Trimmomatic Unknown Trimmer Error for Output File

Question

[Nottuh]

Hi,

I've seen that multiple people have encountered an 'Unknown trimmer' error when using Trimmomatic and unfortunately me too. The code and output I use and receive are written below.

CODE:

for num in {1121292..1121303}
do
    java -jar /software/shared/apps/x86_64/trimmomatic/0.36/trimmomatic-0.36.jar SE -version 0.36 -phred64 SRR$num.fastq.gz SRR$num.trimmed.fastq.gz ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 TOPHRED33
done

OUTPUT:

Picked up JAVA_TOOL_OPTIONS: -XX:ParallelGCThreads=1
0.36
TrimmomaticSE: Started with arguments:
 -version 0.36 -phred64 SRR1121303.fastq.gz SRR1121303_trimmed.fastq.gz ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 TOPHRED33
Automatically using 4 threads
Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: SRR1121303_trimmed.fastq.gz
        at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:70)
        at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59)
        at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:303)
        at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:85)

Based on the output I get, the error should be due to the output name. But as I'm using SE reads there shouldn't be any file naming conventions according to the Trimmomatic manual. I've also tried removing the "extra parameters" such as -phred64 or ILLUMINACAP, as some people seemed to solve their errors when doing so, but I've been unsuccessful in doing so. Removing the parameter '-version 0.36' gives me an error saying that I'm using the trimmomatic command incorrectly, perhaps because there are multiple versions of trimmomatic installed on the server.

Any help would be appreciated as I feel I've spent more time on this problem than I should have.

[finswimmer]

I guess your problem is -version 0.36. I cannot find that this parameter exists.

fin swimmer

[Nottuh]

When trying to load trimmomatic by typing trimmomatic it returns the following output, showing how it is intended to be used.

SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...

Note that I am using version 0.36 of Trimmomatic and the Trimmomatic manual I found online dates from version 0.32. This manual doesn't seem to include the '-version' parameter.

Answer 1

[GenoMax]

$ trimmomatic -version
0.36

You don't need to actually put a version number in your command. As shown above trimmomatic will just print the version number you are using in the output, if you include -version parameter. It is presented in a confusing way but you can make a note that it is also included as a separate option at the end of the in-line help.

   $ trimmomatic 
    Usage: 
           PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
       or: 
           SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
       or: 
           -version

On a different note I don't think the dataset you have is likely to be phred+64 encoded. What makes you think so?

[Nottuh]

Hi Genomax,

I thought the '-version' parameter was optional, but leaving it out gave me the usage output you just posted before. You asked me about phred33 vs phred64 and I was mistaken. I based myself on the following site: https://www.drive5.com/usearch/manual/quality_score.html

But with this information I wrongly interpreted the data I had. Perhaps another dataset that I'm using was in phred64. I'm not sure why I got it wrong. Anyway, after changing phred64 to phred33 and removing the '-version' parameter. Trimmomatic seems to be running. Hopefully that's the end of it. Thanks!