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deng-lab / viroprofiler

A containerized bioinformatics pipeline for viral metagenomic data analysis
https://deng-lab.github.io/viroprofiler
MIT License
23 stars 12 forks source link

--mode "setup" fails with custom --db value: read-only file system #19

Open stas-malavin opened 11 months ago

stas-malavin commented 11 months ago

Description of the bug

Setup fails, complaining about inability to create a subfolder (vibrant) in the folder I supply with the --db argument. Without custom --db works fine, but I don't want the databases to be in my home folder.

Command used and terminal output

Without sudo:

N E X T F L O W  ~  version 23.04.3
Launching `https://github.com/deng-lab/viroprofiler` [tender_austin] DSL2 - revision: c2a1f1871b [main]

----------------------------------------------------------------------------------------------------------------
                                               __                                                                
 oooooo     oooo  o8o                        88  88                        .o88o.  o8o  oooo                     
  `888.     .8'   `"'                       88 ss 88                       888 `"  `"'  `888                     
   `888.   .8'   oooo  oooo d8b  .ooooo.     88__88    oooo d8b  .ooooo.  o888oo  oooo   888   .ooooo.  oooo d8b 
    `888. .8'    `888  `888""8P d88' `88b      ||      `888""8P d88' `88b  888    `888   888  d88' `88b `888""8P 
     `888.8'      888   888     888   888     _||_      888     888   888  888     888   888  888ooo888  888     
      `888'       888   888     888   888   // || \\    888     888   888  888     888   888  888    .o  888     
       `8'       o888o d888b    `Y8bod8P'  //      \\  d888b    `Y8bod8P' o888o   o888o o888o `Y8bod8P' d888b    
  ViroProfiler v0.2.4
----------------------------------------------------------------------------------------------------------------
Core Nextflow options
  revision       : main
  runName        : tender_austin
  containerEngine: singularity
  launchDir      : /media/bioinf/Data/viroprofiler
  workDir        : /media/bioinf/Data/viroprofiler/work
  projectDir     : /home/bioinf/.nextflow/assets/deng-lab/viroprofiler
  userName       : bioinf
  profile        : singularity
  configFiles    : /home/bioinf/.nextflow/assets/deng-lab/viroprofiler/nextflow.config

Input/output options
  mode           : setup
  db             : /media/bioinf/Data/viroprofiler
  outdir         : output

QC
  contamref_idx  : /home/bioinf/viroprofiler/contamination_refs/hg19/ref

Contig library parameters
  assemblies     : scaffolds

Others
  use_iphop      : true
  use_dram       : true

Max job request options
  max_cpus       : 1
  max_memory     : 8.GB
  max_time       : 12.h

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

* The ViroProfiler pipeline
 Ru, Jinlong, et al. "ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis."
 Gut Microbes 15.1 (2023): 2192522. https://doi.org/10.1080/19490976.2023.2192522

