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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

Problem in finding iphop database #16

Open mhmism opened 1 year ago

mhmism commented 1 year ago

Description of the bug

Nextflow is checking Iphop database at the home directory even after specifying another db directory. This will cause error at Iphop step

Command used and terminal output

nextflow run deng-lab/viroprofiler -r main -profile singularity,test -resume –db /gpfs/work5/0/gusr0570/viroprofiler

Output:
N E X T F L O W  ~  version 23.04.1
Launching `https://github.com/deng-lab/viroprofiler` [fervent_jang] DSL2 - revision: c2a1f1871b [main]

----------------------------------------------------------------------------------------------------------------
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  `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                   : fervent_jang
  containerEngine           : singularity
  launchDir                 : /gpfs/work5/0/gusr0570/test
  workDir                   : /gpfs/work5/0/gusr0570/test/work
  projectDir                : /home/mibrahim30/.nextflow/assets/deng-lab/viroprofiler
  userName                  : mibrahim30
  profile                   : singularity,test
  configFiles               : /home/mibrahim30/.nextflow/assets/deng-lab/viroprofiler/nextflow.config

Input/output options
  mode                      : all
  input                     : https://raw.githubusercontent.com/deng-lab/viroprofiler/main/assets/samplesheet.csv
  db                        : /home/mibrahim30/viroprofiler
  outdir                    : output

QC
  contamref_idx             : /home/mibrahim30/viroprofiler/contamination_refs/hg19/ref

