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Trimmomatic errors #18

Closed Evansd36 closed 2 years ago

Evansd36 commented 2 years ago

Hello! I am having some issues with trimmomatic and biostars hasn't seemed to help much. Below are a couple different error messages I got. I am interested in any help you could give regarding what the error message is telling me!

Input: java -jar /home/es180966/anaconda/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 12 -phred33 -basein SRR16646612_1.fastq -baseout SRR16646612_1.fastq ILLUMINACLIP:/home/es180966/anaconda/envs/transect_env/sra_files/Many.truSeq.PE.fa.2.20.10.4 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Output: Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1java -jar

Input: /home/es180966/anaconda/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 12 -phred33 -basein SRR16646612_1.fastq SRR16646612_2.fastq -baseout SRR16646612_1.fastq SRR16646612_2.fastq SRR16646612_1_paired.fastq SRR166464612_1_unpaired.fastq SRR16646612_2_paired.fastq ILLUMINACLIP:/home/es180966/anaconda/envs/transect_env/sra_files/Many.truSeq.PE.fa.2.20.10.4 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Output: Using templated Input files: SRR16646612_1.fastq SRR16646612_2.fastq Using templated Output files: SRR16646612_1_1P.fastq SRR16646612_1_1U.fastq SRR16646612_1_2P.fastq SRR16646612_1_2U.fastq Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: SRR16646612_2.fastq

TonyBolger commented 2 years ago

I guess you have probably resolved this already, but if not - the various parameters to the trimmers need to separated by colons, so "ILLUMINACLIP:/home/es180966/anaconda/envs/transect_env/sra_files/Many.truSeq.PE.fa.2.20.10.4" should be "ILLUMINACLIP:/home/es180966/anaconda/envs/transect_env/sra_files/Many.truSeq.PE.fa:2:20:10:4"