nextflow hangs on first step

[durrantmm]

Hello, I'm running the nextflow pipeline with the command:

nextflow run salzmanlab/compactors \
    -r main \
    -latest \
    -profile test,docker \
    --fastq_samplesheet INPUT/samples/PRJNA256339.paths.filt.nf.csv \
    --anchors_file INPUT/combined_anchors.txt \
    --outdir OUTPUT/compactor_results/PRJNA256339

And left it running overnight on a VM with 8 vCPUs. It hasn't made any progress, here is the output:

N E X T F L O W  ~  version 22.04.5                                                                                                                       
Pulling salzmanlab/compactors ...                                                                                                                         
 Already-up-to-date                                                                                                                                       
Launching `https://github.com/salzmanlab/compactors` [amazing_wescoff] DSL2 - revision: 071fd8d0dd [main]                                                 

WARN: Found unexpected parameters:                                                                                                                        
* --input: https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv                          
* --fasta: genome.fasta                                                                                                                                   
* --genome: R64-1-1                                                                                                                                       
* --recursive_depth: 73                                                                                                                                   
* --branch_threshold: 20                                                                                                                                  
* --epsilon: 0.10                                                                                                                                         
* --max_anchor_reads: 200                                                                                                                                 
* --num_reads: 100000                                                                                                                                     
* --buffer_size: 50                                                                                                                                       
* --anchor_length: 27                                                                                                                                     
* --anchors_file: INPUT/combined_anchors.txt                                                                                                              
* --fastq_samplesheet: INPUT/samples/PRJNA256339.paths.filt.nf.csv                                                                                        
- Ignore this warning: params.schema_ignore_params = "input,fasta,genome,recursive_depth,branch_threshold,epsilon,max_anchor_reads,num_reads,buffer_size,a
nchor_length,anchors_file,fastq_samplesheet"                                                                                                              

------------------------------------------------------                                                                                                    
                                        ,--./,-.                                                                                                          
        ___     __   __   __   ___     /,-._.--~'                                                                                                         
  |\ | |__  __ /  ` /  \ |__) |__         }  {                                                                                                            
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,                                                                                                         
                                        `._,._,'                                                                                                          
  salzmanlab/nf-compactors v1.0dev                                
------------------------------------------------------
Core Nextflow options
  revision                  : main
  runName                   : amazing_wescoff
  containerEngine           : docker
  container                 : kaitlinchaung/nomad:v0.1
  launchDir                 : /home/mdurrant/NOMAD/03.COMPACTORS
  workDir                   : /home/mdurrant/NOMAD/03.COMPACTORS/work
  projectDir                : /home/mdurrant/.nextflow/assets/salzmanlab/compactors
  userName                  : mdurrant
  profile                   : test,docker
  configFiles               : /home/mdurrant/.nextflow/assets/salzmanlab/compactors/nextflow.config

Input/output options
  outdir                    : OUTPUT/compactor_results/PRJNA256339

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                  : 6.h

Other parameters
  fastq_samplesheet         : INPUT/samples/PRJNA256339.paths.filt.nf.csv
  anchors_file              : INPUT/combined_anchors.txt
  num_reads                 : 100000

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

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/salzmanlab/nf-compactors/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (5)
[7f/4f874f] process > NFCORE_COMPACTORS:COMPACTORS:GET_COMPACTORS:MAKE_INTERMEDIARIES (5) [  0%] 0 of 49
[-        ] process > NFCORE_COMPACTORS:COMPACTORS:GET_COMPACTORS:GENERATE_COMPACTORS     -

[durrantmm]

Do you have a test dataset I can troubleshoot on or something?

[durrantmm]

Any update on this?

[chstellar]

You can use SPLASH2 which basically performs the first and second steps, but the classification step is only available here, which further requires information unique to this workflow...

The problem I encounter is that nextflow hangs on the second step...