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Execution for Kneaddata .. Trimmomatic issue #18666
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Same error |
Install trimmomatic without using conda and point to the directory using --trimmomatic. Worked for me. |
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. |
Just a heads up on this issue. Trimmomatic is installed to the bin folder as a symbolic link:
So if you instead give where the link points it should work:
It should work. |
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.
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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. |
Has this issue been solved? I'm pulling the bioconda docker image to a singularity image:
I try to run kneaddata_test:
With this result: Warning: unable to find trimmomatic*.jar. Where could it be?? |
Hi All, Trying to make a reproducible example here. I am having a similar problem. I downloaded installed kneaddata via conda:
and downloaded the tutorial files here
Running this command, I get an error that trimmomatic is not able to be found
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
runs trimmomatdc but yields a different error:
When I copy and paste just the java code, the same message results: But if I remove the
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.
Any suggestions on how to move forward are greatly appreciated! |
Thank you for your solution @aimirza. You save my life, it cost me two days to solve this problem. |
Hi @HollyKArnold were you able to resolve the issue? |
kneaddata has two issues, The second issue is caused by illumina sequencing label which lead to paired-end data as unmatched. Good luck |
Thanks for your response. |
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 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@a9bfd30cd ~/miniconda3/envs/kneaddata |
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:
Trying:
kneaddata -db examples/demo_db -i examples/demo.fastq -o out --trimmomatic /ifs/data/nfs_share/sukmb352/conda/metagenomics-devel/bin/trimmomatic
yields:
Trying:
kneaddata -db examples/demo_db -i examples/demo.fastq -o out --trimmomatic /ifs/data/nfs_share/sukmb352/conda/metagenomics-devel/bin/
yields:
How is this then supposed to work, exactly?
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