Entering edit mode
9 weeks ago
I have applied following in the folder where the data is:
java -jar Trimmomatic-0.39/trimmomatic-0.39.jar PE phred33 /home/*/*R1.fastq.gz /home/*/*R2.fastq.gz *R1.trimmed.fastq.gz *R1.untrimmed.fastq.gz *R2.trimmed.fastq.gz *R2.untrimmed.fastq.gz ILLUMINACLIP:/home/Trimmomatic/adapters/TruSeq3-SE.fa:2:30:7 MINLEN:15
the output i got:
TrimmomaticPE: Started with arguments: phred64 /home/*/*R1.fastq.gz /home/*/*R2.fastq.gz *R1.trimmed.fastq.gz *R1.untrimmed.fastq.gz *R2.trimmed.fastq.gz *R2.untrimmed.fastq.gz ILLUMINACLIP:/home/trimmomatic/adapters/TruSeq3-SE.fa:2:30:7 MINLEN:15 Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: *R2.untrimmed.fastq.gz at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:73) at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59) at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:552) at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)
don't use those stars and use the real files without globbing , and then update your post for a start.
Hi, I used real files only. here I just pasted the format that I used while trimming.
Even if you used real file names,
home/*/seems like a suspect path. Do you have a directory called
homein which ever directory you are running this from? Looks like that may need to start with a
/homeif you are referring to files in your home directory.
A similar issue may exist in this path
Thanks, but it still showing
unknown trimmer: <the output file>
Assuming you have the right number of options provided this is going to be a path issue. Make sure the file with adapter sequence exists. Provide full path to
hi, I provide full path, but it still shows same
Can you post the commandline again here, after you have fixed/implemented all of GenoMax remarks.
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