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nf-core / differentialabundance

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
https://nf-co.re/differentialabundance
MIT License
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Proteomics pipeline does not create the required file for the explotarory plot #198

Closed erdikucuk closed 4 months ago

erdikucuk commented 7 months ago

Description of the bug

Hi,

I'm trying to run the pipeline with the -maxgquant option and encountering a problem in this step, which is running a shiniyngs script:

exploratory_plots.R \
      --sample_metadata "ExperimentalSetup.sample_metadata.tsv" \
      --feature_metadata "matrix_as_anno.feature_metadata.tsv" \
      --assay_files "raw_proteingroups_tab.assay.tsv,normalizeMedian.normalized_proteingroups_tab.assay.tsv" \
      --contrast_variable "condition" \
      --outdir "condition" \
      --sample_id_col "sample" --feature_id_col "Protein IDs" --assay_names "raw,normalised,variance_stabilised" --final_assay "variance_stabilised" --outlier_mad_threshold -5 --palette_name "Set1" --log2_assays ''

It seems like this command is listing three condition names (raw, normalised, variance_stabilised) in the assay_names option but only gives two files as input in assay_files option. Which results in: 

 [1]Error in stringsToNamedVector(elements_string = opt$assay_files, opt$assay_names,  : 
    List in raw_proteingroups_tab.assay.tsv,normalizeMedian.normalized_proteingroups_tab.assay.tsv a different length to raw,normalised,variance_stabilised
   "Reading inputs..."
  Execution halted

I've checked the workdir and there are only two input files there, so I don't know how to produce the third one. I have added the full terminal output and the files I've used for the run. Thanks a lot in advance!

Command used and terminal output

Core Nextflow options
  revision                   : 1.3.1
  runName                    : pensive_hopper
  containerEngine            : singularity
  container                  : [RMARKDOWNNOTEBOOK:biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0]
  launchDir                  : /lustre/projects/bioinfo/data/2023_alahree_Mouse_Proteomics/nfcore
  workDir                    : /lustre/projects/bioinfo/data/2023_alahree_Mouse_Proteomics/nfcore/work
  projectDir                 : /home/kuecuek/.nextflow/assets/nf-core/differentialabundance
  userName                   : kuecuek
  profile                    : singularity
  configFiles                : 

Input/output options
  study_name                 : mouseproteomics_2h
  study_type                 : maxquant
  input                      : /projects/bioinfo/data/2023_alahree_Mouse_Proteomics/nfcore/ExperimentalSetup.tsv
  contrasts                  : /projects/bioinfo/data/2023_alahree_Mouse_Proteomics/nfcore/contrasts_experimental.tsv
  outdir                     : /projects/bioinfo/data/2023_alahree_Mouse_Proteomics/nfcore/output_experimental

Abundance values
  matrix                     : /projects/bioinfo/data/2023_alahree_Mouse_Proteomics/nfcore/input/proteinGroups.tsv
  affy_cel_files_archive     : null
  querygse                   : null

Features options
  features_id_col            : Protein IDs
  features_name_col          : Protein IDs

Affy input options
  affy_cdfname               : null

Proteus input options
  proteus_measurecol_prefix  : Reporter intensity

Limma specific options (microarray only)
  limma_spacing              : null
  limma_block                : null
  limma_correlation          : null

GSEA
  gsea_gene_sets             : null

Shiny app settings
  shinyngs_shinyapps_account : null
  shinyngs_shinyapps_app_name: null

Reporting options
  report_file                : /home/kuecuek/.nextflow/assets/nf-core/differentialabundance/assets/differentialabundance_report.Rmd
  logo_file                  : /home/kuecuek/.nextflow/assets/nf-core/differentialabundance/docs/images/nf-core-differentialabundance_logo_light.png
  css_file                   : /home/kuecuek/.nextflow/assets/nf-core/differentialabundance/assets/nf-core_style.css
  citations_file             : /home/kuecuek/.nextflow/assets/nf-core/differentialabundance/CITATIONS.md
  report_title               : null
  report_author              : null
  report_description         : null

!! 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

executor >  local (7)
[aa/a74b3a] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PROTEUS (condition)                                                                               [100%] 1 of 1 ✔
[e3/7a3792] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (ExperimentalSetup.tsv)                                                                 [100%] 1 of 1 ✔
[c0/7e6927] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:mouseproteomics_2h])                                                     [100%] 1 of 1 ✔
[87/43c2d1] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:LIMMA_DIFFERENTIAL ([id:trial, variable:condition, reference:Control, target:Treated, blocking:]) [100%] 1 of 1 ✔
[3a/6600bb] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)                                                                      [  0%] 0 of 1
[89/58277f] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL (trial)                                                                         [  0%] 0 of 1
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS                                                                       -
[25/97b31c] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP (mouseproteomics_2h)                                                                 [  0%] 0 of 1
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK                                                                                 -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE                                                                                -
ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)'

Caused by:
  Process `NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)` terminated with an error exit status (1)