* The nf-core framework
 Ewels, Philip A., et al. "The nf-core framework for community-curated bioinformatics pipelines."
 Nature biotechnology 38.3 (2020): 276-278. https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/deng-lab/viroprofiler/blob/main/CITATIONS.md
----------------------------------------------------------------------------------------------------------------
[-        ] process > VIROPROFILER:SETUP:DB_CHECKV     -
[-        ] process > VIROPROFILER:SETUP:DB_VIBRANT    -
executor >  local (3)
[-        ] process > VIROPROFILER:SETUP:DB_CHECKV     -
executor >  local (3)
[-        ] process > VIROPROFILER:SETUP:DB_CHECKV     -
executor >  local (3)
[-        ] process > VIROPROFILER:SETUP:DB_CHECKV     -
executor >  local (3)
[-        ] process > VIROPROFILER:SETUP:DB_CHECKV     -
executor >  local (3)
[-        ] process > VIROPROFILER:SETUP:DB_CHECKV     -
executor >  local (3)
[-        ] process > VIROPROFILER:SETUP:DB_CHECKV     -
[84/c6b5c2] process > VIROPROFILER:SETUP:DB_VIBRANT    [100%] 1 of 1, failed: 1 ✘
[ca/f0ce4e] process > VIROPROFILER:SETUP:DB_VIRSORTER2 [100%] 1 of 1, failed: 1 ✘
[-        ] process > VIROPROFILER:SETUP:DB_DRAM       -
[33/246c58] process > VIROPROFILER:SETUP:DB_IPHOP      [100%] 1 of 1, failed: 1 ✘
[-        ] process > VIROPROFILER:SETUP:DB_VREFSEQ    -
Pulling Singularity image docker://denglab/viroprofiler-base:v0.2 [cache /media/bioinf/Data/singularity_cache/denglab-viroprofiler-base-v0.2.img]
Pulling Singularity image docker://denglab/viroprofiler-geneannot:v0.2 [cache /media/bioinf/Data/singularity_cache/denglab-viroprofiler-geneannot-v0.2.img]
Execution cancelled -- Finishing pending tasks before exit
-[ViroProfiler] Pipeline completed with errors-
ERROR ~ Error executing process > 'VIROPROFILER:SETUP:DB_VIBRANT'

Caused by:
  Process `VIROPROFILER:SETUP:DB_VIBRANT` terminated with an error exit status (1)

Command executed:

  if [ ! -d /media/bioinf/Data/viroprofiler/vibrant ]; then
      mkdir -p /media/bioinf/Data/viroprofiler/vibrant
      export VIBRANT_DATA_PATH="/opt/conda/share/vibrant-1.2.1/db"
      download-db.sh /media/bioinf/Data/viroprofiler/vibrant
  else
      echo "VIBRANT database already exists"
  fi

Command exit status:
  1

Command output:
  (empty)

Command error:
  mkdir: cannot create directory ‘/media/bioinf/Data/viroprofiler/vibrant’: Read-only file system

Work dir:
  /media/bioinf/Data/viroprofiler/work/84/c6b5c25b808e8aba045a107cb49ac9

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

Same with sudo:


N E X T F L O W  ~  version 23.04.3
Launching `https://github.com/deng-lab/viroprofiler` [angry_wing] DSL2 - revision: c2a1f1871b [main]

----------------------------------------------------------------------------------------------------------------
                                               __                                                                
 oooooo     oooo  o8o                        88  88                        .o88o.  o8o  oooo                     
  `888.     .8'   `"'                       88 ss 88                       888 `"  `"'  `888                     
   `888.   .8'   oooo  oooo d8b  .ooooo.     88__88    oooo d8b  .ooooo.  o888oo  oooo   888   .ooooo.  oooo d8b 
    `888. .8'    `888  `888""8P d88' `88b      ||      `888""8P d88' `88b  888    `888   888  d88' `88b `888""8P 
     `888.8'      888   888     888   888     _||_      888     888   888  888     888   888  888ooo888  888     
      `888'       888   888     888   888   // || \\    888     888   888  888     888   888  888    .o  888     
       `8'       o888o d888b    `Y8bod8P'  //      \\  d888b    `Y8bod8P' o888o   o888o o888o `Y8bod8P' d888b    
  ViroProfiler v0.2.4
----------------------------------------------------------------------------------------------------------------
Core Nextflow options
  revision       : main
  runName        : angry_wing
  containerEngine: singularity
  launchDir      : /media/bioinf/Data/viroprofiler
  workDir        : /media/bioinf/Data/viroprofiler/work
  projectDir     : /home/bioinf/.nextflow/assets/deng-lab/viroprofiler
  userName       : root
  profile        : singularity
  configFiles    : /home/bioinf/.nextflow/assets/deng-lab/viroprofiler/nextflow.config

Input/output options
  mode           : setup
  db             : /media/bioinf/Data/viroprofiler
  outdir         : output

