SOLUTION: re-run with at least --limitSjdbInsertNsj #156

ZabalaAitor · 2024-07-02T12:08:05Z

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NOTE: Your local project version looks outdated - a different revision is available in the remote repository [4a2d30f69f]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: [email protected]
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

The text was updated successfully, but these errors were encountered:

nictru · 2024-07-02T13:24:15Z

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: [email protected]

ZabalaAitor · 2024-07-02T13:31:16Z

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 · 2024-07-02T13:47:29Z

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 · 2024-07-02T14:11:39Z

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 · 2024-07-02T14:37:48Z

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 · 2024-07-02T14:53:41Z

How can I update the pipeline properly? Using nextflow 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: [email protected]
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: [email protected]
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 · 2024-07-02T16:17:32Z

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 · 2024-07-03T08:10:17Z

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

nictru · 2024-07-03T12:22:56Z

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

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

ZabalaAitor · 2024-07-03T14:22:36Z

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 · 2024-07-03T14:38:28Z

Good to hear!

ZabalaAitor added the bug Something isn't working label Jul 2, 2024

nictru closed this as completed Jul 3, 2024

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SOLUTION: re-run with at least --limitSjdbInsertNsj #156

SOLUTION: re-run with at least --limitSjdbInsertNsj #156

ZabalaAitor commented Jul 2, 2024 •

edited

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nictru commented Jul 2, 2024

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edited

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ZabalaAitor commented Jul 3, 2024 •

edited

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nictru commented Jul 3, 2024

SOLUTION: re-run with at least --limitSjdbInsertNsj #156

SOLUTION: re-run with at least --limitSjdbInsertNsj #156

Comments

ZabalaAitor commented Jul 2, 2024 • edited Loading

Description of the bug

Command used and terminal output

Relevant files

System information

nictru commented Jul 2, 2024

ZabalaAitor commented Jul 2, 2024 • edited Loading

nictru commented Jul 2, 2024

ZabalaAitor commented Jul 2, 2024

nictru commented Jul 2, 2024

ZabalaAitor commented Jul 2, 2024

nictru commented Jul 2, 2024

ZabalaAitor commented Jul 3, 2024

nictru commented Jul 3, 2024

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ZabalaAitor commented Jul 2, 2024 •

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ZabalaAitor commented Jul 2, 2024 •

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ZabalaAitor commented Jul 3, 2024 •

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