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nf-core / circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
https://nf-co.re/circrna
MIT License
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SOLUTION: re-run with at least --limitSjdbInsertNsj #156

Closed ZabalaAitor closed 4 months ago

ZabalaAitor commented 4 months ago

Description of the bug

Hello!

I am trying to solve the following error, but I am not able to use the parameter --limitSjdbInsertNsj to resolve it.

Thank you very much for your time and assistance in resolving this issue.

Command used and terminal output

nextflow pull nf-core/circrna

nextflow run nf-core/circRNA \
    -r dev \
    -profile apptainer \
    --input /data/azabala/RNAseq_MS/samplesheet_circRNA.csv \
    --phenotype /data/azabala/RNAseq_MS/phenotype.csv \
    --module 'circrna_discovery' \
    --outdir /scratch/azabala/circRNA_MS \
    --tool 'circrna_finder' \
    --limitSjdbInsertNsj 1413850 \
    --max_cpus 24 \
    --max_memory 256GB \
    -w /scratch/azabala/circRNA_MS/work_circRNA_MS \
    --genome GRCh38 \
    --save_reference false \
    --gtf /data/azabala/gtf/UCSC/NCBI/hg38.ncbiRefSeq.gtf \
    -resume

Checking nf-core/circrna ...
 Already-up-to-date - revision: 4a2d30f69f [dev]
N E X T F L O W  ~  version 23.04.2
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [4a2d30f69f]
Launching `https://github.com/nf-core/circRNA` [voluminous_rosalind] DSL2 - revision: d4199c40a8 [dev]
WARN: Nextflow self-contained distribution allows only core plugins -- User config plugins will be ignored: nf-validation@1.1.3
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/circrna vdev-gd4199c4
------------------------------------------------------
Core Nextflow options
  revision       : dev
  runName        : voluminous_rosalind
  containerEngine: apptainer
  launchDir      : /scratch/azabala/circRNA_MS
  workDir        : /scratch/azabala/circRNA_MS/work_circRNA_MS
  projectDir     : /home/azabala/.nextflow/assets/nf-core/circRNA
  userName       : azabala
  profile        : apptainer
  configFiles    : 

Input/output options
  input          : /data/azabala/RNAseq_MS/samplesheet_circRNA.csv
  outdir         : /scratch/azabala/circRNA_MS
  phenotype      : /data/azabala/RNAseq_MS/phenotype.csv

Pipeline Options
  tool           : circrna_finder

Reference genome options
  save_reference : false
  genome         : GRCh38
  fasta          : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa
  gtf            : /data/azabala/gtf/UCSC/NCBI/hg38.ncbiRefSeq.gtf
  mature         : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Annotation/SmallRNA/mature.fa

Max job request options
  max_cpus       : 24
  max_memory     : 256GB

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/circrna for your analysis please cite:

* The pipeline

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/circrna/blob/master/CITATIONS.md
------------------------------------------------------
WARN: The following invalid input values have been detected:

* --limitSjdbInsertNsj: 1413850
* --limit-sjdb-insert-nsj: 1413850

Relevant files

No response

System information

Nextflow: 23.04.2 Hardware: HPC Executor: slurm Container: Apptainer OS: Linux nf-core/circrna: dev

nictru commented 4 months ago

This is strange, the according parameter limitSjdbInsertNsj should exist. Not the limit-sjdb-insert-nsj one though.

To eliminate other influences, could you try running the test configuration with the parameter enabled? nextflow run nf-core/circrna -r dev --limitSjdbInsertNsj 1413850 -profile test,apptainer

If it still fails, I think the following line is most suspicious: WARN: Nextflow self-contained distribution allows only core plugins -- User config plugins will be ignored: nf-validation@1.1.3

ZabalaAitor commented 4 months ago

That works!

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/circrna vdev-g4a2d30f
------------------------------------------------------
Core Nextflow options
  revision                  : dev
  runName                   : stoic_brazil
  containerEngine           : apptainer
  launchDir                 : /scratch/azabala
  workDir                   : /scratch/azabala/work
  projectDir                : /home/azabala/.nextflow/assets/nf-core/circrna
  userName                  : azabala
  profile                   : test,apptainer
  configFiles               : 

Input/output options
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/circrna/samples.csv
  outdir                    : results/
  phenotype                 : https://raw.githubusercontent.com/nf-core/test-datasets/circrna/phenotype.csv

Discovery Options
  bsj_reads                 : 2

Alignment Options
  limitSjdbInsertNsj        : 1413850

Reference genome options
  fasta                     : https://raw.githubusercontent.com/nf-core/test-datasets/circrna/reference/chrI.fa
  gtf                       : https://raw.githubusercontent.com/nf-core/test-datasets/circrna/reference/chrI.gtf
  mature                    : https://raw.githubusercontent.com/nf-core/test-datasets/circrna/reference/mature.fa
  species_id                : cel

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Max job request options
  max_cpus                  : 2
  max_memory                : 6 GB
  max_time                  : 6h
nictru commented 4 months ago

Something just caught my eye in your original error message:

NOTE: Your local project version looks outdated - a different revision is available in the remote repository [4a2d30f69f]
Launching `https://github.com/nf-core/circRNA` [voluminous_rosalind] DSL2 - revision: d4199c40a8 [dev]

The commit d4199c40a8 does not contain the parameter limitSjdbInsertNsj yet. So I guess the pipeline pulling did not work as expected? But somehow you have the latest version now

ZabalaAitor commented 4 months ago

You are right. When I try to run my script, it seems like I do not have the latest version, and I get the following message:

NOTE: Your local project version looks outdated - a different revision is available in the remote repository [4a2d30f69f]
Launching `https://github.com/nf-core/circRNA` [voluminous_rosalind] DSL2 - revision: d4199c40a8 [dev]

However, when I run the test code, it appears to be updated.

nictru commented 4 months ago

So I guess there is no pipeline-specific problem here. If you need help updating the pipeline properly let me know, otherwise feel free to close the issue.

