Trimmomatic - unknown trimmer error?

[BioBing]

Hi all,

I am really struggling with Trimmomatic these days and the frustration level is rising (I have to meet a deadline). For multiple days Trimmomatic, on usegalaxy.org, has given me an error as soon as I apply the IlluminaClip:

Fatal error: Exit code 1 () Trimmomatic did not finish successfully

It works like a charm when applying the options for quality trimming, head-crop etc. I reported the error a few days ago, but it is still not working. In order to move along, I installed Trimmomatic on my computer (mac OS Sierra) through the homebrew/science command line application.

When I run Trimmomatic, I continue to get an "unknown trimmer" error and cannot figure out how to fix it. Usage of command line and coding are still fairly new to me.

I have applied following in the folder where the data is:

 
ENSPAC1515:01_Raw_data user$ 
Trimmomatic PE -trimlog L001_adapter.txt  
-basein Reference-Sample-index27_S1_L001_R1_001.fastq.gz 
Reference-Sample-index27_S1_L001_R2_001.fastq.gz 
-baseout L001_adapter_R1_P.fastq.gz L001_adapter_R1_U.fastq.gz
L001_adapter_R2_P.fastq.gz L001_adapter_R2_U.fastq.gz 
ILLUMINACLIP: TruSeq3-PE.fa:2:40:15

And this happens:

TrimmomaticPE: Started with arguments:
-trimlog L001_adapter.txt 
-basein Reference-Sample-index27_S1_L001_R1_001.fastq.gz 
           Reference-Sample-index27_S1_L001_R2_001.fastq.gz
-baseout L001_adapter_R1_P.fq.gz 
              L001_adapter_R1_U.fq.gz 
              L001_adapter_R2_P.fq.gz 
              L001_adapter_R2_U.fq.gz 
ILLUMINACLIP: TruSeq3-PE.fa:2:40:15

Multiple cores found: Using 4 threads

Using templated Input files: 
Reference-Sample-index27_S1_L001_R1_001.fastq.gz 
Reference-Sample-index27_S1_L001_R2_001.fastq.gz

Using templated Output files: 
L001_adapter_R1_P_1P.fq.gz L001_adapter_R1_P_1U.fq.gz
L001_adapter_R1_P_2P.fq.gz L001_adapter_R1_P_2U.fq.gz

Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: 
Reference-Sample-index27_S1_L001_R2_001.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.TrimmomaticPE.run
(TrimmomaticPE.java:536)
at org.usadellab.trimmomatic.Trimmomatic.main
(Trimmomatic.java:80)

I also tried to download the Truseq3-PE.fa and use the path to it in the Illuminaclip (but I get the same error). Hopefully some of you, know how to fix this? You will save my day if you do

Thank you!!

[mastal]

Remove '-basein' and '-baseout', and leave the rest of your command the way it is, I think it should then work. When you specify the full names of all the input and output files, you don't need to use -basein and -baseout.

[BioBing]

Hi Mastal,

Thank you so much for responding. I tried as you suggested, but it is still not working

java -jar trimmomatic-0.36.jar PE –trimlog logfile L001_R1.fastq L001_R2.fastq L001_R1_P.fastq L001_R1_U.fastq L001_R2_P.fastq L001_R2_U.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:40:15

TrimmomaticPE: Started with arguments:
 –trimlog logfile L001_R1.fastq L001_R2.fastq L001_R1_P.fastq L001_R1_U.fastq L001_R2_P.fastq L001_R2_U.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:40:15
Multiple cores found: Using 4 threads
Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: L001_R2_P.fastq
	at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:70)
	at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59)
	at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:536)
	at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

I have no idea what is the issue. This time I tried directly with the java file.

[BioBing]

I solved it!!!

I deleted the -trimlog part, and suddenly it worked!

This is the code I used, in case others have similar issues:

I solved it! By deleting -trimlog, -inbase and -outbase - as well as found a space that should not be there, it worked!

In case others have the same issue, this is how my code looked like (this time I used the homebrew version):

Trimmomatic PE L001_R1.fastq L001_R2.fastq out_L001_R1_P.fastq out_L001_R1_U.fastq out_L001_R2_P.fastq L001_R2_U.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:40:15