Can’t run trinity - Java version

Question

[houssienali]

Hi, Kindly help I can’t run trinity because of java version Error, do not understand options: --max_memory 2G —quality_trimming_params ILLUMINACLIP:/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 MINLEN:25 at ./Trinity.pl line 176.

[biofalconch]

A little bit difficult without a little bit more context, but I think you have to specify the path, but also don't forget the quotations! , since Trinity should have a copy of Trimmomatic, you would have to write something like this :

--quality_trimming_params "ILLUMINACLIP:$TRIMMOMATIC_DIR/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25"