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ERROR ~ Cannot invoke method split() on null object #70

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foreignsand opened this issue Jan 9, 2025 · 1 comment
Open

ERROR ~ Cannot invoke method split() on null object #70

foreignsand opened this issue Jan 9, 2025 · 1 comment

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@foreignsand
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Executing the pipeline with Nextflow using -r dev on my university's core I get the following error:

ERROR ~ Cannot invoke method split() on null object

 -- Check script '/nfs4/FW_HMSC/Levi_Lab/Emily/opt/nxf/assets/sanger-tol/ascc/./workflows/../subworkflows/local/pacbio_barcode_check.nf' at line: 85 or see '.nextflow.log' file for more details

I execute the following script to run the pipeline:

#!/bin/bash

NXF_ASSETS=/nfs4/FW_HMSC/Levi_Lab/Emily/opt/nxf/assets
NXF_TMP=/nfs4/FW_HMSC/Levi_Lab/Emily/opt/nxf/scratch

nextflow run sanger-tol/ascc \
	--input /nfs4/FW_HMSC/Levi_Lab/Emily/marten_data/ascc/ascc_config_marten_cqls.yaml \
	--outdir /nfs4/FW_HMSC/Levi_Lab/Emily/marten_data/ascc/ \
	-profile singularity \
	-entry SANGERTOL_ASCC \
	--include ALL \
	-r dev

The contents of my yaml input file are as follows:

assembly_path: /nfs4/FW_HMSC/Levi_Lab/Emily/marten_data/yahs_scaffolds/ccs_all_scaffolded/yahs.out_scaffolds_final.fa
assembly_title: Humboldt Marten
sci_name: "Martes americana humboldtensis"
taxid: 551455
mito_fasta_path: /nfs4/FW_HMSC/Levi_Lab/Emily/marten_data/mitome/scaffold_644.mito.fa
# plastid_fasta_path: PATH TO PLASTID FASTA
reads_path: /nfs4/FW_HMSC/Levi_Lab/Emily/marten_data/pacbio/7717/subreads/m64047_240219_192555.subreads.fasta
reads_type: "hifi"
pacbio_barcodes: /nfs4/FW_HMSC/Levi_Lab/Emily/opt/pacbio_adaptors/pacbio_adaptors.fa
# pacbio_multiplexing_barcode_names: "bc2008,bc2009" {BARCODES EXPECTED IN DATA} # Not required if you only have one sample, I hope
kmer_len: 7
dimensionality_reduction_methods: "pca,random_trees"
# Available methods: "pca,umap,t-sne,isomap,lle_standard,lle_hessian,lle_modified,mds,se,random_trees,kernel_pca,pca_svd,autoencoder_sigmoid,autoencoder_linear,autoencoder_selu,autoencoder_relu,nmf"
# Include a CSV of the methods you choose to use and reference it when calling the Nextflow ascc pipeline
nt_database: /local/cqls/db/NCBI/latest_blast_db/nt
nt_database_prefix: /local/cqls/db/NCBI/latest_blast_db
nt_kraken_db_path: /local/cqls/db/kraken2/latest/nt # Note: this specifies that the prefix should also be here, not sure how to handle that
ncbi_accessionids_folder: /local/cqls/db/NCBI/accession2taxid
ncbi_taxonomy_path: /local/cqls/db/NCBI/new_taxdump/
ncbi_rankedlineage_path: /local/cqls/db/NCBI/new_taxdump/rankedlineage.dmp
busco_lineages_folder: /local/cqls/db/busco/busco_current/busco_downloads/lineages
fcs_gx_database_path: /fs1/local/cqls/db/NCBI/gxdb_20241115
vecscreen_database_path: /local/cqls/db/NCBI/univec/
diamond_uniprot_database_path: /local/cqls/db/uniprot/reference_proteomes/reference_proteomes.dmnd
diamond_nr_database_path: /local/cqls/db/NCBI/latest_blast_db/nr.dmnd
seqkit:
  sliding: 100000
  window: 6000
n_neighbours: 13
btk_yaml: /nfs4/FW_HMSC/Levi_Lab/Emily/marten_data/ascc/btk_draft.yaml # THIS IS DEFAULT AND ONLY SERVES TO BYPASS GCA REQUIREMENTS OF SANGER-TOL/BLOBTOOLKIT

