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compomics-workflow's Introduction

Update

This project and workflow has been merged into the WOMBAT pipelines.

Please go to https://github.com/wombat-p/WOMBAT-Pipelines

Workflow to analyze label-free data with the compomics pipeline

This workflow is based on a docker image which is available at the docker hub (https://hub.docker.com/repository/docker/veitveit/compomicsworkflow) and is downloaded automatically. If you want to build your own docker image, be aware that it needs to be named veitveit/compomicsworkflow:dev or change the name in the configuration file.

Content

Nextflow folder: Implementation of workflow

data folder: additional data to run the UPS data set (NOT including the RAW files)

Results folder: Results from the running the UPS data set

Getting started

Here is a little script that can be used to test the workflow execution. This script assumes that Docker is available on your system and is targeting Debian/Ubuntu linux distributions.

# Install Java
sudo apt-get install openjdk-8-jdk

# Fix docker permission issue (https://stackoverflow.com/questions/48957195/how-to-fix-docker-got-permission-denied-issue)
# Note: this allows to run docker as non-root user
sudo usermod -aG docker $USER
newgrp docker

# Fetch scripts and data
git clone https://github.com/veitveit/IS_Benchmarking.git
cd ./Compomics-Workflow/Nextflow/data

# Nextflow
cd ..
curl -s https://get.nextflow.io | bash

# Worfklow
./nextflow run main.nf -profile docker,test

Run benchmarking data set

You should have successfully tested the workflow using the procedure above.

Download the raw files from PRIDE: http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD001819

Run the workflow with the following command and parameters after changing RAWFOLDER to the folder where the raw files are located. You will also need to place the files yeast_UPS.fasta and pxd001819.txt into in the current folder. These files is given in the Results folder: https://github.com/veitveit/IS_Benchmarking/tree/master/Compomics/Results

Also adjust the parameter values max_cpus and max_memory to the computing power you have available.

nextflow run main.nf --raws 'RAWFOLDER/*.raw' --fasta '../data/yeast_UPS.fasta' --miscleavages 2 \
  --fragment_mass_tolerance 0.8 --precursor_mass_tolerance 5 --enzyme 'Trypsin (no P rule)' \
  --variable_mods 'Oxidation of M,Acetylation of protein N-term' \
  --experiment_design '../data/pxd001819.txt' \
  --max_cpus 8 --max_memory 8GB \
  -profile docker -with-report -with-trace -with-timeline

compomics-workflow's People

Contributors

veitveit avatar julianu avatar

Stargazers

Ben Neely avatar

Watchers

James Cloos avatar avatar avatar

Forkers

julianu horvatovichlab

compomics-workflow's Issues

Workflow fails at MSqRob step

Step to reproduce :

./nextflow run main.nf --raws "../../data/*.raw" --fasta "../../data/*.fasta" --miscleavages 2 --fragment_mass_tolerance 0.5 --precursor_mass_tolerance 10.0 --enzyme "Trypsin (no P rule)" --variable_mods "Acetylation of protein N-term" --experiment_design "../../data/pxd001819.txt" --max_cpus 16 --max_memory 59GB -profile docker -with-report -with-trace -with-timeline

Main error

  Error in `$<-.data.frame`(`*tmp*`, genotype, value = character(0)) :
    replacement has 0 rows, data has 27

Error log

Error executing process > 'run_msqrob (1)'

Caused by:
  Process `run_msqrob (1)` terminated with an error exit status (1)

Command executed:

  echo "raw_file        exp_condition   biorep" > none
  cp "pxd001819.txt" exp_design.txt
  mv "QuantifiedPeptides.tsv" q_input.txt
  mv "QuantifiedProteins.tsv" q_prot.txt
  Rscript /home/gelonch/dev/jupyterlab_root/wombatp/Compomics-Workflow/Nextflow/scripts/runMSqRob.R

Command exit status:
  1

Command output:
  (empty)

Command error:
  Loading required package: stats4

  Attaching package: ‘S4Vectors’

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

      expand.grid, I, unname

  Loading required package: ProtGenerics

  Attaching package: ‘ProtGenerics’

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

      smooth

executor >  local (112)
[dd/f52dc0] process > convert_raw_mzml (25)      [100%] 27 of 27 ✔
[b4/30bbf3] process > create_decoy_database (1)  [100%] 1 of 1 ✔
[d6/82feb9] process > create_searchgui_paramfile [100%] 1 of 1 ✔
[7f/efd8ad] process > run_searchgui_search (21)  [100%] 27 of 27 ✔
[f6/599bd6] process > run_peptideshaker (27)     [100%] 27 of 27 ✔
[73/366318] process > get_peptideshaker_tsv (24) [100%] 27 of 27 ✔
[8b/7e557c] process > flashLFQ_all               [100%] 1 of 1 ✔
[d9/d587ca] process > run_msqrob (1)             [100%] 1 of 1, failed: 1 ✘
[-        ] process > run_final_qc               -
Error executing process > 'run_msqrob (1)'

Caused by:
  Process `run_msqrob (1)` terminated with an error exit status (1)

Command executed:

  echo "raw_file        exp_condition   biorep" > none
  cp "pxd001819.txt" exp_design.txt
  mv "QuantifiedPeptides.tsv" q_input.txt
  mv "QuantifiedProteins.tsv" q_prot.txt
  Rscript /home/gelonch/dev/jupyterlab_root/wombatp/Compomics-Workflow/Nextflow/scripts/runMSqRob.R

Command exit status:
  1

Command output:
  (empty)

Command error:
  Loading required package: stats4

  Attaching package: ‘S4Vectors’

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

      expand.grid, I, unname

  Loading required package: ProtGenerics

  Attaching package: ‘ProtGenerics’

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

      smooth


  This is MSnbase version 2.20.0
    Visit https://lgatto.github.io/MSnbase/ to get started.


  Attaching package: ‘MSnbase’

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

      trimws

  Loading required package: lme4
  Loading required package: Matrix

  Attaching package: ‘Matrix’

  The following object is masked from ‘package:S4Vectors’:

      expand


  Attaching package: ‘MSqRob’

  The following object is masked from ‘package:lme4’:

      getData

  Warning message:
  In options(stringsAsFactors = T) :
    'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
  Error in `$<-.data.frame`(`*tmp*`, genotype, value = character(0)) :
    replacement has 0 rows, data has 27
  Calls: $<- -> $<-.data.frame
  Execution halted

Work dir:
  /home/gelonch/dev/jupyterlab_root/wombatp/Compomics-Workflow/Nextflow/work/d9/d587caf90a1706fd49a8b2d8f73b71

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

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