Execution for Kneaddata .. Trimmomatic issue

[marchoeppner]

Hi,

I just installed Kneaddata 0.7.3 into an empty Conda environment.

Running a short demo using data provided by the tool authors:

kneaddata -db examples/demo_db -i examples/demo.fastq -o out

yields:

ERROR: Unable to find trimmomatic. Please provide the full path to trimmomatic with --trimmomatic.

Trying:
kneaddata -db examples/demo_db -i examples/demo.fastq -o out --trimmomatic /ifs/data/nfs_share/sukmb352/conda/metagenomics-devel/bin/trimmomatic

yields:

ERROR: Unable to list files in trimmomatic directory: /ifs/data/nfs_share/sukmb352/conda/metagenomics-devel/bin/trimmomatic

Trying:
kneaddata -db examples/demo_db -i examples/demo.fastq -o out --trimmomatic /ifs/data/nfs_share/sukmb352/conda/metagenomics-devel/bin/

yields:

ERROR: The trimmomatic*.jar executable is not included in the directory: /ifs/data/nfs_share/sukmb352/conda/metagenomics-devel/bin

How is this then supposed to work, exactly?

[marcomeola]

Same error

[aimirza]

Install trimmomatic without using conda and point to the directory using --trimmomatic. Worked for me.

[Maryamtarazkar]

Would you please address me how I can install Trimmomatic without using conda on Linux? I followed (http://www.usadellab.org/cms/?page=trimmomatic) but I couldn't find and instruction how to install Trimmomatic.
Thank you for your help in advance

[rpetit3]

Just a heads up on this issue.

Trimmomatic is installed to the bin folder as a symbolic link:

ls -lh /home/rpetit3/miniconda3/envs/kneaddata/bin/trimmomatic
trimmomatic -> ../share/trimmomatic-0.39-1/trimmomatic

So if you instead give where the link points it should work:

kneaddata -db examples/demo_db -i examples/demo.fastq -o out --trimmomatic /home/rpetit3/miniconda3/envs/kneaddata/share/trimmomatic-0.39-1

It should work.

[aimirza]

Would you please address me how I can install Trimmomatic without using conda on Linux? I followed (http://www.usadellab.org/cms/?page=trimmomatic) but I couldn't find and instruction how to install Trimmomatic.
Thank you for your help in advance

In case @rpetit3 solution didn't work, you simply download the binary from the authors web page. Here are the steps I took. At the time of this post, Kneaddata web page requires Trimmomatic version 0.33. Thats what I installed. Though I've seen others install newer versions and it seemed to work for them. idk.

$ cd ~/bin
$ curl -o Trimmomatic-0.33.zip http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.33.zip
$ unzip Trimmomatic-0.33.zip
$ kneaddata --input seq1.fastq --input seq2.fastq -db $DATABASE --output kneaddata_output --trimmomatic ~/bin/Trimmomatic-0.33

[marchoeppner]

Thanks for the suggestions; but this still doesn't sound like a proper solution, Kneaddata should automatically require AND detect trimmomatic within the conda environment - not sure whether this would be best done by wrapping or modifiying the kneaddata executable or linking trimmomatic in a way that kneaddata can see it.

[patrickturko]

Has this issue been solved?

I'm pulling the bioconda docker image to a singularity image:

singularity pull docker://quay.io/biocontainers/kneaddata:0.10.0--pyhdfd78af_0

I try to run kneaddata_test:

singularity exec kneaddata:0.10.0-pyhdfd78af_0.sif kneaddata_test

With this result:

Warning: unable to find trimmomatic*.jar.

Where could it be??

[HollyKArnold]

Hi All, Trying to make a reproducible example here. I am having a similar problem.

I downloaded installed kneaddata via conda:

conda install -c bioconda kneaddata

and downloaded the tutorial files here

https://huttenhower.sph.harvard.edu/kneaddata/

Running this command, I get an error that trimmomatic is not able to be found

$ kneaddata --input input/singleEnd.fastq --reference-db input/demo_db --output kneaddataOutputSingleEnd

ERROR: Unable to find trimmomatic. Please provide the full path to trimmomatic with --trimmomatic.