Here is the stdout from my attempt to run the pipeline and I've attached the .nextflow.log file as well. Any help would be much appreciated:

  Started on:	 cedar0
  Started at:	 Wed Jan  8 06:39:12 PM PST 2025

 N E X T F L O W   ~  version 24.04.3

Launching `https://github.com/sanger-tol/ascc` [cheeky_williams] DSL2 - revision: 0bd7450b27 [dev]

Downloading plugin nf-validation@1.1.4
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`


------------------------------------------------------
  sanger-tol/ascc v1.0dev-g0bd7450
------------------------------------------------------
Core Nextflow options
  revision       : dev
  runName        : cheeky_williams
  containerEngine: singularity
  launchDir      : /nfs4/FW_HMSC/Levi_Lab/Emily/marten_data/ascc
  workDir        : /nfs4/FW_HMSC/Levi_Lab/Emily/marten_data/ascc/work
  projectDir     : /nfs4/FW_HMSC/Levi_Lab/Emily/opt/nxf/assets/sanger-tol/ascc
  userName       : dziedzie
  profile        : singularity
  configFiles    : 

Input/output options
  input          : /nfs4/FW_HMSC/Levi_Lab/Emily/marten_data/ascc/ascc_config_marten_cqls.yaml
  outdir         : /nfs4/FW_HMSC/Levi_Lab/Emily/marten_data/ascc/

Generic options
  tracedir       : /nfs4/FW_HMSC/Levi_Lab/Emily/marten_data/ascc//pipeline_info/

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use sanger-tol/ascc for your analysis please cite:

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

* Software dependencies
  https://github.com/sanger-tol/ascc/blob/master/CITATIONS.md

WARN: Access to undefined parameter `exclude` -- Initialise it to a default value eg. `params.exclude = some_value`
WARN: Access to undefined parameter `btk_busco_run_mode` -- Initialise it to a default value eg. `params.btk_busco_run_mode = some_value`
[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 2 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 3 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 6 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 9 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 10 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 12 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 13 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 16 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 17 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 18 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 20 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 23 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 25 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 27 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 28 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 31 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 32 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 35 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 36 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 40 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 41 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 43 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 44 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 46 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 48 more processes waiting for tasks…

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 48 more processes waiting for tasks…
ERROR ~ Cannot invoke method split() on null object

 -- Check script '/nfs4/FW_HMSC/Levi_Lab/Emily/opt/nxf/assets/sanger-tol/ascc/./workflows/../subworkflows/local/pacbio_barcode_check.nf' at line: 85 or see '.nextflow.log' file for more details
-[sanger-tol/ascc] Pipeline completed with errors-

[-        ] SAN…L_ASCC:ASCC:VALIDATE_TAXID -
[-        ] SAN…TOL_ASCC:ASCC:FILTER_FASTA -
[-        ] SANGERTOL_ASCC:ASCC:GC_CONTENT -
[-        ] SAN…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] SAN…C:GENERATE_GENOME:GNU_SORT -
[-        ] SAN…E_GENOME:GET_LARGEST_SCAFF -
[-        ] SAN…RAILINGNS_CHECK:TRAILINGNS -
[-        ] SAN…RS_PROFILE:GET_KMER_COUNTS -
[-        ] SAN…E:KMER_COUNT_DIM_REDUCTION -
[-        ] SAN…_DIM_REDUCTION_COMBINE_CSV -
[-        ] SAN…ACT_TIARA_HITS:TIARA_TIARA -
[-        ] SAN…CT_NT_BLAST:SEQKIT_SLIDING -
[-        ] SAN…_NT_BLAST:BLAST_BLASTN_MOD -
[-        ] SAN…_BLAST:BLAST_CHUNK_TO_FULL -
[-        ] SAN…LAST:REFORMAT_FULL_OUTFMT6 -
[-        ] SAN…T_BLAST:BLAST_GET_TOP_HITS -
[-        ] SAN…_BLAST:GET_LINEAGE_FOR_TOP -
[-        ] SAN…O_ORGANELLAR_BLAST:SED_SED -
[-        ] SAN…AR_BLAST:BLAST_MAKEBLASTDB -
[-        ] SAN…ANELLAR_BLAST:BLAST_BLASTN -
Plus 48 more processes waiting for tasks…
ERROR ~ Cannot invoke method split() on null object

