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

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

Hello!!

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(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:492)
at java.lang.Integer.parseInt(Integer.java:527)
at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:61)
at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:27)
at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:495)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:35)
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Old 02-23-2016, 01:53 PM   #2
mastal
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Join Date: Mar 2009
Posts: 667
Default

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:

ILLUMINACLIP:./adapters/TruSeq2-PE.fa:2:30:10:8:true

and see if that works.
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Old 02-23-2016, 02:30 PM   #3
patriciacl
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Location: Mexico

Join Date: Feb 2016
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Hello!!

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

Thanks
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