As noted above, within conda, the trimmomatic is a link that points to the shared folder. Specifying the direct link to where the trimmomatic.jar is with the following command

kneaddata --input input/seq1.fastq --input input/seq2.fastq --reference-db input/demo_db --output kneaddataOutputPairedEnd --trimmomatic ../share/trimmomatic-0.39-2/

runs trimmomatdc but yields a different error:

Initial number of reads ( ~/input/seq1.fastq ): 42473 Initial number of reads ( ~/input/seq2.fastq ): 42473 Running Trimmomatic ...

CRITICAL ERROR: Error executing: java -Xmx500m -d64 -jar ~/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 1 -phred33 ~/input/seq1.fastq ~/input/seq2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.1.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.1.fastq ~/kneaddataTutorial/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.2.fastq SLIDINGWINDOW:4:20 MINLEN:122

Error message returned from Trimmomatic : Unrecognized option: -d64 Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.

When I copy and paste just the java code, the same message results:
java -Xmx500m -d64 -jar ~/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 1 -phred33 ~/input/seq1.fastq ~/input/seq2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.1.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.1.fastq ~/kneaddataTutorial/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.2.fastq SLIDINGWINDOW:4:20 MINLEN:122

But if I remove the -d64 and rerun, the program completes
java -Xmx500m -jar ~/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 1 -phred33 ~/input/seq1.fastq ~/input/seq2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.1.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.1.fastq ~/kneaddataTutorial/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.2.fastq SLIDINGWINDOW:4:20 MINLEN:122

TrimmomaticPE: Completed Successfully

However, this presents the problem that then the rest of the workflow for kneaddata is not run. I tried checking to see if perhaps I have the wrong version of java installed. The URL link is broken (#4 Java runtime environment link listed here: https://huttenhower.sph.harvard.edu/kneaddata/) to kneaddata's required java runtime environment.

java --version openjdk 10.0.2 2018-07-17 OpenJDK Runtime Environment Zulu10.3+5 (build 10.0.2+13) OpenJDK 64-Bit Server VM Zulu10.3+5 (build 10.0.2+13, mixed mode)

Any suggestions on how to move forward are greatly appreciated!

[Yunliang81]

Thank you for your solution @aimirza. You save my life, it cost me two days to solve this problem.

[shrez28]

Hi All, Trying to make a reproducible example here. I am having a similar problem.

I downloaded installed kneaddata via conda:

conda install -c bioconda kneaddata

and downloaded the tutorial files here

https://huttenhower.sph.harvard.edu/kneaddata/

Running this command, I get an error that trimmomatic is not able to be found

$ kneaddata --input input/singleEnd.fastq --reference-db input/demo_db --output kneaddataOutputSingleEnd

ERROR: Unable to find trimmomatic. Please provide the full path to trimmomatic with --trimmomatic.

As noted above, within conda, the trimmomatic is a link that points to the shared folder. Specifying the direct link to where the trimmomatic.jar is with the following command

kneaddata --input input/seq1.fastq --input input/seq2.fastq --reference-db input/demo_db --output kneaddataOutputPairedEnd --trimmomatic ../share/trimmomatic-0.39-2/

runs trimmomatdc but yields a different error:

Initial number of reads ( ~/input/seq1.fastq ): 42473 Initial number of reads ( ~/input/seq2.fastq ): 42473 Running Trimmomatic ...

CRITICAL ERROR: Error executing: java -Xmx500m -d64 -jar ~/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 1 -phred33 ~/input/seq1.fastq ~/input/seq2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.1.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.1.fastq ~/kneaddataTutorial/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.2.fastq SLIDINGWINDOW:4:20 MINLEN:122

Error message returned from Trimmomatic : Unrecognized option: -d64 Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.

