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)
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)
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