Trimmomatic

Question

[sehriban.buyukkilic]

Hi everyone,

I have one problem with my code, but I couldn't understand what is it. Anyone can say what is wrong with me code, please.

Thank you so much.

java -jar /truba/home/sbuyukkilic/trimmomatic/Trimmomatic-0.39/trimmomatic-0.39.jar PE /truba/home/sbuyukkilic/fastqc_tool/sehriban SRR11192680_1.fastq.gz SRR11192680_2.fastq.gz SRR11192680_1_trimmed.fastq SRR11192680_1_unpaired.fastq SRR11192680_2_trimmed.fastq SRR11192680_2_unpaired.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36

[Pierre Lindenbaum]

I have one problem with my code

see https://meta.stackexchange.com/questions/147616

[sehriban.buyukkilic]

-bash-4.2$ java -jar /truba/home/sbuyukkilic/trimmomatic/Trimmomatic-0.39/trimmomatic-0.39.jar PE /truba/home/sbuyukkilic/fastqc_tool/sehriban SRR11192680_1.fastq.gz SRR11192680_2.fastq.gz SRR11192680_1_trimmed.fastq SRR11192680_1_unpaired.fastq SRR11192680_2_trimmed.fastq SRR11192680_2_unpaired.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36
TrimmomaticPE: Started with arguments:
 /truba/home/sbuyukkilic/fastqc_tool/sehriban SRR11192680_1.fastq.gz SRR11192680_2.fastq.gz SRR11192680_1_trimmed.fastq SRR11192680_1_unpaired.fastq SRR11192680_2_trimmed.fastq SRR11192680_2_unpaired.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36
Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: SRR11192680_2_unpaired.fastq

[sehriban.buyukkilic]

it's giving error like that

Answer 1

[Matthias Zepper]

Mind that it complains that SRR11192680_2_unpaired.fastq is an unknown trimmer. Evidently, it interprets your filename as a different parameter.

The software expects a fixed number of input and output files to work on. Your path /truba/home/sbuyukkilic/fastqc_tool/sehriban is interpreted as input_forward.fq.gz. Thus, you have a misalignment within your parameters.

[Felix]

As Matthias says, there is an extra parameter. Maybe you meant:

cd /truba/home/sbuyukkilic/fastqc_tool/sehriban
java -jar /truba/home/sbuyukkilic/trimmomatic/Trimmomatic-0.39/trimmomatic-0.39.jar PE  SRR11192680_1.fastq.gz SRR11192680_2.fastq.gz SRR11192680_1_trimmed.fastq SRR11192680_1_unpaired.fastq SRR11192680_2_trimmed.fastq SRR11192680_2_unpaired.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36

Btw. I find it clearer to use the parameters -basein and -baseout instead of the 6 file names, but that's just my preference.

[sehriban.buyukkilic]

thank you so much, Problem solved. It was about path, I was running Trimmomatic in the folder. In this situation no need to path.