Contig library parameters
  assemblies                : scaffolds

Others
  use_iphop                 : true
  use_dram                  : true

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                  : 24.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 (3)
[f7/b6f3b4] process > VIROPROFILER:FASTQC (UC21)               [100%] 5 of 5, cached: 5 ✔
[13/f89bd9] process > VIROPROFILER:FASTP (UC21)                [100%] 5 of 5, cached: 5 ✔
[1c/9970e8] process > VIROPROFILER:SPADES (UC21)               [100%] 5 of 5, cached: 5 ✔
[1f/2ad85a] process > VIROPROFILER:CONTIGLIB                   [100%] 1 of 1, cached: 1 ✔
[14/94debb] process > VIROPROFILER:CHECKV                      [100%] 1 of 1, cached: 1 ✔
[37/5cbccf] process > VIROPROFILER:CONTIGLIB_CLUSTER           [100%] 1 of 1, cached: 1 ✔
[53/1726a0] process > VIROPROFILER:GENEPRED4CTG                [100%] 1 of 1, cached: 1 ✔
[ee/75a2fe] process > VIROPROFILER:NRPROT                      [100%] 1 of 1, cached: 1 ✔
[ff/bc6c4a] process > VIROPROFILER:NRGENE                      [100%] 1 of 1, cached: 1 ✔
[4c/68df51] process > VIROPROFILER:CONTIGINDEX                 [100%] 1 of 1, cached: 1 ✔
[d6/52905e] process > VIROPROFILER:MAPPING2CONTIGS2 (UC24)     [100%] 5 of 5, cached: 5 ✔
[cd/67df91] process > VIROPROFILER:ABUNDANCE                   [100%] 1 of 1, cached: 1 ✔
[60/5962a0] process > VIROPROFILER:VIBRANT                     [100%] 1 of 1, cached: 1 ✔
[39/607e3e] process > VIROPROFILER:DVF                         [100%] 1 of 1, cached: 1 ✔
[24/59b7a5] process > VIROPROFILER:VIRCONTIGS_PRE              [100%] 1 of 1, cached: 1 ✔
[60/9874c0] process > VIROPROFILER:VIRSORTER2                  [  0%] 0 of 1
[-        ] process > VIROPROFILER:DRAMV                       -
[ea/a33ffa] process > VIROPROFILER:TAXONOMY_VCONTACT           [  0%] 0 of 1
[72/ec9a16] process > VIROPROFILER:TAXONOMY_MMSEQS             [100%] 1 of 1, cached: 1 ✔
[-        ] process > VIROPROFILER:TAXONOMY_MERGE              -
[10/bc6e46] process > VIROPROFILER:VIRALHOST_IPHOP             [  0%] 0 of 1
executor >  local (3)
[f7/b6f3b4] process > VIROPROFILER:FASTQC (UC21)               [100%] 5 of 5, cached: 5 ✔
[13/f89bd9] process > VIROPROFILER:FASTP (UC21)                [100%] 5 of 5, cached: 5 ✔
[1c/9970e8] process > VIROPROFILER:SPADES (UC21)               [100%] 5 of 5, cached: 5 ✔
[1f/2ad85a] process > VIROPROFILER:CONTIGLIB                   [100%] 1 of 1, cached: 1 ✔
[14/94debb] process > VIROPROFILER:CHECKV                      [100%] 1 of 1, cached: 1 ✔
[37/5cbccf] process > VIROPROFILER:CONTIGLIB_CLUSTER           [100%] 1 of 1, cached: 1 ✔
[53/1726a0] process > VIROPROFILER:GENEPRED4CTG                [100%] 1 of 1, cached: 1 ✔
[ee/75a2fe] process > VIROPROFILER:NRPROT                      [100%] 1 of 1, cached: 1 ✔
[ff/bc6c4a] process > VIROPROFILER:NRGENE                      [100%] 1 of 1, cached: 1 ✔
[4c/68df51] process > VIROPROFILER:CONTIGINDEX                 [100%] 1 of 1, cached: 1 ✔
[d6/52905e] process > VIROPROFILER:MAPPING2CONTIGS2 (UC24)     [100%] 5 of 5, cached: 5 ✔
[cd/67df91] process > VIROPROFILER:ABUNDANCE                   [100%] 1 of 1, cached: 1 ✔
[60/5962a0] process > VIROPROFILER:VIBRANT                     [100%] 1 of 1, cached: 1 ✔
[39/607e3e] process > VIROPROFILER:DVF                         [100%] 1 of 1, cached: 1 ✔
[24/59b7a5] process > VIROPROFILER:VIRCONTIGS_PRE              [100%] 1 of 1, cached: 1 ✔
[60/9874c0] process > VIROPROFILER:VIRSORTER2                  [  0%] 0 of 1
[-        ] process > VIROPROFILER:DRAMV                       -
[ea/a33ffa] process > VIROPROFILER:TAXONOMY_VCONTACT           [  0%] 0 of 1
[72/ec9a16] process > VIROPROFILER:TAXONOMY_MMSEQS             [100%] 1 of 1, cached: 1 ✔
[-        ] process > VIROPROFILER:TAXONOMY_MERGE              -
[10/bc6e46] process > VIROPROFILER:VIRALHOST_IPHOP             [100%] 1 of 1, failed: 1 ✘
[03/855f3f] process > VIROPROFILER:BACPHLIP                    [100%] 1 of 1, cached: 1 ✔
[-        ] process > VIROPROFILER:RESULTS_TSE                 -
[-        ] process > VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS -
[-        ] process > VIROPROFILER:MULTIQC                     -
executor >  local (3)
[f7/b6f3b4] process > VIROPROFILER:FASTQC (UC21)               [100%] 5 of 5, cached: 5 ✔
[13/f89bd9] process > VIROPROFILER:FASTP (UC21)                [100%] 5 of 5, cached: 5 ✔
[1c/9970e8] process > VIROPROFILER:SPADES (UC21)               [100%] 5 of 5, cached: 5 ✔
[1f/2ad85a] process > VIROPROFILER:CONTIGLIB                   [100%] 1 of 1, cached: 1 ✔
[14/94debb] process > VIROPROFILER:CHECKV                      [100%] 1 of 1, cached: 1 ✔
[37/5cbccf] process > VIROPROFILER:CONTIGLIB_CLUSTER           [100%] 1 of 1, cached: 1 ✔
[53/1726a0] process > VIROPROFILER:GENEPRED4CTG                [100%] 1 of 1, cached: 1 ✔
[ee/75a2fe] process > VIROPROFILER:NRPROT                      [100%] 1 of 1, cached: 1 ✔
[ff/bc6c4a] process > VIROPROFILER:NRGENE                      [100%] 1 of 1, cached: 1 ✔
[4c/68df51] process > VIROPROFILER:CONTIGINDEX                 [100%] 1 of 1, cached: 1 ✔
[d6/52905e] process > VIROPROFILER:MAPPING2CONTIGS2 (UC24)     [100%] 5 of 5, cached: 5 ✔
[cd/67df91] process > VIROPROFILER:ABUNDANCE                   [100%] 1 of 1, cached: 1 ✔
[60/5962a0] process > VIROPROFILER:VIBRANT                     [100%] 1 of 1, cached: 1 ✔
[39/607e3e] process > VIROPROFILER:DVF                         [100%] 1 of 1, cached: 1 ✔
[24/59b7a5] process > VIROPROFILER:VIRCONTIGS_PRE              [100%] 1 of 1, cached: 1 ✔
[-        ] process > VIROPROFILER:VIRSORTER2                  -
[-        ] process > VIROPROFILER:DRAMV                       -
[-        ] process > VIROPROFILER:TAXONOMY_VCONTACT           -
[72/ec9a16] process > VIROPROFILER:TAXONOMY_MMSEQS             [100%] 1 of 1, cached: 1 ✔
[-        ] process > VIROPROFILER:TAXONOMY_MERGE              -
[10/bc6e46] process > VIROPROFILER:VIRALHOST_IPHOP             [100%] 1 of 1, failed: 1 ✘
[03/855f3f] process > VIROPROFILER:BACPHLIP                    [100%] 1 of 1, cached: 1 ✔
[-        ] process > VIROPROFILER:RESULTS_TSE                 -
[-        ] process > VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS -
[-        ] process > VIROPROFILER:MULTIQC                     -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'VIROPROFILER:VIRALHOST_IPHOP'

