[62/149eb0] NOTE: Process `EURYALE:ALIGNMENT:DIAMOND_BLASTX (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1)
+Error executing process > 'EURYALE:ALIGNMENT:DIAMOND_BLASTX (WT_REP1)'
Caused by:
- Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137)
+ Process `EURYALE:ALIGNMENT:DIAMOND_BLASTX (WT_REP1)` terminated with an error exit status (137)
Command executed:
STAR \
@@ -264,7 +258,7 @@ Resource requests
(empty)
Command error:
- .command.sh: line 9: 30 Killed STAR --genomeDir star --readFilesIn WT_REP1_trimmed.fq.gz --runThreadN 2 --outFileNamePrefix WT_REP1. <TRUNCATED>
+ .command.sh: line 9: 30 Killed
Work dir:
/home/pipelinetest/work/9d/172ca5881234073e8d76f2a19c88fb
@@ -273,28 +267,30 @@ Resource requests
For beginners
A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefor you can try to increase the resource for the parameters --max_cpus, --max_memory, and --max_time. Based on the error above, you have to increase the amount of memory. Therefore you can go to the parameter documentation of rnaseq and scroll down to the show hidden parameter button to get the default value for --max_memory. In this case 128GB, you than can try to run your pipeline again with --max_memory 200GB -resume to skip all process, that were already calculated. If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below.
Advanced option on process level
-To bypass this error you would need to find exactly which resources are set by the STAR_ALIGN process. The quickest way is to search for process STAR_ALIGN in the nf-core/rnaseq Github repo.
-We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the modules/ directory and so, based on the search results, the file we want is modules/nf-core/star/align/main.nf.
-If you click on the link to that file you will notice that there is a label directive at the top of the module that is set to label process_high.
+
To bypass this error you would need to find exactly which resources are set by the DIAMOND_BLASTX process. The quickest way is to search for process DIAMOND_BLASTX in the dalmolingroup/euryale Github repo.
+We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the modules/ directory and so, based on the search results, the file we want is modules/nf-core/diamond/blastx/main.nf.
+If you click on the link to that file you will notice that there is a label directive at the top of the module that is set to label process_high.
The Nextflow label directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements.
-The default values for the process_high label are set in the pipeline's base.config which in this case is defined as 72GB.
-Providing you haven't set any other standard nf-core parameters to cap the maximum resources used by the pipeline then we can try and bypass the STAR_ALIGN process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB.
+The default values for the process_high label are set in the pipeline's base.config which in this case is defined as 72GB.
+Providing you haven't set any other standard nf-core parameters to cap the maximum resources used by the pipeline then we can try and bypass the DIAMOND_BLASTX process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 300GB.
The custom config below can then be provided to the pipeline via the -c parameter as highlighted in previous sections.
process {
- withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN' {
- memory = 100.GB
+ withName: 'EURYALE:ALIGNMENT:DIAMOND_BLASTX' {
+ memory = 300.GB
}
}
-NB: We specify the full process name i.e. NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN in the config file because this takes priority over the short name (STAR_ALIGN) and allows existing configuration using the full process name to be correctly overridden.
+NB: We specify the full process name i.e. EURYALE:ALIGNMENT:DIAMOND_BLASTX in the config file because this takes priority over the short name (DIAMOND_BLASTX) and allows existing configuration using the full process name to be correctly overridden.
If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly.
Updating containers (advanced users)
-The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the process name and override the Nextflow container definition for that process using the withName declaration. For example, in the nf-core/viralrecon pipeline a tool called Pangolin has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via -c custom.config.
+The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the process name and override the Nextflow container definition for that process using the withName declaration.
+For example, in the dalmolingroup/euryale pipeline a tool called Kraken2 is being used.
+You can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via -c custom.config.
-- Check the default version used by the pipeline in the module file for Pangolin
-- Find the latest version of the Biocontainer available on Quay.io
+- Check the default version used by the pipeline in the module file for Kraken2
+- Find the latest version of the Biocontainer available on Quay.io
-
Create the custom config accordingly:
@@ -302,8 +298,8 @@ Updating containers (advanced users)
For Docker:
nextflow
process {
- withName: PANGOLIN {
- container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0'
+ withName: KRAKEN2 {
+ container = 'quay.io/biocontainers/kraken2:2.1.3--pl5321hdcf5f25_2'
}
}
@@ -311,8 +307,8 @@ Updating containers (advanced users)
For Singularity:
nextflow
process {
- withName: PANGOLIN {
- container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0'
+ withName: KRAKEN2 {
+ container = 'https://depot.galaxyproject.org/singularity/kraken2%3A2.1.3--pl5321hdcf5f25_2'
}
}
@@ -321,13 +317,13 @@ Updating containers (advanced users)
nextflow
process {
withName: PANGOLIN {
- conda = 'bioconda::pangolin=3.0.5'
+ conda = 'bioconda::kraken2=2.1.3'
}
}
-NB: If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the work/ directory otherwise the -resume ability of the pipeline will be compromised and it will restart from scratch.
+NB: If you wish to periodically update individual tool-specific results (e.g. Kraken2) generated by the pipeline then you must ensure to keep the work/ directory otherwise the -resume ability of the pipeline will be compromised and it will restart from scratch.
Running in the background
Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.