Try 1: failed! 

(kneaddata) qiime2@qiime2core2020-11:~$ usr/share/trimmomatic
bash: usr/share/trimmomatic: No such file or directory

Try 2:(kneaddata) qiime2@qiime2core2020-11:~$ locate trimmomatic 
got a list of options 
/home/qiime2/Trimmomatic-0.33/trimmomatic-0.33.jar
/home/qiime2/miniconda/envs/kneaddata/bin/trimmomatic
/home/qiime2/miniconda/envs/kneaddata/conda-meta/trimmomatic-0.39-hdfd78af_2.json
/home/qiime2/miniconda/envs/kneaddata/share/trimmomatic
/home/qiime2/miniconda/envs/kneaddata/share/trimmomatic-0.39-2
/home/qiime2/miniconda/envs/kneaddata/share/trimmomatic-0.39-2/LICENSE
/home/qiime2/miniconda/envs/kneaddata/share/trimmomatic-0.39-2/adapters
/home/qiime2/miniconda/envs/kneaddata/share/trimmomatic-0.39-2/build_env_setup.sh
/home/qiime2/miniconda/envs/kneaddata/share/trimmomatic-0.39-2/conda_build.sh
/home/qiime2/miniconda/envs/kneaddata/share/trimmomatic-0.39-2/metadata_conda_debug.yaml
/home/qiime2/miniconda/envs/kneaddata/share/trimmomatic-0.39-2/trimmomatic
/home/qiime2/miniconda/envs/kneaddata/share/trimmomatic-0.39-2/trimmomatic.jar
/home/qiime2/miniconda/envs/kneaddata/share/trimmomatic-0.39-2/adapters/NexteraPE-PE.fa
/home/qiime2/miniconda/envs/kneaddata/share/trimmomatic-0.39-2/adapters/TruSeq2-PE.fa
/home/qiime2/miniconda/envs/kneaddata/share/trimmomatic-0.39-2/adapters/TruSeq2-SE.fa
/home/qiime2/miniconda/envs/kneaddata/share/trimmomatic-0.39-2/adapters/TruSeq3-PE-2.fa
/home/qiime2/miniconda/envs/kneaddata/share/trimmomatic-0.39-2/adapters/TruSeq3-PE.fa
/home/qiime2/miniconda/envs/kneaddata/share/trimmomatic-0.39-2/adapters/TruSeq3-SE.fa
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2.tar.bz2
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/bin
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/bin/trimmomatic
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/about.json
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/files
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/git
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/has_prefix
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/hash_input.json
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/index.json
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/link.json
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/paths.json
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/repodata_record.json
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/test
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/0.32
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/0.33
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/0.35
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/build.sh
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/conda_build_config.yaml
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/meta.yaml
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/meta.yaml.template
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/trimmomatic.py
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/0.32/build.sh
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/0.32/meta.yaml
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/0.32/trimmomatic.sh
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/0.33/build.sh
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/0.33/meta.yaml
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/0.33/trimmomatic.sh
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/0.35/build.sh
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/0.35/meta.yaml
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/recipe/0.35/trimmomatic.sh
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/test/run_test.bat
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/info/test/run_test.sh
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share/trimmomatic
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share/trimmomatic-0.39-2
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share/trimmomatic-0.39-2/LICENSE
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share/trimmomatic-0.39-2/adapters
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share/trimmomatic-0.39-2/build_env_setup.sh
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share/trimmomatic-0.39-2/conda_build.sh
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share/trimmomatic-0.39-2/metadata_conda_debug.yaml
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share/trimmomatic-0.39-2/trimmomatic
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share/trimmomatic-0.39-2/trimmomatic.jar
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share/trimmomatic-0.39-2/adapters/NexteraPE-PE.fa
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share/trimmomatic-0.39-2/adapters/TruSeq2-PE.fa
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share/trimmomatic-0.39-2/adapters/TruSeq2-SE.fa
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share/trimmomatic-0.39-2/adapters/TruSeq3-PE-2.fa
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share/trimmomatic-0.39-2/adapters/TruSeq3-PE.fa
/home/qiime2/miniconda/pkgs/trimmomatic-0.39-hdfd78af_2/share/trimmomatic-0.39-2/adapters/TruSeq3-SE.fa