When I copy and paste just the java code, the same message results: java -Xmx500m -d64 -jar ~/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 1 -phred33 ~/input/seq1.fastq ~/input/seq2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.1.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.1.fastq ~/kneaddataTutorial/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.2.fastq SLIDINGWINDOW:4:20 MINLEN:122

But if I remove the -d64 and rerun, the program completes java -Xmx500m -jar ~/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 1 -phred33 ~/input/seq1.fastq ~/input/seq2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.1.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.1.fastq ~/kneaddataTutorial/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.2.fastq SLIDINGWINDOW:4:20 MINLEN:122

TrimmomaticPE: Completed Successfully

However, this presents the problem that then the rest of the workflow for kneaddata is not run. I tried checking to see if perhaps I have the wrong version of java installed. The URL link is broken (#4 Java runtime environment link listed here: https://huttenhower.sph.harvard.edu/kneaddata/) to kneaddata's required java runtime environment.

java --version openjdk 10.0.2 2018-07-17 OpenJDK Runtime Environment Zulu10.3+5 (build 10.0.2+13) OpenJDK 64-Bit Server VM Zulu10.3+5 (build 10.0.2+13, mixed mode)

Any suggestions on how to move forward are greatly appreciated!

Hi @HollyKArnold were you able to resolve the issue?
Thanks!

[Yunliang81]

Hi All, Trying to make a reproducible example here. I am having a similar problem.
I downloaded installed kneaddata via conda:
conda install -c bioconda kneaddata
and downloaded the tutorial files here
https://huttenhower.sph.harvard.edu/kneaddata/
Running this command, I get an error that trimmomatic is not able to be found
$ kneaddata --input input/singleEnd.fastq --reference-db input/demo_db --output kneaddataOutputSingleEnd
ERROR: Unable to find trimmomatic. Please provide the full path to trimmomatic with --trimmomatic.
As noted above, within conda, the trimmomatic is a link that points to the shared folder. Specifying the direct link to where the trimmomatic.jar is with the following command
kneaddata --input input/seq1.fastq --input input/seq2.fastq --reference-db input/demo_db --output kneaddataOutputPairedEnd --trimmomatic ../share/trimmomatic-0.39-2/
runs trimmomatdc but yields a different error:
Initial number of reads ( ~/input/seq1.fastq ): 42473 Initial number of reads ( ~/input/seq2.fastq ): 42473 Running Trimmomatic ...
CRITICAL ERROR: Error executing: java -Xmx500m -d64 -jar ~/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 1 -phred33 ~/input/seq1.fastq ~/input/seq2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.1.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.1.fastq ~/kneaddataTutorial/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.2.fastq SLIDINGWINDOW:4:20 MINLEN:122
Error message returned from Trimmomatic : Unrecognized option: -d64 Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.
When I copy and paste just the java code, the same message results: java -Xmx500m -d64 -jar ~/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 1 -phred33 ~/input/seq1.fastq ~/input/seq2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.1.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.1.fastq ~/kneaddataTutorial/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.2.fastq SLIDINGWINDOW:4:20 MINLEN:122
But if I remove the -d64 and rerun, the program completes java -Xmx500m -jar ~/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 1 -phred33 ~/input/seq1.fastq ~/input/seq2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.1.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.1.fastq ~/kneaddataTutorial/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.2.fastq SLIDINGWINDOW:4:20 MINLEN:122
TrimmomaticPE: Completed Successfully
However, this presents the problem that then the rest of the workflow for kneaddata is not run. I tried checking to see if perhaps I have the wrong version of java installed. The URL link is broken (#4 Java runtime environment link listed here: https://huttenhower.sph.harvard.edu/kneaddata/) to kneaddata's required java runtime environment.
java --version openjdk 10.0.2 2018-07-17 OpenJDK Runtime Environment Zulu10.3+5 (build 10.0.2+13) OpenJDK 64-Bit Server VM Zulu10.3+5 (build 10.0.2+13, mixed mode)
Any suggestions on how to move forward are greatly appreciated!

