Error in kneaddata

[Muneer111]

Hi @ EcoJulia
Hope you are fine and doing good
I am trying to run kneaddata and got this unexpected error

 **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.**

kindly suggest further

[kescobo]

Hi @Muneer111 thanks for trying out the package!

This error is from kneaddata itself, rather than the wrapper provided by this package, so it needs to be fixed with the underlying installation. Did you install this with BiobakeryUtils.install_deps(), or some other way?

I don't think I've ever seen this specific error before, but I've definitely seen problems with the trimmomatic dependency, see eg here

[Muneer111]

Hi @kescobo
thank you so much
No, I installed the kneaddata by this way
$ conda create --name kneaddata
$ source activate kneaddata
$ conda install -c cyclus java-jre
$ conda install -c bioconda fastqc
$ conda install -c bioconda trf
$ conda install -c bioconda kneaddata
$ conda install pip
$ pip install kneaddata
Then I installed Trimmomatic version 0.33 (but no through conda)
$ curl -o Trimmomatic-0.33.zip http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.33.zip
$ unzip Trimmomatic-0.33.zip
and finally installed the reference database
$ kneaddata_database --download human_genome bowtie2 <path/to/install/kneaddata_database.
And after successful installation ran the above mentioned command and resulted in error.
Thanks and Regards

[kescobo]

Hi @Muneer111 - So, that's a problem upstream of this package. I would recommend the following:

• If you are using this package to run kneaddata() from julia, try using BiobakeryUtils.install_deps()
• If you already have a conda environment, using conda to install trimmomatic
  • you may need to also set tbb=2020.2, see here

Note: this package is just a wrapper around biobakery, and not directly affiliated with them. If you have issues with biobakery command line functionality, please ask on their help forum https://forum.biobakery.org/

[Muneer111]

Hi @kescobo
Thank you for your help.
meanwhile I tried to download biobakery workflow
I followed this tutorial
https://github.com/biobakery/biobakery_workflows/wiki/Installing-the-workflows-with-pip
and successfully installed biobakery_workflows_databases --install wmgx.
Now which tutorial I will follow to run my samples.
Thanks and Regards

[Muneer111]

Hi@ Kescobo
Hope you are fine and doing good.
Today I installed kneaddata and ran i sample, it started well but after few minutes gave error
Problem 1
**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/bowtie2/ --output kneadata_81 **
Reformatting file sequence identifiers …

Reformatting file sequence identifiers …

Reordering read identifiers …

Initial number of reads ( /home/qiime2/kneadata_81/reordered_7yj33gia_reformatted_identifiers7tpvjx6v_81_R1 ): 22625162.0
Initial number of reads ( /home/qiime2/kneadata_81/reordered_xxlw0fsb_reformatted_identifiersmuluit7e_81_R2 ): 22625162.0
**Running Trimmomatic … **
CRITICAL ERROR: Error executing: java -Xmx500m -jar /home/qiime2/miniconda/envs/kneaddata/bin/trimmomatic PE -threads 1 -phred33 /home/qiime2/kneadata_81/reordered_7yj33gia_reformatted_identifiers7tpvjx6v_81_R1 /home/qiime2/kneadata_81/reordered_xxlw0fsb_reformatted_identifiersmuluit7e_81_R2 /home/qiime2/kneadata_81/81_R1_kneaddata.trimmed.1.fastq /home/qiime2/kneadata_81/81_R1_kneaddata.trimmed.single.1.fastq /home/qiime2/kneadata_81/81_R1_kneaddata.trimmed.2.fastq /home/qiime2/kneadata_81/81_R1_kneaddata.trimmed.single.2.fastq MINLEN:60 ILLUMINACLIP:/home/qiime2/miniconda/envs/kneaddata/lib/python3.10/site-packages/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:75

Error message returned from Trimmomatic :
java: symbol lookup error: java: undefined symbol: JLI_StringDup

Problem 2
I then tried to install biobakery_workflow_databses and got this error

biobakery_workflows_databases --install wmgx
Installing humann utility mapping database
Download URL: http://huttenhower.sph.harvard.edu/humann2_data/full_mapping_v201901.tar.gz
Downloading file of size: 2.55 GB

2.55 GB 100.00 % 1.49 MB/sec 0 min -0 sec
Extracting: /home/qiime2/biobakery_workflows_databases/humann/full_mapping_v201901.tar.gz

Database installed: /home/qiime2/biobakery_workflows_databases/humann/utility_mapping

HUMAnN configuration file updated: database_folders : utility_mapping = /home/qiime2/biobakery_workflows_databases/humann/utility_mapping
Generating strainphlan fasta database
Could not locate a Bowtie index corresponding to basename “/home/qiime2/miniconda/envs/kneaddata/lib/python3.8/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901”
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home/qiime2/miniconda/envs/abmiguez kneaddata/bin/bowtie2-inspect-s --wrapper basic-0 /home/qiime2/miniconda/envs/kneaddata/lib/python3.8/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901
Unable to install database. Error running command: bowtie2-inspect /home/qiime2/miniconda/envs/kneaddata/lib/python3.8/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901 > /home/qiime2/biobakery_workflows_databases/strainphlan_db_markers/all_markers.fasta

Problem 3
If success in installation please suggest what tutorial to follow for further analysis
thanks and regards

[kescobo]

Hi @Muneer111, it does not appear that you are using this package. Again, BiobakeryUtils.jl is a wrapper package for the julia language. I do not maintain the tools in the bioBakery.

Please direct your questions to https://forum.biobakery.org/