Numberformatexception error in Trimmomatic

[mariruilo]

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.

[JackieBadger]

maybe delete the space between "MINLEN:" and "100"?


The error:
For input string: ""

Is saying it doesn't recognize what is in between the ""
In this case I am betting it is refering to the space directly after MINLEN: as it is expecting a number directly after the colon

[mariruilo]

Thank you so much, I think I had changed everything except for that. Actually I hadn't seen the space...
It seems to be working now.