MOP_MOD error: compore_polish_flow:NANOCOMPORE_SAMPLE_COMPARE:sampleCompare (mod vs wt)

[Iris-QAQ]

Hi there,

I am trying to use the mop_mod pipeline with test data that I have already piped into the same output with mop_preprocess. I am using singularity as my virtualization software. And I mannually downloaded all the imgs which the singularity needed.

Here is my params.config

    input_path         = "$baseDir/../mop_preprocess/output/"
    comparison         = "$baseDir/comparison.tsv"

    reference           = "$baseDir/../anno/yeast_rRNA_ref.fa.gz"
    
    output             = "$baseDir/output_mod"

    pars_tools         = "$baseDir/tools_opt.tsv"
    
    // flows 
    epinano       = "YES"
    nanocompore   = "YES"
    tombo_lsc     = "YES"
    tombo_msc     = "YES"

    // epinano plots
    epinano_plots = "YES"

    email              = ""
}

Here is my tools_opt.tsv

#flows  tool    extrapars
epinano epinano ""
nanocompore     nanopolish      ""
nanocompore     nanocompore     " --downsample_high_coverage 5000"
tombo_resquiggling      tombo   ""
tombo_msc       tombo   ""
tombo_lsc       tombo   ""

However, the nanocompore part of the nextflow pipeline throws up the following error (pulled from the log.txt file):

ERROR ~ Error executing process > 'compore_polish_flow:NANOCOMPORE_SAMPLE_COMPARE:sampleCompare (mod vs wt)'

Caused by:
  Process `compore_polish_flow:NANOCOMPORE_SAMPLE_COMPARE:sampleCompare (mod vs wt)` terminated with an error exit status (1)

Command executed:

  nanocompore sampcomp --nthreads 1    --file_list1 mod_collapsed_align_events/out_eventalign_collapse.tsv     --file_list2 wt_col
lapsed_align_events/out_eventalign_collapse.tsv     --label1 mod     --label2 wt     --fasta reference.fa     --outpath ./mod-wt_n
anocompore/      --downsample_high_coverage 5000 --pvalue_thr 1 --outprefix mod_vs_wt --logit --comparison_methods GMM,KS,MW,TT --
overwrite 
       gzip mod-wt_nanocompore/*_results.tsv

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Converting SIF file to temporary sandbox...
WARNING: Skipping mount /home/jingjiaxian/anaconda3/envs/mamba/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.
conf doesn't exist in container
  /usr/local/lib/python3.8/site-packages/nanocompore/SampCompDB.py:332: SyntaxWarning: "is" with a literal. Did you mean "=="?
    if convert is "ensembl_to_ucsc":
  /usr/local/lib/python3.8/site-packages/nanocompore/SampCompDB.py:334: SyntaxWarning: "is" with a literal. Did you mean "=="?
    elif convert is "ucsc_to_ensembl":
  /usr/local/lib/python3.8/site-packages/nanocompore/SampCompDB.py:342: SyntaxWarning: "is" with a literal. Did you mean "=="?
    if convert is "ensembl_to_ucsc":
  /usr/local/lib/python3.8/site-packages/nanocompore/SampCompDB.py:344: SyntaxWarning: "is" with a literal. Did you mean "=="?
    elif convert is "ucsc_to_ensembl":
  generated new fontManager
  /usr/local/lib/python3.8/site-packages/sklearn/utils/deprecation.py:144: FutureWarning: The sklearn.mixture.gaussian_mixture mod
ule is  deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be im
ported from sklearn.mixture. Anything that cannot be imported from sklearn.mixture is now part of the private API.
    warnings.warn(message, FutureWarning)
  Initialising SampComp and checking options
  Only 1 replicate found for condition mod
  This is not recommended. The statistics will be calculated with the logit method
  Only 1 replicate found for condition wt
  This is not recommended. The statistics will be calculated with the logit method
  Traceback (most recent call last):
    File "/usr/local/bin/nanocompore", line 11, in <module>
      sys.exit(main())
    File "/usr/local/lib/python3.8/site-packages/nanocompore/__main__.py", line 139, in main
      args.func(args)
    File "/usr/local/lib/python3.8/site-packages/nanocompore/__main__.py", line 154, in sampcomp_main
      s = SampComp(
    File "/usr/local/lib/python3.8/site-packages/nanocompore/SampComp.py", line 163, in __init__
      raise NanocomporeError("The minimum number of threads is 3")
  nanocompore.common.NanocomporeError: The minimum number of threads is 3
  INFO:    Cleaning up image...

It seems like Looks like there is something wrong with python3.8, but I'm sure the ./MOP2/singularity have quay.io-biocontainers-nanocompore-1.0.0rc3.post1--py38_0.img.

Could you please help me with that? Thanks

Best,
Iris