ZabalaAitor commented 4 months ago

How can I update the pipeline properly? Usingnextflow pull nf-core/circrna only updated the test code script.

(base) 16:41:42-azabala@hyperion-login-02:/scratch/azabala$ nextflow pull nf-core/circrna
Checking nf-core/circrna ...
 Already-up-to-date - revision: 4a2d30f69f [dev]
(base) 16:50:08-azabala@hyperion-login-02:/scratch/azabala$ nextflow run nf-core/circRNA -r dev -profile apptainer --input /data/azabala/RNAseq_MS/samplesheet_circRNA.csv --phenotype /data/azabala/RNAseq_MS/phenotype.csv --module 'circrna_discovery' --outdir /scratch/azabala/limit/ --tool 'circrna_finder' --limitSjdbInsertNsj 1413850 --max_cpus 2 --max_memory 6GB -w /scratch/azabala/limit/work_circRNA_MS --genome GRCh38 --save_reference false --gtf /data/azabala/gtf/UCSC/NCBI/hg38.ncbiRefSeq.gtf 
N E X T F L O W  ~  version 23.04.2
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [4a2d30f69f]
Launching `https://github.com/nf-core/circRNA` [high_goldwasser] DSL2 - revision: d4199c40a8 [dev]
WARN: Nextflow self-contained distribution allows only core plugins -- User config plugins will be ignored: nf-validation@1.1.3
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/circrna vdev-gd4199c4
------------------------------------------------------
Core Nextflow options
  revision       : dev
  runName        : high_goldwasser
  containerEngine: apptainer
  launchDir      : /scratch/azabala
  workDir        : /scratch/azabala/limit/work_circRNA_MS
  projectDir     : /home/azabala/.nextflow/assets/nf-core/circRNA
  userName       : azabala
  profile        : apptainer
  configFiles    : 

Input/output options
  input          : /data/azabala/RNAseq_MS/samplesheet_circRNA.csv
  outdir         : /scratch/azabala/limit/
  phenotype      : /data/azabala/RNAseq_MS/phenotype.csv

Pipeline Options
  tool           : circrna_finder

Reference genome options
  save_reference : false
  genome         : GRCh38
  fasta          : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa
  gtf            : /data/azabala/gtf/UCSC/NCBI/hg38.ncbiRefSeq.gtf
  mature         : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Annotation/SmallRNA/mature.fa

Max job request options
  max_cpus       : 2
  max_memory     : 6GB

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/circrna for your analysis please cite:

* The pipeline

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/circrna/blob/master/CITATIONS.md
------------------------------------------------------
WARN: The following invalid input values have been detected:

* --limitSjdbInsertNsj: 1413850
* --limit-sjdb-insert-nsj: 1413850
* * 
(base) 16:50:30-azabala@hyperion-login-02:/scratch/azabala$ nextflow run nf-core/circrna -r dev --limitSjdbInsertNsj 1413850 -profile test,apptainer
N E X T F L O W  ~  version 23.04.2
Launching `https://github.com/nf-core/circrna` [romantic_mandelbrot] DSL2 - revision: 4a2d30f69f [dev]
WARN: Nextflow self-contained distribution allows only core plugins -- User config plugins will be ignored: nf-validation@1.1.3
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/circrna vdev-g4a2d30f
------------------------------------------------------
Core Nextflow options
  revision                  : dev
  runName                   : romantic_mandelbrot
  containerEngine           : apptainer
  launchDir                 : /scratch/azabala
  workDir                   : /scratch/azabala/work
  projectDir                : /home/azabala/.nextflow/assets/nf-core/circrna
  userName                  : azabala
  profile                   : test,apptainer
  configFiles               : 

Input/output options
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/circrna/samples.csv
  outdir                    : results/
  phenotype                 : https://raw.githubusercontent.com/nf-core/test-datasets/circrna/phenotype.csv

Discovery Options
  bsj_reads                 : 2

Alignment Options
  limitSjdbInsertNsj        : 1413850

Reference genome options
  fasta                     : https://raw.githubusercontent.com/nf-core/test-datasets/circrna/reference/chrI.fa
  gtf                       : https://raw.githubusercontent.com/nf-core/test-datasets/circrna/reference/chrI.gtf
  mature                    : https://raw.githubusercontent.com/nf-core/test-datasets/circrna/reference/mature.fa
  species_id                : cel

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Max job request options
  max_cpus                  : 2
  max_memory                : 6 GB
  max_time                  : 6h

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/circrna for your analysis please cite:

* The pipeline

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/circrna/blob/master/CITATIONS.md
------------------------------------------------------
nictru commented 4 months ago

Interesting, as both runs refer to /home/azabala/.nextflow/assets/nf-core/circrna as projectDir - should have the same content for both runs, so I don't really understand how this can happen

I would probably delete /home/azabala/.nextflow/assets/nf-core/circrna and try again

ZabalaAitor commented 4 months ago

Deleting /home/azabala/.nextflow/assets/nf-core/circrna did not solve the problem.

nictru commented 4 months ago

There's not really much I can do to help you with this, but I can give you some hints:

  1. /home/azabala/.nextflow/assets/nf-core/circrna should be a git directory, so you can play around a bit there
  2. You can always clone the github repository to any local directory and execute the nextflow run command with the path of that directory
ZabalaAitor commented 4 months ago

It seems that the /home/azabala/.nextflow/assets/nf-core/circrna directory was not deleted properly. After removing it, I was able to update the pipeline correctly and run the script with no problems.

Thanks for your help!

nictru commented 4 months ago

Good to hear!