Comments (4)
dgoswamia
commented on June 26, 2024
1
Hello @WackerO , Thank you for your quick input,
After running: docker image prune -a
I able to run the whole nf-core/differentialabundance analysis pipeline. no issue.
Thanks again !!
Please close the ticket
from differentialabundance.
dgoswamia
commented on June 26, 2024
change profile to
profile : rnaseq,conda
still a similar error with atlas gene annotation manipulation package
N E X T F L O W ~ version 23.10.1
Launching https://github.com/nf-core/differentialabundance [friendly_heyrovsky] DSL2 - revision: a3d664c [master]
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
There is a problem with your Conda configuration!
You will need to set-up the conda-forge and bioconda channels correctly.
Please refer to https://bioconda.github.io/
The observed channel order is
[defaults]
but the following channel order is required:
[conda-forge, bioconda, defaults]
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/differentialabundance v1.4.0-ga3d664c
------------------------------------------------------
Core Nextflow options
revision : master
runName : friendly_heyrovsky
container : [RMARKDOWNNOTEBOOK:biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0]
launchDir : /user1/running_nextflow/differentialabundance
workDir : /user1/running_nextflow/differentialabundance/work
projectDir : /user1/.nextflow/assets/nf-core/differentialabundance
userName : wami
profile : rnaseq,conda
configFiles :
Input/output options
input : input_data/samplesheet_copy/samplesheet_RNASeq_v2.csv
contrasts : input_data/contrasts_observations/contrasts_file.csv
outdir : input_data/output_03_14_2024
Abundance values
matrix : input_data/countmatrix/salmon.merged.gene_counts.tsv
affy_cel_files_archive : null
querygse : null
Affy input options
affy_cdfname : null
Proteus input options
proteus_round_digits : -1
Filtering
filtering_min_abundance : 1
filtering_min_samples : 1
Differential analysis
differential_min_fold_change: 2
differential_max_pval : 1
Limma specific options (microarray only)
limma_spacing : null
limma_block : null
limma_correlation : null
limma_p_value : 1
GSEA
gsea_gene_sets : null
Shiny app settings
shinyngs_shinyapps_account : null
shinyngs_shinyapps_app_name : null
Reporting options
report_file : /user1/.nextflow/assets/nf-core/differentialabundance/assets/differentialabundance_report.Rmd
logo_file : /user1/.nextflow/assets/nf-core/differentialabundance/docs/images/nf-core-differentialabundance_logo_light.png
css_file : /user1/.nextflow/assets/nf-core/differentialabundance/assets/nf-core_style.css
citations_file : /user1/.nextflow/assets/nf-core/differentialabundance/CITATIONS.md
report_title : null
report_author : null
report_description : null
Reference genome options
gtf : input_data/gtf_annotation/gencode.v21.chr_patch_hapl_scaff.annotation.gtf
Institutional config options
config_profile_name : RNA-seq profile
config_profile_description : Settings for RNA-seq analysis
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/differentialabundance for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.7568000
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/differentialabundance/blob/master/CITATIONS.md
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE -
ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE'
Caused by:
Conda environment file does not exist: modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml
-- Check '.nextflow.log' file for details
-[nf-core/differentialabundance] Pipeline completed with errors-
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK -
[- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE -
ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE'
Caused by:
Conda environment file does not exist: modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml
from differentialabundance.
WackerO
commented on June 26, 2024
Hello @dgoswamia, this seems to be not a pipeline problem, but an issue with docker. Not sure how much I can help with this, but you could try pruning your docker images?
from differentialabundance.
dgoswamia
commented on June 26, 2024
Thanks to @WackerO for quick comment
from differentialabundance.
Related Issues (20)
- Remove parameter --gsea_run HOT 1
- URGENT: pin nf-validation version HOT 2
- Dev version: On parameters website list parameter gene_sets_files in section GSEA HOT 1
- Name of blocking variable not correctly recognized HOT 7
- Continuous covariates HOT 6
- Please pin the version of the nf-validation plugin! HOT 1
- Error with samplesheet.csv with two column headers that have prefix in common HOT 8
- release differentialabundance
- Error in TABULAR_TO_GSEA_CHIP HOT 1
- GSEA html reports have broken links to png and TSV files HOT 1
- Failed to publish file => double forward slashes
- Auto-format sample names HOT 2
- PosixFileAttributeView
- Missing colour and hover labels in interactive report volcano plot HOT 1
- Normalized/Raw data mishap on the report HOT 1
- Provide a parameter to disable rmarkdown report creation in the differential abundance pipeline HOT 1
- Requests: Enhancements to DESeq2 csv outputs and PDF outputs
- For spike-in analysis, remove control features from outputs
- How to use `--transcript_length_matrix` with nf-core/rnaseq `--aligner star_rsem` output? HOT 1
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