Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Trimmomatic error Saeideh Bioinformatics 6 09-13-2015 07:10 AM
Trimmomatic error while executing Irina Pulyakhina Bioinformatics 15 07-03-2015 04:44 AM
Trimmomatic error dvanic Bioinformatics 31 04-06-2015 01:24 AM
Numberformatexception error in Trimmomatic mariruilo Bioinformatics 2 04-01-2013 11:08 AM
Trimmomatic Help Single Reads Error Hilary April Smith Bioinformatics 3 10-17-2012 06:05 AM

Thread Tools
Old 02-23-2016, 10:54 AM   #1
Junior Member
Location: Mexico

Join Date: Feb 2016
Posts: 2
Default On Trimmomatic Error. PE reads


I've got 12,438,019 Illumina paired end reads which I'm trying to preprocess in Trimommatic V 0.32 as follows:

java -jar trimmomatic-0.32.jar PE -threads 8 -phred33 -basein /home/DMEL-2/SRR042489_H3_1.fastq -baseout /home/DMEL-2/MOSCAPP ILLUMINACLIP:TruSeq2-PE.fa:2:30:10:true SLIDINGWINDOW:6:10 HEADCROP:10 MINLEN:32

However, I'm getting the below message.
I've not seen this error before. Please advise.

Thanks for your help.

TrimmomaticPE: Started with arguments: -threads 8 -phred33 -basein /home/pcarvajal04/DMEL-2/SRR042489_H3_1.fastq -baseout /home/pcarvajal04/DMEL-2/MOSCAPP ILLUMINACLIP:./adapters/TruSeq2-PE.fa:2:30:10:true SLIDINGWINDOW:6:10 HEADCROP:10 MINLEN:32
Using templated Input files: /home/DMEL-2/SRR042489_H3_1.fastq/home/DMEL-2/SRR042489_H3_2.fastq
Using templated Output files: /home/DMEL-2/MOSCAPP_1P /home/DMEL-2/MOSCAPP_1U /home/DMEL-2/MOSCAPP_2P /home/DMEL-2/MOSCAPP_2U
Exception in thread "main" java.lang.NumberFormatException: For input string: "true"
at java.lang.NumberFormatException.forInputString(
at java.lang.Integer.parseInt(
at java.lang.Integer.parseInt(
at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(
at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(
at org.usadellab.trimmomatic.Trimmomatic.main(
patriciacl is offline   Reply With Quote
Old 02-23-2016, 01:53 PM   #2
Senior Member
Location: uk

Join Date: Mar 2009
Posts: 667

Have you used that version of the Illuminaclip command before?

The error message looks like it's expecting a number instead of the string 'true'.

According to the manual, the command is:
LLUMINACLIP:<fastaWithAdaptersEtc>:<seed mismatches>:<palindrome clip threshold>:<simple clip threshold>:<minAdapterLength>:<keepBothReads>

the default minAdapterLength is 8, so you could try rewriting the command as:


and see if that works.
mastal is offline   Reply With Quote
Old 02-23-2016, 02:30 PM   #3
Junior Member
Location: Mexico

Join Date: Feb 2016
Posts: 2


You're right, it worked.
Thank you.

In regards to the question, I think I've used it before, though it seems than I need to pay more attention to details on PE

patriciacl is offline   Reply With Quote


Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:15 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO