[Bug]: FASTCAT command not found

[NHPttt]

What happened?

Hi I am running this workflow and I can't get passed this error. Please see below.

Operating System

macOS

Workflow Execution

Command line

Workflow Execution - EPI2ME Labs Versions

No response

Workflow Execution - Execution Profile

No response

Workflow Version

N E X T F L O W ~ version 22.10.0

Relevant log output

(micromamba3) [nhamil2@node1903 COVIDWorkflow]$ nextflow run epi2me-labs/wf-artic --fastq FAU09485_pass_barcode40_c1fe13a7_1.fastq.gz -profile conda
N E X T F L O W  ~  version 22.10.0
Launching `https://github.com/epi2me-labs/wf-artic` [kickass_brenner] DSL2 - revision: a60a1e1e73 [master]

WARN: Found unexpected parameters:
* --scheme_dir: primer_schemes
- Ignore this warning: params.schema_ignore_params = "scheme_dir" 

Core Nextflow options
  revision   : master
  runName    : kickass_brenner
  launchDir  : /scratch1/nhamil2/COVIDWorkflow
  workDir    : /scratch1/nhamil2/COVIDWorkflow/work
  projectDir : /home/nhamil2/.nextflow/assets/epi2me-labs/wf-artic
  userName   : nhamil2
  profile    : conda
  configFiles: /home/nhamil2/.nextflow/assets/epi2me-labs/wf-artic/nextflow.config

Basic Input/Output Options
  fastq      : FAU09485_pass_barcode40_c1fe13a7_1.fastq.gz

Advanced options
  normalise  : 200

!! 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

      ------------------------------------
      Available Primer Schemes:
      ------------------------------------

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

      ------------------------------------

Checking fastq input.
Single file input detected.
executor >  local (6)
[46/880a7b] process > handleSingleFile (1)    [100%] 1 of 1 ✔
executor >  local (6)
[46/880a7b] process > handleSingleFile (1)    [100%] 1 of 1 ✔
[-        ] process > pipeline:getVersions    -
[94/5dbe9c] process > pipeline:getParams      [100%] 1 of 1 ✔
[-        ] process > pipeline:copySchemeDir  -
[88/ad2075] process > pipeline:preArticQC (1) [100%] 1 of 1, failed: 1 ✘
[-        ] process > pipeline:runArtic       -
[-        ] process > pipeline:combineDepth   -
[-        ] process > pipeline:allConsensus   -
[-        ] process > pipeline:allVariants    [  0%] 0 of 1
[42/5c1386] process > pipeline:prep_nextclade [100%] 1 of 1 ✔
[-        ] process > pipeline:nextclade      -
[-        ] process > pipeline:pangolin       -
[-        ] process > pipeline:telemetry      -
[-        ] process > pipeline:report         -
[-        ] process > output                  -
Error executing process > 'pipeline:preArticQC (1)'

Caused by:
  Process `pipeline:preArticQC (1)` terminated with an error exit status (127)

Command executed:

  fastcat -s FAU09485_pass_barcode40_c1fe13a7_1 -r FAU09485_pass_barcode40_c1fe13a7_1.stats -x FAU09485_pass_barcode40_c1fe13a7_1 > /dev/null

Command exit status:
  127

Command output:
  (empty)

Command error:
  ps: /software/spackages/linux-rocky8-x86_64/gcc-9.5.0/anaconda3-2022.05-zyrazrj6uvrtukupqzhaslr63w7hj6in/lib/libuuid.so.1: no version information available (required by /lib64/libblkid.so.1)
  .command.sh: line 2: fastcat: command not found

Work dir:
  /scratch1/nhamil2/COVIDWorkflow/work/88/ad207512e7c1a4129f0885f0da5fab

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

[mattdmem]

Hello,

Thanks for your bug report. I would recommend using -profile docker or -profile singularity rather than conda.

Matt