QC
  contamref_idx  : /home/bioinf/viroprofiler/contamination_refs/hg19/ref

Contig library parameters
  assemblies     : scaffolds

Others
  use_iphop      : true
  use_dram       : true

Max job request options
  max_cpus       : 1
  max_memory     : 8.GB
  max_time       : 12.h

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

* The ViroProfiler pipeline
 Ru, Jinlong, et al. "ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis."
 Gut Microbes 15.1 (2023): 2192522. https://doi.org/10.1080/19490976.2023.2192522

* The nf-core framework
 Ewels, Philip A., et al. "The nf-core framework for community-curated bioinformatics pipelines."
 Nature biotechnology 38.3 (2020): 276-278. https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/deng-lab/viroprofiler/blob/main/CITATIONS.md
----------------------------------------------------------------------------------------------------------------
executor >  local (2)
[-        ] process > VIROPROFILER:SETUP:DB_CHECKV     -
executor >  local (3)
[-        ] process > VIROPROFILER:SETUP:DB_CHECKV     -
executor >  local (3)
[-        ] process > VIROPROFILER:SETUP:DB_CHECKV     -
executor >  local (3)
[-        ] process > VIROPROFILER:SETUP:DB_CHECKV     -
executor >  local (3)
[-        ] process > VIROPROFILER:SETUP:DB_CHECKV     -
executor >  local (3)
[-        ] process > VIROPROFILER:SETUP:DB_CHECKV     -
[e9/2a8e6a] process > VIROPROFILER:SETUP:DB_VIBRANT    [100%] 1 of 1, failed: 1 ✘
[6b/e97a14] process > VIROPROFILER:SETUP:DB_VIRSORTER2 [100%] 1 of 1, failed: 1 ✘
[-        ] process > VIROPROFILER:SETUP:DB_DRAM       -
[24/3376dc] process > VIROPROFILER:SETUP:DB_IPHOP      [100%] 1 of 1, failed: 1 ✘
[-        ] process > VIROPROFILER:SETUP:DB_VREFSEQ    -
Pulling Singularity image docker://denglab/viroprofiler-geneannot:v0.2 [cache /media/bioinf/Data/singularity_cache/denglab-viroprofiler-geneannot-v0.2.img]
Pulling Singularity image docker://denglab/viroprofiler-base:v0.2 [cache /media/bioinf/Data/singularity_cache/denglab-viroprofiler-base-v0.2.img]
Execution cancelled -- Finishing pending tasks before exit
-[ViroProfiler] Pipeline completed with errors-
ERROR ~ Error executing process > 'VIROPROFILER:SETUP:DB_VIBRANT'

Caused by:
  Process `VIROPROFILER:SETUP:DB_VIBRANT` terminated with an error exit status (1)

Command executed:

  if [ ! -d /media/bioinf/Data/viroprofiler/vibrant ]; then
      mkdir -p /media/bioinf/Data/viroprofiler/vibrant
      export VIBRANT_DATA_PATH="/opt/conda/share/vibrant-1.2.1/db"
      download-db.sh /media/bioinf/Data/viroprofiler/vibrant
  else
      echo "VIBRANT database already exists"
  fi

Command exit status:
  1

Command output:
  (empty)

Command error:
  mkdir: cannot create directory ‘/media/bioinf/Data/viroprofiler/vibrant’: Read-only file system

Work dir:
  /media/bioinf/Data/viroprofiler/work/e9/2a8e6a55c8e400100dbd97ec403619

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

.nextflow.log

System information

$ nextflow -v
nextflow version 23.04.3.5875
$ cat /etc/*release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=22.04
DISTRIB_CODENAME=jammy
DISTRIB_DESCRIPTION="Ubuntu 22.04.3 LTS"
PRETTY_NAME="Ubuntu 22.04.3 LTS"
NAME="Ubuntu"
VERSION_ID="22.04"
VERSION="22.04.3 LTS (Jammy Jellyfish)"
VERSION_CODENAME=jammy
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=jammy

Executed locally Viroprofile v. 0.2.4 Containers: current example is with Singularity, but I've tried Docker with the same result.