Hi Folks,
I'm running trimmomatic, and get an error I've never found before, and don't know how to solve. I think my command line is fine, although so far I've only run single reads, and this is my first pair end run. I would appreciate any input. Thanks!!!
This is my command line:
java -classpath /Users/lab/Documents/Trimmomatic-0.25/Trimmomatic-0.25.jar org.usadellab.trimmomatic.TrimmomaticPE -phred33 -trimlog RC31.txt SampleSheet-R1-2597.fastq SampleSheet-R2-2597.fastq RC31_30100_forward_paired.fq.gz RC31_30100_forward_unpaired.fq.gz RC31_30100_reverse_paired.fq.gz RC31_30100_reverse_unpaired.fq.gz SLIDINGWINDOW:15:20 LEADING:30 TRAILING:30 MINLEN: 100
And this is the error I get,
Exception in thread "main" java.lang.NumberFormatException: For input string: ""
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:48)
at java.lang.Integer.parseInt(Integer.java:470)
at java.lang.Integer.parseInt(Integer.java:499)
at org.usadellab.trimmomatic.fastq.trim.MinLenTrimmer.<init>(MinLenTrimmer.java:11)
at org.usadellab.trimmomatic.fastq.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:47)
at org.usadellab.trimmomatic.TrimmomaticPE.main(TrimmomaticPE.java:346)
Thanks for your help again.
I'm running trimmomatic, and get an error I've never found before, and don't know how to solve. I think my command line is fine, although so far I've only run single reads, and this is my first pair end run. I would appreciate any input. Thanks!!!
This is my command line:
java -classpath /Users/lab/Documents/Trimmomatic-0.25/Trimmomatic-0.25.jar org.usadellab.trimmomatic.TrimmomaticPE -phred33 -trimlog RC31.txt SampleSheet-R1-2597.fastq SampleSheet-R2-2597.fastq RC31_30100_forward_paired.fq.gz RC31_30100_forward_unpaired.fq.gz RC31_30100_reverse_paired.fq.gz RC31_30100_reverse_unpaired.fq.gz SLIDINGWINDOW:15:20 LEADING:30 TRAILING:30 MINLEN: 100
And this is the error I get,
Exception in thread "main" java.lang.NumberFormatException: For input string: ""
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:48)
at java.lang.Integer.parseInt(Integer.java:470)
at java.lang.Integer.parseInt(Integer.java:499)
at org.usadellab.trimmomatic.fastq.trim.MinLenTrimmer.<init>(MinLenTrimmer.java:11)
at org.usadellab.trimmomatic.fastq.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:47)
at org.usadellab.trimmomatic.TrimmomaticPE.main(TrimmomaticPE.java:346)
Thanks for your help again.
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