeating "SRR12182130_1_fastqc.zip" :

PE SRR12182130_1_fastqc.zip SRR12182130_1_fastqc.zip

I think you must have 2.