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Error in trimmomatic

Open Muneer111 opened this issue 1 year ago • 0 comments

Hi @timflutre Hope you are fine and keeping safe I am running kneaddata, but it gave and error with Trimmomatic **kneaddata –input1 /media/sf_Shared_folder/ovas/Final/81_R1.fastq --input2 /media/sf_Shared_folder/ovas/Final/81_R2.fastq --reference-db /home/qiime2/ref_dtabase/ --output kneaddata_81 --trimmomatic /home/qiime2/Trimmomatic-0.33 Reformatting file sequence identifiers …

Reformatting file sequence identifiers …

Reordering read identifiers …

Initial number of reads ( /home/qiime2/kneaddata_81/reordered_qhik9bbx_reformatted_identifierse3uxy95f_81_R1 ): 22625162.0 Initial number of reads ( /home/qiime2/kneaddata_81/reordered_enctz3x3_reformatted_identifiersd8ic66o3_81_R2 ): 22625162.0 Running Trimmomatic … CRITICAL ERROR: Error executing: java -Xmx500m -jar /home/qiime2/Trimmomatic-0.33/trimmomatic-0.33.jar PE -threads 1 -phred33 /home/qiime2/kneaddata_81/reordered_qhik9bbx_reformatted_identifierse3uxy95f_81_R1 /home/qiime2/kneaddata_81/reordered_enctz3x3_reformatted_identifiersd8ic66o3_81_R2 /home/qiime2/kneaddata_81/81_R1_kneaddata.trimmed.1.fastq /home/qiime2/kneaddata_81/81_R1_kneaddata.trimmed.single.1.fastq /home/qiime2/kneaddata_81/81_R1_kneaddata.trimmed.2.fastq /home/qiime2/kneaddata_81/81_R1_kneaddata.trimmed.single.2.fastq MINLEN:60 ILLUMINACLIP:/home/qiime2/miniconda/envs/kneaddata/lib/python3.8/site-packages/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:75

Error message returned from Trimmomatic : <JAVA_HOME>/lib/ext exists, extensions mechanism no longer supported; Use -classpath instead. .Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit** I posted not biobakery forum, but didn't got any response yet can understand the time constraints and busy schedule of every one there). Kindly guide how to overcome this issue.

Muneer111 avatar Aug 04 '23 06:08 Muneer111