Error in executing read_classification (Kraken2)

[Krysasp]

Hi @replikation, i ran into following problem, i have pulled most recent updates and re-installed my kraken2 and singularity. What could be the cause of error at this step?

Error executing process > 'read_classification_wf:download_database_kraken2' Caused by: Process read_classification_wf:download_database_kraken2 terminated with an error exit status (127) Command executed: null Command exit status: 127 Command output: (empty) Command error: .command.sh: line 2: null: command not found Work dir: /home/ihcm-ubuntu/work/nextflow-poreCov-ihcm-ubuntu/e9/c99ec597af62845b30e46c58c7208b

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

[hoelzer]

Hi @Krysasp , whats the content fo /home/ihcm-ubuntu/work/nextflow-poreCov-ihcm-ubuntu/e9/c99ec597af62845b30e46c58c7208b/.command.log

It looks like the inital download of the kraken2 database fails which is not really realted to kraken2 itself and Singularity.

[replikation]

Could you please provide the full nextflow command.

[Krysasp]

thanks for the quick response! I'm running the following command: nextflow run replikation/poreCov --fastq_pass NANOPORE_DATA/R60/basecall/fastqpass/ -r 0.10.1 --cores 14 --output NANOPORE_DATA/R60/result/ -profile local,singularity

after error execution, i can only trace 3 'kraken.tar.gz' empty files there aren't any log i can trace directly in /work/nextflow-poreCov-ihcm-ubuntu/

should i rebuild manually the kraken2 databases?

[replikation]

• you got an exit 127 error, could it be that some disk or hardware stuff is not enough when executing the process. error null (i think) appears when it was not able to download from source one or two. (see the process below). otherwise it is a straight ubunut wget process. can you attach the execution HTML file? this shows us all the process - i think id was retrying it a few times before causing the error

    script:
    if (task.attempt.toString() == '0')
        """
        wget https://zenodo.org/record/4534746/files/GRCh38.p13_SC2_2021-02-08.tar.gz -O kraken.tar.gz
        """
    if (task.attempt.toString() == '1')
        """
        wget https://osf.io/eprfq/download -O kraken.tar.gz
        """

[Krysasp]

i attached them as text files. i have enough storage and ram, have been running revision 0.8.0 with no issue, but only noticed this issue after some recent installations of kraken2-dependent tools...

execution_report.txt execution_timeline.txt

thanks having a look..

[replikation]

@Krysasp i identified the issues. both databases are not downloadable at the moment. i need to prepare a fix

[Krysasp]

Thank you ! hope to see great tool back online : >

[replikation]

currently preparing a new release and doing some extensive testing will be included in the new release. and thanks for reporting

[replikation]

@Krysasp fixed in release 0.11.0

[Krysasp]

thank you for the release :) @replikation