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failed to create symbolic link '/opt/conda/db2': Read-only file system #18

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wanghang7410 opened this issue Aug 31, 2023 · 0 comments
Open

failed to create symbolic link '/opt/conda/db2': Read-only file system #18

wanghang7410 opened this issue Aug 31, 2023 · 0 comments
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bug Something isn't working

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@wanghang7410
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Description of the bug

An error occurs when I execute the command "nextflow run deng-lab/viroprofiler -r main-profile singularity,test"

Command used and terminal output

(base) [root@develop viroprofiler]# nextflow run deng-lab/viroprofiler -r main -profile singularity,test
N E X T F L O W  ~  version 23.04.1
Launching `https://github.com/deng-lab/viroprofiler` [ridiculous_wright] 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                   : ridiculous_wright
  containerEngine           : singularity
  launchDir                 : /root/wanghang/viroprofiler/viropor/viroprofiler
  workDir                   : /root/wanghang/viroprofiler/viropor/viroprofiler/work
  projectDir                : /root/.nextflow/assets/deng-lab/viroprofiler
  userName                  : root
  profile                   : singularity,test
  configFiles               : /root/.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                        : /root/wanghang/viroprofiler/viropor/viroprofiler
  outdir                    : output

QC
  contamref_idx             : /root/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
----------------------------------------------------------------------------------------------------------------
[-        ] process > VIROPROFILER:FASTQC                      -
[-        ] process > VIROPROFILER:FASTP                       -
[-        ] process > VIROPROFILER:FASTQC                      -
[-        ] process > VIROPROFILER:FASTP                       -
[-        ] process > VIROPROFILER:SPADES                      -
executor >  local (2)
[63/8195fe] process > VIROPROFILER:FASTQC (HT04)               [  0%] 0 of 2
[-        ] process > VIROPROFILER:FASTP                       [  0%] 0 of 1
executor >  local (4)
[63/8195fe] process > VIROPROFILER:FASTQC (HT04)               [  0%] 0 of 2
[97/67fff5] process > VIROPROFILER:FASTP (HT04)                [  0%] 0 of 2
executor >  local (4)
[63/8195fe] process > VIROPROFILER:FASTQC (HT04)               [  0%] 0 of 2
[97/67fff5] process > VIROPROFILER:FASTP (HT04)                [  0%] 0 of 2
executor >  local (4)
[63/8195fe] process > VIROPROFILER:FASTQC (HT04)               [  0%] 0 of 2
[97/67fff5] process > VIROPROFILER:FASTP (HT04)                [  0%] 0 of 2
executor >  local (4)
[63/8195fe] process > VIROPROFILER:FASTQC (HT04)               [  0%] 0 of 2
[97/67fff5] process > VIROPROFILER:FASTP (HT04)                [  0%] 0 of 2
executor >  local (6)
[29/7fe6d1] process > VIROPROFILER:FASTQC (UC20)               [  0%] 0 of 3
[74/30fe30] process > VIROPROFILER:FASTP (UC20)                [  0%] 0 of 3
executor >  local (6)
[29/7fe6d1] process > VIROPROFILER:FASTQC (UC20)               [  0%] 0 of 3
[74/30fe30] process > VIROPROFILER:FASTP (UC20)                [  0%] 0 of 3
executor >  local (6)
[63/8195fe] process > VIROPROFILER:FASTQC (HT04)               [ 66%] 2 of 3
[74/30fe30] process > VIROPROFILER:FASTP (UC20)                [  0%] 0 of 3
executor >  local (8)
