Closed Krysasp closed 2 years ago
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.
Could you please provide the full nextflow command.
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?
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
"""
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..
@Krysasp i identified the issues. both databases are not downloadable at the moment. i need to prepare a fix
Thank you ! hope to see great tool back online : >
currently preparing a new release and doing some extensive testing will be included in the new release. and thanks for reporting
@Krysasp fixed in release 0.11.0
thank you for the release :) @replikation
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/c99ec597af62845b30e46c58c7208bTip: when you have fixed the problem you can continue the execution adding the option
-resume
to the run command line