Output missing

[MartinPippel]

I tried to use the pipeline but I am not getting all the expected outputs - though the pipeline claims to have finished successfully. I guess some inputs are not provided in the correct format? Any advice would be highly appreciated.

outputs:

outputs/
├── base_content
│   ├── asm_dinuc_windows.tsv.gz
│   ├── asm_freq_windows.tsv.gz
│   ├── asm_mononuc_windows.tsv.gz
│   ├── asm_tetranuc_windows.tsv.gz
│   └── asm_trinuc_windows.tsv.gz
├── multiqc
│   ├── multiqc_data
│   │   ├── multiqc_citations.txt
│   │   ├── multiqc_data.json
│   │   ├── multiqc.log
│   │   ├── multiqc_software_versions.txt
│   │   └── multiqc_sources.txt
│   └── multiqc_report.html
├── pipeline_info
│   └── blobtoolkit
│       ├── blobtoolkit_software_mqc_versions.yml
│       ├── execution_report_2025-07-04_15-28-37.html
│       ├── execution_timeline_2025-07-04_15-28-37.html
│       ├── execution_trace_2025-07-04_15-28-37.txt
│       ├── params_2025-07-04_15-28-41.json
│       └── pipeline_dag_2025-07-04_15-28-37.html
├── read_mapping
│   ├── pacbio
│   │   ├──  qcLitStygr1_pacbio.bam
│   │   └── qcLitStygr1_pacbio.coverage.1k.bed.gz
│   └── hic
│       ├── qcLitStygr1_hic.bam
│       └── qcLitStygr1_hic.coverage.1k.bed.gz
└── resources
    └── new_taxdump.json

pipeline:

  sanger-tol/blobtoolkit 0.8.0
------------------------------------------------------
Input/output options
  input              : samplesheet.csv
  align              : true
  outdir             : outputs

Reference genome options
  taxon              : 2750798
  fasta              : asm.fa

Databases
  busco              : /sw/data/BUSCO_data/latest/rackham/v5_lineage_sets/lineages
  lineage_tax_ids    : /home/pippel/.nextflow/assets/sanger-tol/blobtoolkit/assets/mapping_taxids-busco_dataset_name.2019-12-16.txt
  blastp             : /sw/data/diamond_databases/reference_proteomes/latest/reference_proteomes.dmnd
  blastx             : /sw/data/diamond_databases/reference_proteomes/latest/reference_proteomes.dmnd
  blastn             : /sw/data/blast_databases
  taxdump            : /sw/data/ncbi_taxonomy/latest/new_taxdump

Generic options
  trace_report_suffix: 2025-07-04_15-07-13

Core Nextflow options
  revision           : main
  runName            : determined_maxwell
  containerEngine    : singularity
  launchDir          : /crex/proj/snic2021-6-194/private/martin/Lithobius/run_02/curation/EAR/post2/btk
  workDir            : /crex/proj/snic2021-6-194/private/martin/Lithobius/run_02/curation/EAR/post2/btk/nxf-work
  projectDir         : /home/pippel/.nextflow/assets/sanger-tol/blobtoolkit
  userName           : pippel
  profile            : pelle
  configFiles        :

[yumisims]

Hi,

Could you share the command you ran, including the parameters and the sample CSV?

[MartinPippel]

sample sheet:

sample,datatype,datafile,library_layout
qcLitStygr1_hic,hic,/proj/snic2022-6-208/private/martin/Lithobius/run_02/curation/sanger/HIC2/L.cram,PAIRED
qcLitStygr1_pacbio,pacbio,/proj/snic2022-6-208/private/martin/Lithobius/run_02/curation/sanger/PB/pb.fasta.gz,SINGLE

run command:

    PROFILE="pelle"

    STORAGEALLOC="/proj/snic2021-6-194"                           # NAISS storage allocation (path)
    WORKDIR="nxf-work" # Nextflow work directory
    RESULTS="outputs"      # Path to store results from Nextflow

    # Path to Nextflow script. Pulls from Github
    WORKFLOW="${WORKFLOW:-sanger-tol/blobtoolkit}"
    # Workflow version or branch to use (default: main)
    BRANCH="${BRANCH:-main}"

    REMOTE_OPTS="-r $BRANCH -latest"

    # Run nextflow
    nextflow run "$WORKFLOW" \
        $REMOTE_OPTS \
        -profile "$PROFILE" \
        -work-dir "$WORKDIR" \
        -resume \
        -ansi-log false \
        -params-file workflow_parameters.yml \
        --outdir "$RESULTS"

and workflow_parameters.yml:

project: 'uppmax2025-2-58'
input: 'samplesheet.csv'
align: true
taxon: 2750798
fasta: 'asm.fa'
blastp: '/sw/data/diamond_databases/reference_proteomes/latest/reference_proteomes.dmnd'
blastx: '/sw/data/diamond_databases/reference_proteomes/latest/reference_proteomes.dmnd'
blastn: '/sw/data/blast_databases'
taxdump: '/sw/data/ncbi_taxonomy/latest/new_taxdump'
busco: '/sw/data/BUSCO_data/latest/rackham/v5_lineage_sets/lineages'

[yumisims]

Hi,
Thanks for providing the details. Since I can’t see the contents of the results, it doesn’t look like the BlobToolKit analysis has been performed. Have you included a general BUSCO lineage in the analysis? Thanks.

[MartinPippel]

thanks for your quick feedback. I thought the busco lineages are automatically chosen based on the taxon. How do I specify one or multiple lineages?

The lineages path that I provided via busco: '/sw/data/BUSCO_data/latest/rackham/v5_lineage_sets/lineages' contains all busco lineages:

acari_odb12/
acetobacteraceae_odb12/
acetobacter_odb12/
acholeplasmataceae_odb12/
achromobacter_odb12/
acidobacteriaceae_odb12/
acidobacteria_odb10/
acidobacteriota_odb12/
...

[yumisims]

We haven't tested the pipeline on odb12 yet, but you can choose a general BUSCO lineage using --busco_lineages something_odb10, depending on the taxon you are working with. Please let me know if it is working, thank you.