Try 3: (kneaddata) qiime2@qiime2core2020-11:~$ locate Trimmomatic-0.33

/home/qiime2/Trimmomatic-0.33
/home/qiime2/Trimmomatic-0.33.zip
/home/qiime2/Trimmomatic-0.33/LICENSE
/home/qiime2/Trimmomatic-0.33/adapters
/home/qiime2/Trimmomatic-0.33/trimmomatic-0.33.jar
/home/qiime2/Trimmomatic-0.33/adapters/NexteraPE-PE.fa
/home/qiime2/Trimmomatic-0.33/adapters/TruSeq2-PE.fa
/home/qiime2/Trimmomatic-0.33/adapters/TruSeq2-SE.fa
/home/qiime2/Trimmomatic-0.33/adapters/TruSeq3-PE-2.fa
/home/qiime2/Trimmomatic-0.33/adapters/TruSeq3-PE.fa
/home/qiime2/Trimmomatic-0.33/adapters/TruSeq3-SE.fa


then back to command line 

 kneaddata --input1 /media/sf_Shared_folder/examples/demoR_1.fastq --input2 /media/sf_Shared_folder/examples/demoR_2.fastq --reference-db /home/qiime2/bowtie2/ --output kneedata_demo --trimmomatic /home/qiime2/Trimmomatic-0.33
Reformatting file sequence identifiers ...

Reformatting file sequence identifiers ...

Initial number of reads ( /home/qiime2/kneedata_demo/reformatted_identifierszt1wbpgy_demoR_1 ): 400.0
Initial number of reads ( /home/qiime2/kneedata_demo/reformatted_identifiersq75a9j4b_demoR_2 ): 400.0
Running Trimmomatic ... 
CRITICAL ERROR: Error executing: java -Xmx500m -jar /home/qiime2/Trimmomatic-0.33/trimmomatic-0.33.jar PE -threads 1 -phred33 /home/qiime2/kneedata_demo/reformatted_identifierszt1wbpgy_demoR_1 /home/qiime2/kneedata_demo/reformatted_identifiersq75a9j4b_demoR_2 /home/qiime2/kneedata_demo/demoR_1_kneaddata.trimmed.1.fastq /home/qiime2/kneedata_demo/demoR_1_kneaddata.trimmed.single.1.fastq /home/qiime2/kneedata_demo/demoR_1_kneaddata.trimmed.2.fastq /home/qiime2/kneedata_demo/demoR_1_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:50

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.

(kneaddata) qiime2@qiime2core2020-11:~$ kneaddata --input1 /media/sf_Shared_folder/examples/demoR_1.fastq --input2 /media/sf_Shared_folder/examples/demoR_2.fastq --reference-db /home/qiime2/bowtie2/ --output kneedata_demo --trimmomatic /home/qiime2/miniconda/envs/kneaddata/bin/trimmomatic 
ERROR: Unable to list files in trimmomatic directory: /home/qiime2/miniconda/envs/kneaddata/bin/trimmomatic

(kneaddata) qiime2@qiime2core2020-11:~$ kneaddata --input1 /media/sf_Shared_folder/examples/demoR_1.fastq --input2 /media/sf_Shared_folder/examples/demoR_2.fastq --reference-db /home/qiime2/bowtie2/ --output kneedata_demo --trimmomatic /home/qiime2/miniconda/envs/kneaddata/share/trimmomatic
Reformatting file sequence identifiers ...

Reformatting file sequence identifiers ...

Initial number of reads ( /home/qiime2/kneedata_demo/reformatted_identifiers60gpx85r_demoR_1 ): 400.0
Initial number of reads ( /home/qiime2/kneedata_demo/reformatted_identifiersha0rwy5__demoR_2 ): 400.0
Running Trimmomatic ... 
CRITICAL ERROR: Error executing: java -Xmx500m -jar /home/qiime2/miniconda/envs/kneaddata/share/trimmomatic/trimmomatic PE -threads 1 -phred33 /home/qiime2/kneedata_demo/reformatted_identifiers60gpx85r_demoR_1 /home/qiime2/kneedata_demo/reformatted_identifiersha0rwy5__demoR_2 /home/qiime2/kneedata_demo/demoR_1_kneaddata.trimmed.1.fastq /home/qiime2/kneedata_demo/demoR_1_kneaddata.trimmed.single.1.fastq /home/qiime2/kneedata_demo/demoR_1_kneaddata.trimmed.2.fastq /home/qiime2/kneedata_demo/demoR_1_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:50

Error message returned from Trimmomatic :
Error: Invalid or corrupt jarfile /home/qiime2/miniconda/envs/kneaddata/share/trimmomatic/trimmomatic