haatales.blogg.se - Script gb kill

Example error: Error executing process > 'FASTQC (hct116_h3k4me1_IP_R1_T1)' Then the error message of that tool will be displayed.

While generating outputs: if an expected process output is missing, Nextflow will fail with the message Missing output file(s). Check script '/home/lfaller/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq.nf' at line: 603 or see '.nextflow.log' file for more detailsĭuring run: for errors that occur while a pipeline is running or generating outputs it might be helpful to check log files as explained below. Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` command.sh: line 3: rsem-prepare-reference: command not found This type of error might also be related to a missing command required to run the pipeline. Check '.nextflow.log' file for detailsĭuring the first process: when an error appears during the first process it might indicate an issue with software dependencies, to specify how Nextflow should handle dependencies you need to select a configuration profile. Launching `./main.nf` - revision: bb0fa33a13ĮRROR ~ Unknown config attribute: projectDir - check config file: An example error is: N E X T F L O W ~ version 0.27.3 Docker daemon is running (if you are using Docker to manage dependencies).įor this step you try to identify when the error occurs:īefore the first process: errors that occur before the first process might be related to an outdated version of Nextflow, updating to the newest version could help solving the issue.There is enough disk space, this will avoid running out of space while you are running the pipeline.Use nextflow self-update to update a typical installation or conda update nextflow for a Bioconda installation. You might also want to check the following: There is an issue with the installation or configuration of Nextflow or software management tool, rather than a pipeline error. The Getting Started tutorial for further information. If Docker is not installed, you can replace docker with singularity or conda, see Start smallīefore using the pipeline with your data, make sure to run a test using: nextflow run nf-core/ -profile test,docker These are the recommended steps for troubleshooting a pipeline. My pipeline update doesn't seem to do anything.

Crashed pipeline with an error but Nextflow is still running.

I get a exceeded job memory limit error.

My pipeline crashes part way through a run at a certain step with a non 0 exit code.

Cannot find input files when using Singularity.

The pipeline crashes almost immediately with an early pipeline step.

Output for only a single sample although I specified multiple with wildcards.

Manual debugging on clusters using schedulers.

Read the log and check the work directory.