 -- Check script '/nfs4/FW_HMSC/Levi_Lab/Emily/opt/nxf/assets/sanger-tol/ascc/./workflows/../subworkflows/local/pacbio_barcode_check.nf' at line: 85 or see '.nextflow.log' file for more details

nextflow.01.log

Originally posted by @foreignsand in #69 (comment)
@foreignsand
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I seem to have found a workaround for this by assigning pacbio_multiplexing_barcode_names to "bc1001" in my input yaml file. So my input yaml file now looks like this:

assembly_path: /nfs4/FW_HMSC/Levi_Lab/Emily/marten_data/yahs_scaffolds/ccs_all_scaffolded/yahs.out_scaffolds_final.fa
assembly_title: Humboldt Marten
sci_name: "Martes americana humboldtensis"
taxid: 551455
mito_fasta_path: /nfs4/FW_HMSC/Levi_Lab/Emily/marten_data/mitome/scaffold_644.mito.fa
# plastid_fasta_path: PATH TO PLASTID FASTA
reads_path: /nfs4/FW_HMSC/Levi_Lab/Emily/marten_data/pacbio/7717/subreads/m64047_240219_192555.subreads.fasta
reads_type: "hifi"
pacbio_barcodes: /nfs4/FW_HMSC/Levi_Lab/Emily/opt/pacbio_adaptors/pacbio_adaptors.fa
pacbio_multiplexing_barcode_names: "bc1001" # {BARCODES EXPECTED IN DATA} Not required if you only have one sample, I hope
kmer_len: 7
dimensionality_reduction_methods: "pca"
# Available methods: "pca,umap,t-sne,isomap,lle_standard,lle_hessian,lle_modified,mds,se,random_trees,kernel_pca,pca_svd,autoencoder_sigmoid,autoencoder_linear,autoencoder_selu,autoencoder_relu,nmf"
# Include a CSV of the methods you choose to use and reference it when calling the Nextflow ascc pipeline
nt_database: /local/cqls/db/NCBI/latest_blast_db/nt
nt_database_prefix: /local/cqls/db/NCBI/latest_blast_db
nt_kraken_db_path: /local/cqls/db/kraken2/latest/nt # Note: this specifies that the prefix should also be here, not sure how to handle that
ncbi_accessionids_folder: /local/cqls/db/NCBI/accession2taxid
ncbi_taxonomy_path: /local/cqls/db/NCBI/new_taxdump/
ncbi_rankedlineage_path: /local/cqls/db/NCBI/new_taxdump/rankedlineage.dmp
busco_lineages_folder: /local/cqls/db/busco/busco_current/busco_downloads/lineages
fcs_gx_database_path: /fs1/local/cqls/db/NCBI/gxdb_20241115
vecscreen_database_path: /local/cqls/db/NCBI/univec/
diamond_uniprot_database_path: /local/cqls/db/uniprot/reference_proteomes/reference_proteomes.dmnd
diamond_nr_database_path: /local/cqls/db/NCBI/latest_blast_db/nr.dmnd
seqkit:
  sliding: 100000
  window: 6000
n_neighbours: 13
btk_yaml: /nfs4/FW_HMSC/Levi_Lab/Emily/marten_data/ascc/btk_draft.yaml # THIS IS DEFAULT AND ONLY SERVES TO BYPASS GCA REQUIREMENTS OF SANGER-TOL/BLOBTOOLKIT

This allows the pipeline to continue, although I'm not sure this is the best way to handle the issue because my run wasn't multiplexed so there aren't any barcodes associated with the sample used for the PacBio sequencing run that produced the data for this assembly.

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