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Old 06-27-2017, 01:58 PM   #1
Junior Member
Location: Oklahoma City, OK

Join Date: Sep 2016
Posts: 1
Default Trimmomatic not working correctly

Hello all,
I am very new to trimmomatic and running into problems. My command line is:

C:\Users\Munster>java -jar "c:\Program Files\Trimmomatic-0.36\trimmomatic-0.36.jar" PE -phred33 -threads 8 -trimlog 33_blood_log.txt 33_blood_67__brain_R1_001.fastq.gz 33_blood_67__brain_R2_001.fastq.gz 33_blood_TRSW_1P.fq 33_blood_TRSW_1U.fq 33_blood_TRSW_2P.fq 33_blood_TRSW_2U.fq ILLUMINACLIP:"c:\Program Files\Trimmomatic-0.36\adapters\TruSeq3-PE.fa":2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

This is what I get when I run the command:

TrimmomaticPE: Started with arguments:
-phred33 -threads 8 -trimlog 33_blood_log.txt 33_blood_67__brain_R1_001.fastq.g
z 33_blood_67__brain_R2_001.fastq.gz 33_blood_TRSW_1P.fq 33_blood_TRSW_1U.fq 33_
blood_TRSW_2P.fq 33_blood_TRSW_2U.fq ILLUMINACLIP:c:\Program Files\Trimmomatic-0
.36\adapters\TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLE
Exception in thread "main" java.lang.NumberFormatException: For input string: "\
Program Files\Trimmomatic-0.36\adapters\TruSeq3-PE.fa"
at java.lang.NumberFormatException.forInputString(NumberFormatException.
at java.lang.Integer.parseInt(
at java.lang.Integer.parseInt(
at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaCl
at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFact
at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(
at org.usadellab.trimmomatic.Trimmomatic.main(

What do these errors mean? Any suggestions for how to get this to work correctly? I am working on a PC and using the command window to run commands. THANKS!!!
munsters is offline   Reply With Quote
Old 06-30-2017, 04:41 AM   #2
Location: Europe

Join Date: Oct 2016
Posts: 56

Hello munsters,

I guess the problem is the path to the adapter file, as it contains "c:" and trimmomatic understand the ":" as a delimiter.

Try using a path without the device name.

fin swimmer
finswimmer is offline   Reply With Quote

java, trimmomatic

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