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

Command executed:

  iphop predict --fa_file putative_vcontigs_pref1.fasta --out_dir out_iphop --db_dir /home/mibrahim30/viroprofiler/iphop/Sept_2021_pub --num_threads 1

  cat <<-END_VERSIONS > versions.yml
  "VIROPROFILER:VIRALHOST_IPHOP":
      iPHoP: $(iphop --version | head -n1 | sed 's/iPHoP v//;s/: .*//')
      seqkit: $( seqkit | sed '3!d; s/Version: //' )
  END_VERSIONS

Command exit status:
  1

Command output:
  Pblm, I could not find directory /home/mibrahim30/viroprofiler/iphop/Sept_2021_pub. Maybe the host database directory was not specified with the --db_dir and is not the default "db/" directory ?

Command error:
  INFO:    Converting SIF file to temporary sandbox...
  Pblm, I could not find directory /home/mibrahim30/viroprofiler/iphop/Sept_2021_pub. Maybe the host database directory was not specified with the --db_dir and is not the default "db/" directory ?
  INFO:    Cleaning up image...

Work dir:
  /gpfs/work5/0/gusr0570/test/work/10/bc6e46cecc313ca37702b0c62428f1

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

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

Relevant files

command.log of 10/bc6e46......

INFO: Converting SIF file to temporary sandbox... Pblm, I could not find directory /home/mibrahim30/viroprofiler/iphop/Sept_2021_pub. Maybe the host database directory was not specified with the --db_dir and is not the default "db/" directory ? INFO: Cleaning up image...

System information

Nextflow version 23.04.1 Hardware HPC Executor slurm

rujinlong commented 1 year ago

Hi @mhmism. The db parameter should be set as --db "/gpfs/work5/0/gusr0570/viroprofiler"

mhmism commented 1 year ago

I have set the db parameter as you suggested but also does not work out. Also tried to bind the directory in singularity (as writable), but no luck. I tried multiple solutions so far with no luck.