Command executed:

  exploratory_plots.R \
      --sample_metadata "ExperimentalSetup.sample_metadata.tsv" \
      --feature_metadata "matrix_as_anno.feature_metadata.tsv" \
      --assay_files "raw_proteingroups_tab.assay.tsv,normalizeMedian.normalized_proteingroups_tab.assay.tsv" \
      --contrast_variable "condition" \
      --outdir "condition" \
      --sample_id_col "sample" --feature_id_col "Protein IDs" --assay_names "raw,normalised,variance_stabilised" --final_assay "variance_stabilised" --outlier_mad_threshold -5 --palette_name "Set1" --log2_assays ''

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
      r-shinyngs: $(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
  END_VERSIONS

Command exit status:
  1

Command output:
  [1] "Reading inputs..."
executor >  local (7)
[aa/a74b3a] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PROTEUS (condition)                                                                               [100%] 1 of 1 ✔
[e3/7a3792] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (ExperimentalSetup.tsv)                                                                 [100%] 1 of 1 ✔
[c0/7e6927] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:mouseproteomics_2h])                                                     [100%] 1 of 1 ✔
[87/43c2d1] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:LIMMA_DIFFERENTIAL ([id:trial, variable:condition, reference:Control, target:Treated, blocking:]) [100%] 1 of 1 ✔
[3a/6600bb] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)                                                                      [100%] 1 of 1, failed: 1 ✘
[89/58277f] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL (trial)                                                                         [  0%] 0 of 1
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS                                                                       -
[25/97b31c] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP (mouseproteomics_2h)                                                                 [  0%] 0 of 1
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK                                                                                 -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE                                                                                -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)'

Caused by:
  Process `NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)` terminated with an error exit status (1)

Command executed:

  exploratory_plots.R \
      --sample_metadata "ExperimentalSetup.sample_metadata.tsv" \
      --feature_metadata "matrix_as_anno.feature_metadata.tsv" \
      --assay_files "raw_proteingroups_tab.assay.tsv,normalizeMedian.normalized_proteingroups_tab.assay.tsv" \
      --contrast_variable "condition" \
      --outdir "condition" \
      --sample_id_col "sample" --feature_id_col "Protein IDs" --assay_names "raw,normalised,variance_stabilised" --final_assay "variance_stabilised" --outlier_mad_threshold -5 --palette_name "Set1" --log2_assays ''

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
      r-shinyngs: $(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
  END_VERSIONS

Command exit status:
  1

Command output:
  [1] "Reading inputs..."
executor >  local (7)
[aa/a74b3a] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PROTEUS (condition)                                                                               [100%] 1 of 1 ✔
[e3/7a3792] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (ExperimentalSetup.tsv)                                                                 [100%] 1 of 1 ✔
[c0/7e6927] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:mouseproteomics_2h])                                                     [100%] 1 of 1 ✔
[87/43c2d1] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:LIMMA_DIFFERENTIAL ([id:trial, variable:condition, reference:Control, target:Treated, blocking:]) [100%] 1 of 1 ✔
[3a/6600bb] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)                                                                      [100%] 1 of 1, failed: 1 ✘
[89/58277f] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL (trial)                                                                         [  0%] 0 of 1 ✔
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS                                                                       -
[25/97b31c] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP (mouseproteomics_2h)                                                                 [  0%] 0 of 1
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK                                                                                 -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE                                                                                -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)'

Caused by:
  Process `NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)` terminated with an error exit status (1)

Command executed:

  exploratory_plots.R \
      --sample_metadata "ExperimentalSetup.sample_metadata.tsv" \
      --feature_metadata "matrix_as_anno.feature_metadata.tsv" \
      --assay_files "raw_proteingroups_tab.assay.tsv,normalizeMedian.normalized_proteingroups_tab.assay.tsv" \
      --contrast_variable "condition" \
      --outdir "condition" \
      --sample_id_col "sample" --feature_id_col "Protein IDs" --assay_names "raw,normalised,variance_stabilised" --final_assay "variance_stabilised" --outlier_mad_threshold -5 --palette_name "Set1" --log2_assays ''

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
      r-shinyngs: $(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
  END_VERSIONS

Command exit status:
  1

Command output:
  [1] "Reading inputs..."
executor >  local (7)
[aa/a74b3a] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PROTEUS (condition)                                                                               [100%] 1 of 1 ✔
[e3/7a3792] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (ExperimentalSetup.tsv)                                                                 [100%] 1 of 1 ✔
[c0/7e6927] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:mouseproteomics_2h])                                                     [100%] 1 of 1 ✔
[87/43c2d1] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:LIMMA_DIFFERENTIAL ([id:trial, variable:condition, reference:Control, target:Treated, blocking:]) [100%] 1 of 1 ✔
[3a/6600bb] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)                                                                      [100%] 1 of 1, failed: 1 ✘
[89/58277f] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL (trial)                                                                         [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS                                                                       -
[25/97b31c] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP (mouseproteomics_2h)                                                                 [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK                                                                                 -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE                                                                                -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/differentialabundance] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)'

Caused by:
  Process `NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)` terminated with an error exit status (1)