[5f/4f4192] process > VIROPROFILER:FASTQC (UC21)               [ 50%] 2 of 4
[57/dab04a] process > VIROPROFILER:FASTP (UC21)                [  0%] 0 of 4
executor >  local (10)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24)               [ 40%] 2 of 5
[7a/9b09f2] process > VIROPROFILER:FASTP (UC24)                [  0%] 0 of 5
executor >  local (10)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24)               [ 40%] 2 of 5
[84/f3c856] process > VIROPROFILER:FASTP (HT02)                [ 20%] 1 of 5
[-        ] process > VIROPROFILER:SPADES                      -
executor >  local (10)
[29/7fe6d1] process > VIROPROFILER:FASTQC (UC20)               [ 60%] 3 of 5
[84/f3c856] process > VIROPROFILER:FASTP (HT02)                [ 20%] 1 of 5
[-        ] process > VIROPROFILER:SPADES                      -
executor >  local (10)
[5f/4f4192] process > VIROPROFILER:FASTQC (UC21)               [ 80%] 4 of 5
[84/f3c856] process > VIROPROFILER:FASTP (HT02)                [ 20%] 1 of 5
[-        ] process > VIROPROFILER:SPADES                      -
executor >  local (11)
[5f/4f4192] process > VIROPROFILER:FASTQC (UC21)               [ 80%] 4 of 5
[84/f3c856] process > VIROPROFILER:FASTP (HT02)                [ 20%] 1 of 5
[01/d0ee0f] process > VIROPROFILER:SPADES (HT02)               [  0%] 0 of 1
executor >  local (11)
[5f/4f4192] process > VIROPROFILER:FASTQC (UC21)               [ 80%] 4 of 5
[84/f3c856] process > VIROPROFILER:FASTP (HT02)                [ 20%] 1 of 5
[01/d0ee0f] process > VIROPROFILER:SPADES (HT02)               [  0%] 0 of 1
executor >  local (11)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24)               [100%] 5 of 5 ✔
[84/f3c856] process > VIROPROFILER:FASTP (HT02)                [ 20%] 1 of 5
[01/d0ee0f] process > VIROPROFILER:SPADES (HT02)               [  0%] 0 of 1
executor >  local (12)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24)               [100%] 5 of 5 ✔
[57/dab04a] process > VIROPROFILER:FASTP (UC21)                [ 40%] 2 of 5
[68/8fca3d] process > VIROPROFILER:SPADES (UC21)               [  0%] 0 of 2
executor >  local (13)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24)               [100%] 5 of 5 ✔
[97/67fff5] process > VIROPROFILER:FASTP (HT04)                [ 60%] 3 of 5
[96/8ea940] process > VIROPROFILER:SPADES (HT04)               [  0%] 0 of 3
executor >  local (13)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24)               [100%] 5 of 5 ✔
[97/67fff5] process > VIROPROFILER:FASTP (HT04)                [ 60%] 3 of 5
[96/8ea940] process > VIROPROFILER:SPADES (HT04)               [  0%] 0 of 3
executor >  local (15)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24)               [100%] 5 of 5 ✔
[7a/9b09f2] process > VIROPROFILER:FASTP (UC24)                [100%] 5 of 5 ✔
[b9/fad586] process > VIROPROFILER:SPADES (UC24)               [  0%] 0 of 5
executor >  local (15)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24)               [100%] 5 of 5 ✔
[7a/9b09f2] process > VIROPROFILER:FASTP (UC24)                [100%] 5 of 5 ✔
[01/d0ee0f] process > VIROPROFILER:SPADES (HT02)               [ 20%] 1 of 5
executor >  local (15)
executor >  local (15)
executor >  local (16)
executor >  local (17)
executor >  local (19)
executor >  local (19)
executor >  local (21)
executor >  local (21)
executor >  local (22)
executor >  local (22)
executor >  local (22)
executor >  local (22)
executor >  local (32)
executor >  local (33)
executor >  local (34)
executor >  local (34)
executor >  local (34)
executor >  local (37)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24)               [100%] 5 of 5 ✔