Hi @HollyKArnold were you able to resolve the issue? Thanks!

kneaddata has two issues,
one is trimmomatic, we need to remove trimmomatic under ~/miniconda3/envs/kneaddata/bin/
download trimmomatic-0.39 and copy Trimmomatic-0.39.jar to ~/miniconda3/envs/kneaddata/bin/

The second issue is caused by illumina sequencing label which lead to paired-end data as unmatched.
to fix it, we need edit "./lib/python3.10/site-packages/kneaddata/utilities.py" according to the guidance in biobakery/kneaddata@a9bfd30

Good luck

[shrez28]

Hi All, Trying to make a reproducible example here. I am having a similar problem.
I downloaded installed kneaddata via conda:
conda install -c bioconda kneaddata
and downloaded the tutorial files here
https://huttenhower.sph.harvard.edu/kneaddata/
Running this command, I get an error that trimmomatic is not able to be found
$ kneaddata --input input/singleEnd.fastq --reference-db input/demo_db --output kneaddataOutputSingleEnd
ERROR: Unable to find trimmomatic. Please provide the full path to trimmomatic with --trimmomatic.
As noted above, within conda, the trimmomatic is a link that points to the shared folder. Specifying the direct link to where the trimmomatic.jar is with the following command
kneaddata --input input/seq1.fastq --input input/seq2.fastq --reference-db input/demo_db --output kneaddataOutputPairedEnd --trimmomatic ../share/trimmomatic-0.39-2/
runs trimmomatdc but yields a different error:
Initial number of reads ( ~/input/seq1.fastq ): 42473 Initial number of reads ( ~/input/seq2.fastq ): 42473 Running Trimmomatic ...
CRITICAL ERROR: Error executing: java -Xmx500m -d64 -jar ~/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 1 -phred33 ~/input/seq1.fastq ~/input/seq2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.1.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.1.fastq ~/kneaddataTutorial/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.2.fastq SLIDINGWINDOW:4:20 MINLEN:122
Error message returned from Trimmomatic : Unrecognized option: -d64 Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.
When I copy and paste just the java code, the same message results: java -Xmx500m -d64 -jar ~/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 1 -phred33 ~/input/seq1.fastq ~/input/seq2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.1.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.1.fastq ~/kneaddataTutorial/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.2.fastq SLIDINGWINDOW:4:20 MINLEN:122
But if I remove the -d64 and rerun, the program completes java -Xmx500m -jar ~/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 1 -phred33 ~/input/seq1.fastq ~/input/seq2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.1.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.1.fastq ~/kneaddataTutorial/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.2.fastq SLIDINGWINDOW:4:20 MINLEN:122
TrimmomaticPE: Completed Successfully
However, this presents the problem that then the rest of the workflow for kneaddata is not run. I tried checking to see if perhaps I have the wrong version of java installed. The URL link is broken (#4 Java runtime environment link listed here: https://huttenhower.sph.harvard.edu/kneaddata/) to kneaddata's required java runtime environment.
java --version openjdk 10.0.2 2018-07-17 OpenJDK Runtime Environment Zulu10.3+5 (build 10.0.2+13) OpenJDK 64-Bit Server VM Zulu10.3+5 (build 10.0.2+13, mixed mode)
Any suggestions on how to move forward are greatly appreciated!

Hi @HollyKArnold were you able to resolve the issue? Thanks!

kneaddata has two issues, one is trimmomatic, we need to remove trimmomatic under ~/miniconda3/envs/kneaddata/bin/ download trimmomatic-0.39 and copy Trimmomatic-0.39.jar to ~/miniconda3/envs/kneaddata/bin/

The second issue is caused by illumina sequencing label which lead to paired-end data as unmatched. to fix it, we need edit "./lib/python3.10/site-packages/kneaddata/utilities.py" according to the guidance in biobakery/kneaddata@a9bfd30

Good luck

Thanks for your response.
Have you tried to install with git? https://github.com/biobakery/biobakery/wiki/kneaddata
Install from source:
STEP 1 : $ git clone https://github.com/biobakery/kneaddata.git
STEP 2 : $ cd kneaddata
STEP 3 : $ python setup.py install

[Yunliang81]

