trimmomatic error correcting problem

[fnn4]

Hi all,

I use trimmomatic to trim and error correct. Commands are as below
trimmomatic PE -threads 16 forward.fastq.gz reverse.fastq.gz paired-1.fastq.gz unpaired-1.fastq.gz paired-2.fastq.gz unpaired-2.fastq.gz ILLUMINACLIP:/opt/Trimmomatic-0.32/adapters/NexteraPE-PE.fa:2:30:10*LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15MINLEN:36

When I take out the error correcting part (starting LEADING to the end), it was able to finish trimmomatic. When I include that part, it gave error. Please see below: Any one can help? Thank you!

TrimmomaticPE: Started with arguments: -threads 16 forward.fastq.gz reverse.fastq.gz paired-1.fastq.gz unpaired-1.fastq.gz paired-2.fastq.gz unpaired-2.fastq.gz ILLUMINACLIP:/opt/Trimmomatic-0.32/adapters/NexteraPE-PE.fa:2:30:10*LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15MINLEN:36
Exception in thread "main" java.lang.NumberFormatException: For input string: "10*LEADING"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.parseInt(Integer.java:615)
at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:55)
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)

[mastal]

You should have a space between the different commands, and it looks like there isn't a space between the end of the parameters for the ILLUMINACLIP command and the LEADING command.

[fnn4]

Thank you for replying! I checked my commands and reran it. It did have space in between. And with space, it still shows errors:

TrimmomaticPE: Started with arguments: -threads 16 forward.fastq.gz reverse.fastq.gz paired-1.fastq.gz unpaired-1.fastq.gz paired-2.fastq.gz unpaired-2.fastq.gz ILLUMINACLIP:/opt/Trimmomatic-0.32/adapters/NexteraPE-PE.fa:2:30:10*LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Exception in thread "main" java.lang.NumberFormatException: For input string: "10*LEADING"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.parseInt(Integer.java:615)
at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:55)
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)

[mastal]

If you have a space and not a '*' before LEADING, you might have some kind of control character present, because trimmomatic seems to be interpreting your command as containing the characters '10*LEADING', which it doesn't recognise, and it is giving an error.