[7a/9b09f2] process > VIROPROFILER:FASTP (UC24)                [100%] 5 of 5 ✔
[97/17e074] process > VIROPROFILER:SPADES (UC20)               [100%] 5 of 5 ✔
[c7/e36f95] process > VIROPROFILER:CONTIGLIB                   [100%] 1 of 1 ✔
[ce/17b9fa] process > VIROPROFILER:CHECKV                      [100%] 1 of 1 ✔
executor >  local (37)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24)               [100%] 5 of 5 ✔
[7a/9b09f2] process > VIROPROFILER:FASTP (UC24)                [100%] 5 of 5 ✔
[97/17e074] process > VIROPROFILER:SPADES (UC20)               [100%] 5 of 5 ✔
[c7/e36f95] process > VIROPROFILER:CONTIGLIB                   [100%] 1 of 1 ✔
[ce/17b9fa] process > VIROPROFILER:CHECKV                      [100%] 1 of 1 ✔
[64/46c405] process > VIROPROFILER:CONTIGLIB_CLUSTER           [100%] 1 of 1 ✔
[9b/5486d6] process > VIROPROFILER:GENEPRED4CTG                [100%] 1 of 1 ✔
[40/c60cf7] process > VIROPROFILER:NRPROT                      [100%] 1 of 1 ✔
[23/21ca21] process > VIROPROFILER:NRGENE                      [100%] 1 of 1 ✔
[00/d2bd9c] process > VIROPROFILER:CONTIGINDEX                 [100%] 1 of 1 ✔
[9b/381bbf] process > VIROPROFILER:MAPPING2CONTIGS2 (HT04)     [100%] 5 of 5 ✔
[ad/6d2e49] process > VIROPROFILER:ABUNDANCE                   [100%] 1 of 1 ✔
[86/6145cc] process > VIROPROFILER:VIBRANT                     [100%] 1 of 1 ✔
[39/c98340] process > VIROPROFILER:DVF                         [100%] 1 of 1 ✔
[51/f7a743] process > VIROPROFILER:VIRCONTIGS_PRE              [100%] 1 of 1 ✔
[aa/37b52b] process > VIROPROFILER:VIRSORTER2                  [100%] 1 of 1 ✔
[83/b54606] process > VIROPROFILER:DRAMV                       [100%] 1 of 1, failed: 1 ✘
[20/bf03f7] process > VIROPROFILER:TAXONOMY_VCONTACT           [  0%] 0 of 1
[02/f44345] process > VIROPROFILER:TAXONOMY_MMSEQS             [100%] 1 of 1 ✔
[-        ] process > VIROPROFILER:TAXONOMY_MERGE              -
[aa/fc290e] process > VIROPROFILER:VIRALHOST_IPHOP             [  0%] 0 of 1
[28/2c527b] process > VIROPROFILER:BACPHLIP                    [100%] 1 of 1 ✔
[-        ] process > VIROPROFILER:RESULTS_TSE                 -
[-        ] process > VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS -
[-        ] process > VIROPROFILER:MULTIQC                     -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'VIROPROFILER:DRAMV'

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

Command executed:

  # Due to limitation of container, DRAM database path is hardset to /opt/conda/db2
  # So we need to create a soft link for the database path
  ln -s /root/wanghang/viroprofiler/viropor/viroprofiler /opt/conda/db2
  export DRAM_CONFIG_LOCATION=/root/wanghang/viroprofiler/viropor/viroprofiler/dram/CONFIG

  DRAM-v.py annotate -i final-viral-combined-for-dramv.fa -v viral-affi-contigs-for-dramv.tab -o dramv-annotate --threads 1 --min_contig_size 3000
  DRAM-v.py distill -i dramv-annotate/annotations.tsv -o dramv-distill

  cat <<-END_VERSIONS > versions.yml
  "VIROPROFILER:DRAMV":
      DRAM: 1.3
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  ln: failed to create symbolic link '/opt/conda/db2': Read-only file system

Work dir:
  /root/wanghang/viroprofiler/viropor/viroprofiler/work/83/b54606e343f92eaef4840413574f01

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

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

Relevant files

No response

System information

No response
@wanghang7410 wanghang7410 added the bug Something isn't working label Aug 31, 2023
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