Command executed:

  exploratory_plots.R \
      --sample_metadata "ExperimentalSetup.sample_metadata.tsv" \
      --feature_metadata "matrix_as_anno.feature_metadata.tsv" \
      --assay_files "raw_proteingroups_tab.assay.tsv,normalizeMedian.normalized_proteingroups_tab.assay.tsv" \
      --contrast_variable "condition" \
      --outdir "condition" \
      --sample_id_col "sample" --feature_id_col "Protein IDs" --assay_names "raw,normalised,variance_stabilised" --final_assay "variance_stabilised" --outlier_mad_threshold -5 --palette_name "Set1" --log2_assays ''

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
      r-shinyngs: $(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
  END_VERSIONS

Command exit status:
  1

Command output:
  [1] "Reading inputs..."
executor >  local (7)
[aa/a74b3a] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PROTEUS (condition)                                                                               [100%] 1 of 1 ✔
[e3/7a3792] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (ExperimentalSetup.tsv)                                                                 [100%] 1 of 1 ✔
[c0/7e6927] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:mouseproteomics_2h])                                                     [100%] 1 of 1 ✔
[87/43c2d1] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:LIMMA_DIFFERENTIAL ([id:trial, variable:condition, reference:Control, target:Treated, blocking:]) [100%] 1 of 1 ✔
[3a/6600bb] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)                                                                      [100%] 1 of 1, failed: 1 ✘
[89/58277f] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL (trial)                                                                         [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS                                                                       -
[25/97b31c] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP (mouseproteomics_2h)                                                                 [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK                                                                                 -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE                                                                                -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/differentialabundance] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)'

Caused by:
  Process `NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)` terminated with an error exit status (1)

Command executed:

  exploratory_plots.R \
      --sample_metadata "ExperimentalSetup.sample_metadata.tsv" \
      --feature_metadata "matrix_as_anno.feature_metadata.tsv" \
      --assay_files "raw_proteingroups_tab.assay.tsv,normalizeMedian.normalized_proteingroups_tab.assay.tsv" \
      --contrast_variable "condition" \
      --outdir "condition" \
      --sample_id_col "sample" --feature_id_col "Protein IDs" --assay_names "raw,normalised,variance_stabilised" --final_assay "variance_stabilised" --outlier_mad_threshold -5 --palette_name "Set1" --log2_assays ''

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
      r-shinyngs: $(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
  END_VERSIONS

Command exit status:
  1

Command output:
  [1] "Reading inputs..."

Command error:
      Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
      table, tapply, union, unique, unsplit, which.max, which.min

  Loading required package: S4Vectors

  Attaching package: ‘S4Vectors’

  The following object is masked from ‘package:utils’:

      findMatches

  The following objects are masked from ‘package:base’:

      expand.grid, I, unname

  Loading required package: IRanges
  Loading required package: GenomeInfoDb
  Loading required package: Biobase
  Welcome to Bioconductor

      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.

  Attaching package: ‘Biobase’

  The following object is masked from ‘package:MatrixGenerics’:

      rowMedians

  The following objects are masked from ‘package:matrixStats’:

      anyMissing, rowMedians

  Attaching package: ‘shinyngs’

  The following object is masked from ‘package:MatrixGenerics’:

      colMedians

  The following object is masked from ‘package:matrixStats’:

      colMedians

  [1]Error in stringsToNamedVector(elements_string = opt$assay_files, opt$assay_names,  : 
    List in raw_proteingroups_tab.assay.tsv,normalizeMedian.normalized_proteingroups_tab.assay.tsv a different length to raw,normalised,variance_stabilised
   "Reading inputs..."
  Execution halted

Work dir:
  /lustre/projects/bioinfo/data/2023_alahree_Mouse_Proteomics/nfcore/work/3a/6600bb6bba93236336b8e68268b2be

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details

Relevant files

call_experimental.txt contrasts_experimental.txt ExperimentalSetup.txt proteinGroups.txt

System information

No response

WackerO commented 7 months ago

Hey @erdikucuk, could you add the following parameters to you bash script and try rerunning?

    --exploratory_assay_names "raw,normalised" \
    --exploratory_final_assay "normalised" \
    --differential_feature_id_column "Protein IDs" \
    --differential_fc_column "logFC" \
    --differential_pval_column "adj.P.Val" \
    --differential_qval_column "P.Value" \
    --differential_file_suffix ".limma.results.tsv" \
    --features_metadata_cols 'Protein IDs' \
etlioglu commented 4 months ago

I have experienced the same issue as @erdikucuk documented and I can confirm that the additional parameters, that was suggested by @WackerO, solved the issue, my run with proteomics samples completed successfully.

erdikucuk commented 4 months ago

Hi,

Sorry I forgot the report, this also solved the issue for me.

etlioglu commented 4 months ago

I believe there is a small error in the following bit:

    --differential_pval_column "adj.P.Val" \
    --differential_qval_column "P.Value" \

That should have read:

    --differential_pval_column "P.Value" \
    --differential_qval_column "adj.P.Val" \