Why I am getting a Command Trace Error

[navyn007]

Operating System

Other Linux (please specify below)

Other Linux

Linux Mint 21.1 Cinnamon

Workflow Version

N E X T F L O W ~ version 23.04.1

Workflow Execution

EPI2ME Desktop application

EPI2ME Version

EPI2ME V5.1.0

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

Hiya, I'm very new to linux, sequence analysis, docker and epi2me

I have been trying to run the demo dataset on the wf-arctic pipeline using epi2me and i'm always getting this error,

Command error: touch: cannot touch '.command.trace': Permission denied

I tried editing the nextflow config file to modify the docker runoptions, but i'm not sure if i am doing it right ?

runOptions = '-u $(id -u):$(id -g)'

Again i am really new to all of this do i do apologise if my error is something rather pathetic

thank you so much for your time :)

Relevant log output

N E X T F L O W  ~  version 23.04.1
Launching `/home/navin/epi2melabs/workflows/epi2me-labs/wf-artic/main.nf` [hungry_visvesvaraya] DSL2 - revision: 966ee35cc0
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-artic v0.3.30
--------------------------------------------------------------------------------
Core Nextflow options
  runName        : hungry_visvesvaraya
  containerEngine: docker
  launchDir      : /home/navin/epi2melabs/instances/wf-artic_cfc7af0a-f7b8-46ae-be0a-948f6d0b1371
  workDir        : /home/navin/epi2melabs/instances/wf-artic_cfc7af0a-f7b8-46ae-be0a-948f6d0b1371/work
  projectDir     : /home/navin/epi2melabs/workflows/epi2me-labs/wf-artic
  userName       : navin
  profile        : standard
  configFiles    : /home/navin/epi2melabs/workflows/epi2me-labs/wf-artic/nextflow.config, /home/navin/epi2melabs/instances/wf-artic_cfc7af0a-f7b8-46ae-be0a-948f6d0b1371/demo.config
Input Options
  fastq          : /home/navin/epi2melabs/demo/epi2me-labs/wf-artic/v0.3.30/wf-artic-demo/fastq
Primer Scheme Selection
  scheme_version : Midnight-ONT/V3
Sample Options
  sample_sheet   : /home/navin/epi2melabs/demo/epi2me-labs/wf-artic/v0.3.30/wf-artic-demo/sample_sheet.csv
Output Options
  out_dir        : /home/navin/epi2melabs/instances/wf-artic_cfc7af0a-f7b8-46ae-be0a-948f6d0b1371/output
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-artic for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-artic v0.3.30.
--------------------------------------------------------------------------------
WARN: Nextflow version 23.04.1 does not match workflow required version: >=23.04.2 -- Execution will continue, but things may break!
      ------------------------------------
      Available Primer Schemes:
      ------------------------------------

  Name      Version
  SARS-CoV-2    Midnight-IDT/V2 
  SARS-CoV-2    Midnight-IDT/V1 
  SARS-CoV-2    Midnight-ONT/V3 
  SARS-CoV-2    Midnight-ONT/V2 
  SARS-CoV-2    Midnight-ONT/V1 
  SARS-CoV-2    NEB-VarSkip/v2  
  SARS-CoV-2    NEB-VarSkip/v1a 
  SARS-CoV-2    NEB-VarSkip/v1a-long    
  SARS-CoV-2    NEB-VarSkip/v2b 
  SARS-CoV-2    ARTIC/V3    
  SARS-CoV-2    ARTIC/V2    
  SARS-CoV-2    ARTIC/V4    
  SARS-CoV-2    ARTIC/V5.3.2    
  SARS-CoV-2    ARTIC/V4.1  
  SARS-CoV-2    ARTIC/V1    
      ------------------------------------

Checking fastq input.
[12/02922a] Submitted process > pipeline:prep_nextclade
[a1/975cbc] Submitted process > pipeline:getVersions
[73/82bf7e] Submitted process > validate_sample_sheet
[df/92bb7a] Submitted process > pipeline:lookup_medaka_variant_model (1)
[5e/6159d6] Submitted process > pipeline:getParams
ERROR ~ Error executing process > 'pipeline:lookup_medaka_variant_model (1)'
Caused by:
  Process `pipeline:lookup_medaka_variant_model (1)` terminated with an error exit status (1)
Command executed:
  medaka_model=$(workflow-glue resolve_medaka_model lookup_table 'dna_r9.4.1_450bps_hac' "medaka_variant")
  echo -n $medaka_model
Command exit status:
  1
Command output:
  (empty)
Command error:
  touch: cannot touch '.command.trace': Permission denied
Work dir:
  /home/navin/epi2melabs/instances/wf-artic_cfc7af0a-f7b8-46ae-be0a-948f6d0b1371/work/df/92bb7a914a77424b58759f53aeae27
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
 -- Check '/home/navin/epi2melabs/instances/wf-artic_cfc7af0a-f7b8-46ae-be0a-948f6d0b1371/nextflow.log' file for details
WARN: Input directory 'barcode64' was found, but sample sheet '/home/navin/epi2melabs/demo/epi2me-labs/wf-artic/v0.3.30/wf-artic-demo/sample_sheet.csv' has no such entry.
WARN: Input tuple does not match input set cardinality declared by process `pipeline:allVariants` -- offending value: []
ERROR ~ Unexpected error [NullPointerException]
 -- Check '/home/navin/epi2melabs/instances/wf-artic_cfc7af0a-f7b8-46ae-be0a-948f6d0b1371/nextflow.log' file for details
WARN: Killing running tasks (4)

Application activity log entry

Nothing is listed in Red

[mattdmem]

Hi @navyn007 - Are you still having issues? My immediate thought is you're running with sudo or within a dir where you don't have permissions. Let me know if you still need assistance!

[cjw85]

The error here appears reminiscent of other reports that we have with the use of Docker Desktop. (e.g. here).

Have you installed Docker Desktop? If so can I recommend that you follow the instructions here to install the docker.io package on your system:

https://labs.epi2me.io/installation/#installing-docker-on-linux-without-docker-desktop

[cjw85]

As an aside I noticed you commented:

I'm very new to linux, sequence analysis, docker and epi2me

Have you considered using EPI2ME Desktop on Windows?

[cjw85]

Closing due to lack of response.