Hi All, Trying to make a reproducible example here. I am having a similar problem.
I downloaded installed kneaddata via conda:
conda install -c bioconda kneaddata
and downloaded the tutorial files here
https://huttenhower.sph.harvard.edu/kneaddata/
Running this command, I get an error that trimmomatic is not able to be found
$ kneaddata --input input/singleEnd.fastq --reference-db input/demo_db --output kneaddataOutputSingleEnd
ERROR: Unable to find trimmomatic. Please provide the full path to trimmomatic with --trimmomatic.
As noted above, within conda, the trimmomatic is a link that points to the shared folder. Specifying the direct link to where the trimmomatic.jar is with the following command
kneaddata --input input/seq1.fastq --input input/seq2.fastq --reference-db input/demo_db --output kneaddataOutputPairedEnd --trimmomatic ../share/trimmomatic-0.39-2/
runs trimmomatdc but yields a different error:
Initial number of reads ( ~/input/seq1.fastq ): 42473 Initial number of reads ( ~/input/seq2.fastq ): 42473 Running Trimmomatic ...
CRITICAL ERROR: Error executing: java -Xmx500m -d64 -jar ~/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 1 -phred33 ~/input/seq1.fastq ~/input/seq2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.1.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.1.fastq ~/kneaddataTutorial/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.2.fastq SLIDINGWINDOW:4:20 MINLEN:122
Error message returned from Trimmomatic : Unrecognized option: -d64 Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.
When I copy and paste just the java code, the same message results: java -Xmx500m -d64 -jar ~/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 1 -phred33 ~/input/seq1.fastq ~/input/seq2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.1.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.1.fastq ~/kneaddataTutorial/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.2.fastq SLIDINGWINDOW:4:20 MINLEN:122
But if I remove the -d64 and rerun, the program completes java -Xmx500m -jar ~/share/trimmomatic-0.39-2/trimmomatic.jar PE -threads 1 -phred33 ~/input/seq1.fastq ~/input/seq2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.1.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.1.fastq ~/kneaddataTutorial/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.2.fastq ~/kneaddataOutputPairedEnd/seq1_kneaddata.trimmed.single.2.fastq SLIDINGWINDOW:4:20 MINLEN:122
TrimmomaticPE: Completed Successfully
However, this presents the problem that then the rest of the workflow for kneaddata is not run. I tried checking to see if perhaps I have the wrong version of java installed. The URL link is broken (#4 Java runtime environment link listed here: https://huttenhower.sph.harvard.edu/kneaddata/) to kneaddata's required java runtime environment.
java --version openjdk 10.0.2 2018-07-17 OpenJDK Runtime Environment Zulu10.3+5 (build 10.0.2+13) OpenJDK 64-Bit Server VM Zulu10.3+5 (build 10.0.2+13, mixed mode)
Any suggestions on how to move forward are greatly appreciated!

Hi @HollyKArnold were you able to resolve the issue? Thanks!

kneaddata has two issues, one is trimmomatic, we need to remove trimmomatic under ~/miniconda3/envs/kneaddata/bin/ download trimmomatic-0.39 and copy Trimmomatic-0.39.jar to ~/miniconda3/envs/kneaddata/bin/
The second issue is caused by illumina sequencing label which lead to paired-end data as unmatched. to fix it, we need edit "./lib/python3.10/site-packages/kneaddata/utilities.py" according to the guidance in biobakery/kneaddata@a9bfd30
Good luck

Thanks for your response. Have you tried to install with git? https://github.com/biobakery/biobakery/wiki/kneaddata Install from source: STEP 1 : $ git clone https://github.com/biobakery/kneaddata.git STEP 2 : $ cd kneaddata STEP 3 : $ python setup.py install

No, I used conda install ..

The following code for your reference

kneaddata has two issues, one is trimmomatic, we need to remove trimmomatic under ~/miniconda3/envs/kneaddata/bin/

download trimmomatic-0.39 and copy Trimmomatic-0.39.jar to ~/miniconda3/envs/kneaddata/bin/

wget https://github.com/usadellab/Trimmomatic/files/5854859/Trimmomatic-0.39.zip
unzip Trimmomatic-0.39.zip
cp Trimmomatic-0.39/Trimmomatic-0.39.jar ~/miniconda3/envs/kneaddata/bin/

The second issue is caused by illumina sequencing label which lead to paired-end data as unmatched.

to fix it, we need edit "./lib/python3.10/site-packages/kneaddata/utilities.py" according to the guidance in biobakery/kneaddata@a9bfd30

cd ~/miniconda3/envs/kneaddata
find -name utilities.py
nano ./lib/python3.10/site-packages/kneaddata/utilities.py # please add "if...." marked in green to line 391, see the attached graph at bottom