Unable to finish picking assemblies

Pipeline is getting stuck in picking assemblies by the tsv files it needs but can't find. Here's the error message I got, and .nextflow.log says the same thing. Any ideas? Thanks!

[ac/db06fd] NOTE: Process PATHOGENSURVEILLANCE:PREPARE_INPUT:PICK_ASSEMBLIES (H1_18_18_7_S180_L002) terminated with an error exit status (1) -- Execution is retried (1)
[56/cbf319] NOTE: Process PATHOGENSURVEILLANCE:PREPARE_INPUT:PICK_ASSEMBLIES (H1_14_14_10_S138_L002) terminated with an error exit status (1) -- Execution is retried (1)
[f6/3ee247] NOTE: Process PATHOGENSURVEILLANCE:PREPARE_INPUT:PICK_ASSEMBLIES (H1_12_52_3_S254_L003) terminated with an error exit status (1) -- Execution is retried (1)
[6d/1cc26a] NOTE: Process PATHOGENSURVEILLANCE:PREPARE_INPUT:PICK_ASSEMBLIES (H1_1_21_5A_S144_L002) terminated with an error exit status (1) -- Execution is retried (1)
ERROR ~ Error executing process > 'PATHOGENSURVEILLANCE:PREPARE_INPUT:PICK_ASSEMBLIES (H1_5_5_8_S244_L003)'

Caused by:
  Process PATHOGENSURVEILLANCE:PREPARE_INPUT:PICK_ASSEMBLIES (H1_5_5_8_S244_L003) terminated with an error exit status (1)

Command executed:

  pick_assemblies.R H1_5_5_8_S244_L003_families.txt H1_5_5_8_S244_L003_genera.txt H1_5_5_8_S244_L003_species.txt 30 20 10 H1_5_5_8_S244_L003.tsv 

  cat <<-END_VERSIONS > versions.yml
  "PATHOGENSURVEILLANCE:PREPARE_INPUT:PICK_ASSEMBLIES":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.R version //; s/ .$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Error in file(file, "rt") : cannot open the connection
  Calls: lapply -> FUN -> read.csv -> read.table -> file
  In addition: Warning message:
  In file(file, "rt") :
    cannot open file 'H1_5_5_8_S244_L003.tsv': No such file or directory
  Execution halted

Work dir:
  /nfs7/BPP/Chang_Lab/paradarc/paper1_bra/scripts/new_pipeline/pathogensurveillance/work/69/fc2ce323ae5f9d5e6d103aabfae673

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

 -- Check '.nextflow.log' file for details
-[nf-core/plantpathsurveil] Sent summary e-mail to buchanri@oregonstate.edu (sendmail)-
WARN: Access to undefined parameter `outdir` -- Initialise it to a default value eg. `params.outdir = some_value`
-[nf-core/plantpathsurveil] Pipeline completed with errors

 To clean the cache, run the command:
 nextflow clean amazing_avogadro -f

WARN: Killing running tasks (118)

nf-core / pathogensurveillance

Unable to finish picking assemblies #93