Critical error help

[adamber1187]

Hi all,

New to using kneaddata and trying to play around with some .fastq files. I keep getting the following error, any recommendations to solve? Thanks in advance.

(sequencing) berlinba@RHEUM-HJJPCS2:/mnt/c/Users/berlinba/documents$ kneaddata --input mega_test.fastq --reference-db kneaddata_reference --output kneaddata_megatest

Initial number of reads ( /mnt/c/Users/berlinba/documents/mega_test.fastq ): 149610.0

Running Trimmomatic ...

CRITICAL ERROR: Error executing: java -Xmx500m -jar /mnt/c/Users/berlinba/Documents/Trimmomatic-0.39/trimmomatic-0.39.jar SE -threads 1 -phred33 /mnt/c/Users/berlinba/documents/mega_test.fastq /mnt/c/Users/berlinba/documents/kneaddata_megatest/mega_test_kneaddata.trimmed.fastq ILLUMINACLIP:/home/berlinba/anaconda3/envs/sequencing/lib/python3.6/site-packages/kneaddata/adapters/TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:150

[Lauren McIver]

Hello, It looks like an issue running trimmomatic. If you would try running that java command directly it should give us more details about the specific error. Please feel free to post the error message if you would like help debugging.

Thanks,

Lauren

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[adamber1187]

Hi Lauren,

You are absolutely right, it was an issue with running trimmomatic. Turns out my JRE was outdated, and updated fixed the issue. Thanks a bunch for the reply.

-Adam

On Monday, September 9, 2019 at 10:09:58 AM UTC-6, Lauren McIver wrote:

Hello, It looks like an issue running trimmomatic. If you would try running that java command directly it should give us more details about the specific error. Please feel free to post the error message if you would like help debugging.

Thanks,

Lauren

On Mon, Sep 9, 2019 at 9:01 AM adamber1187 <adam.be...@gmail.com> wrote:

Hi all,

New to using kneaddata and trying to play around with some .fastq files. I keep getting the following error, any recommendations to solve? Thanks in advance.

(sequencing) berlinba@RHEUM-HJJPCS2:/mnt/c/Users/berlinba/documents$ kneaddata --input mega_test.fastq --reference-db kneaddata_reference --output kneaddata_megatest

Initial number of reads ( /mnt/c/Users/berlinba/documents/mega_test.fastq ): 149610.0

Running Trimmomatic ...

CRITICAL ERROR: Error executing: java -Xmx500m -jar /mnt/c/Users/berlinba/Documents/Trimmomatic-0.39/trimmomatic-0.39.jar SE -threads 1 -phred33 /mnt/c/Users/berlinba/documents/mega_test.fastq /mnt/c/Users/berlinba/documents/kneaddata_megatest/mega_test_kneaddata.trimmed.fastq ILLUMINACLIP:/home/berlinba/anaconda3/envs/sequencing/lib/python3.6/site-packages/kneaddata/adapters/TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:150

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