Issue with fix strain names bulk

[aoshaver]

command run:

nextflow run andersenlab/nemascan \
--vcf 20210803 \
--traitfile /home/ashaver5/vast-eande106/projects/Amanda/projects/NemaScan/traitfiles/ABZ_ASSAY1_medians.tsv \
--sthresh EIGEN \
--species c_briggsae \
--out /home/ashaver5/vast-eande106/projects/Amanda/projects/NemaScan/output

error:

ERROR ~ Error executing process > 'fix_strain_names_bulk (BULK TRAIT)'

Caused by:
  Process `fix_strain_names_bulk (BULK TRAIT)` terminated with an error exit status (1)


Command executed:

  # for now, don't fix isotypes for non elegans
  Rscript --vanilla Fix_Isotype_names_bulk.R ABZ_ASSAY1_medians.tsv fix strain_isotype_lookup.tsv
  
  # check to make sure there are more than 40 strains for a mapping.
  if [[ $(wc -l <Phenotyped_Strains.txt) -le 40 ]]
  then
      echo "ERROR: Please provide at least 40 strains for a GWAS mapping."
      exit 1
  fi

Command exit status:
  1

Command output:
  (empty)

Command error:
  
  Attaching package: ‘dplyr’
  
  The following objects are masked from ‘package:stats’:
  
      filter, lag
  
  The following objects are masked from ‘package:base’:
  
      intersect, setdiff, setequal, union
  
  Warning message:
  package ‘dplyr’ was built under R version 3.6.3 
  Warning message:
  package ‘tidyr’ was built under R version 3.6.3 
  Warning message:
  package ‘ggplot2’ was built under R version 3.6.3 
  
  Attaching package: ‘glue’
  
  The following object is masked from ‘package:dplyr’:
  
      collapse
  
  Warning message:
  package ‘purrr’ was built under R version 3.6.3 
  
  Attaching package: ‘data.table’
  
  The following object is masked from ‘package:purrr’:
  
      transpose
  
  The following objects are masked from ‘package:dplyr’:
  
      between, first, last

Work dir:
  /scratch4/eande106/Amanda/e8/0213559658ce41a106a2e6e63b0b66

Container:
  /vast/eande106/singularity/andersenlab-nemascan-20220407173056db3227.img

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

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