Introduction Usage Parameters Output Releases

Introduction

This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.

The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps:

Initial clustering:

  • MMseqs2 initial clustering of input amino acid sequences and filtering with membership threshold

Multiple sequence alignment:

  • FAMSA aligner option. Best speed and sensitivity option to build seed multiple sequence alignment for the families
  • mafft aligner option. Fast but not as sensitive as FAMSA to build seed multiple sequence alignment for the families
  • ClipKIT to optionally clip gapped portions of the multiple sequence alignment (MSA)

Generating family models:

  • hmmer to build the family HMM (hmmbuild) and to optionally ‘fish’ additional sequences from the input fasta file (hmmsearch), with given thresholds, into the family and also build the family full MSA (hmmalign)

Removing redundancy:

  • hmmer to match family representative sequences against other family models in order to keep non redundant ones
  • MMseqs2 to strictly cluster the sequences within each of the remaining families, in order to still capture the evolutionary diversity within a family, but without keeping all the almost identical sequences
  • FAMSA aligner option. Re-align full MSA with final set of sequences
  • mafft aligner option. Re-align full MSA with final set of sequences

Updating families:

  • untar to decompress tarballs of existing hmms and msas
  • hmmer to match input sequences to existing families with hmmsearch as well as for rebuilding models with newly recruited sequences with hmmbuild
  • SeqKit to extract fasta formatted family sequences from their MSA files
  • MMseqs2 to strictly cluster the sequences within each of the families to update
  • FAMSA aligner option. Re-align full MSA with final set of sequences
  • mafft aligner option. Re-align full MSA with final set of sequences
  • ClipKIT to optionally clip gapped portions of the multiple sequence alignment (MSA)

Reporting:

  • Extract family representatives to produce the final metadata file along with a fasta of all family representative sequences (can be used downstream for structural prediction).
  • MultiQC - Aggregate report describing results and QC from the whole pipeline
  • Pipeline information - Report metrics generated during the workflow execution

MMseqs2

Output files
  • mmseqs/
    • initial_clustering/
      • mmseqs_createtsv/
        • <samplename>.tsv: tab-separated table containing 2 columns; the first one with the cluster representative sequences, and the second with the cluster members
      • mmseqs_createdb/
        • <samplename>/
          • *: (optional) mmseqs format db of fasta sequences. Can be turned on with —save_mmseqs_db
      • mmseqs_linclust/
        • <samplename>/
          • *: (optional) mmseqs format clustered db. Can be turned on with —save_mmseqs_clustering
      • mmseqs_cluster/
        • <samplename>/
          • *: (optional) mmseqs format clustered db. Can be turned on with —save_mmseqs_clustering
      • filtered_fasta_chunks/
        • <samplename>/
          • chunked_fasta/
            • *.fasta: (optional) fasta files with amino acid sequences of each cluster above the membership threshold

The mmseqs_createtsv/<samplename>.tsv contains the mmseqs clustering of sequences, which will then be filtered by size and split into chunks for further parallel processing. The optionally saved chunked_fasta folder contains these fasta files of sequences for each cluster. These per cluster fasta files act as input to produce downstream families in the next steps of the pipeline. The original mmseqs db and the clustered mmseqs db can be optional saved to the output folder, but they won’t be further utilised in this pipeline.

MMseqs2 clusters amino acid fasta files via either the ‘cluster’ or the ‘linclust’ algorithms.

FAMSA aligner

Output files
  • seed_msa/
    • famsa_align/
      • <samplename>/
        • <samplename>_*.aln: fasta files with aligned amino acid sequences

This folder contains the generated seed MSA family files, if famsa was chosen as the --alignment_tool. These MSA files only contain the original sequences of each cluster as calculated by mmseqs.

FAMSA is a progressive algorithm for large-scale multiple sequence alignments.

mafft aligner

Output files
  • seed_msa/
    • mafft_align/
      • <samplename>/
        • <samplename>_*.fas: fasta files with aligned amino acid sequences

This folder contains the generated seed MSA family files, if mafft was chosen as the --alignment_tool. These MSA files only contain the original sequences of each cluster as calculated by mmseqs.

mafft is a fast but not very sensitive multiple sequence alignment tool.

ClipKIT

Output files
  • seed_msa/
    • clipkit/
      • <samplename>/
        • <samplename>_*.clipkit: gap-clipped (start, middle, end) fasta files of aligned amino acid sequences
    • clip_ends/
      • <samplename>/
        • <samplename>_*.clipends: gap-clipped (only start and end) fasta files of aligned amino acid sequences

If the --trim_msa parameter was set to true, then depending on the --clipping_tool, and according to the --gap_threshold either clipkit is run and gaps (above threshold) are removed throughout the alignment, or clip_ends is run and gaps (above threshold) are removed only at the ends. Results are stored in the seed_msa folder.

ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others.

hmmer

Output files
  • hmmer/
    • hmmbuild/
      • <samplename>/
        • <samplename>_*.hmm.gz: compressed hmm model for the family
        • <samplename>_*.hmmbuild.txt: (optional) hmmbuild execution log
    • hmmsearch/
      • <samplename>/
        • <samplename>_*.domtbl.gz: (optional) hmmsearch results along parameters info. Can be turned on with —save_hmmsearch_results
        • <samplename>_*.txt.gz: (optional) hmmsearch execution log. Can be turned on with —save_hmmsearch_results
  • full_msa/
    • pre_non_redundant/
      • <samplename>/
        • <samplename>_*.sto.gz: compressed family full MSA produced by hmmalign (before checking for redundancy)

The hmmer/hmmbuild folder contains all originally created family HMMs. These models will be used downstream used to ‘fish’ extra sequences in each family if --recruit_sequences_with_models is set to true, and/or to remove between-families redundancy if --remove_family_redundancy is set to true. The models can also be used in the update_families execution mode of the pipeline, along with the families’ respective MSAs, to recruit sequences from a new input fasta file into the families, updating both family HMM and MSA files.

hmmer is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others.

hmmer for redundancy removal

Output files
  • remove_redundancy/
    • hmmer/
      • concatenated/
        • <samplename>.hmm.gz: (optional) concatenated compressed hmm model for all families in a given sample (pre redundancy removal)
      • hmmsearch/
        • <samplename>/
          • <samplename>_*.domtbl.gz: (optional) hmmsearch results of family reps against families’ HMMs
    • family_reps/
      • <samplename>/
        • <samplename>_meta_mqc.csv: (optional) csv with metadata (Sample Name,Family Id,Size,Representative Length,Representative Id,Sequence)
        • <samplename>_reps.fa: (optional) fasta file of all family representative sequences (one sequence per family)
    • non_redundant_fams/
      • <samplename>/
        • non_redundant/
          • <samplename>_*.fasta.gz: (optional) compressed family full MSA (after checking for family redundancy)

If --remove_family_redundancy is set to true, the hmmer/hmmsearch module is used to identify family representative sequences that are highly identical to other family HMMs. In these cases, the smaller sized families are deemed redundant and flagged for removal. These remove_redundancy optional folders only contain intermediate pipeline results that by default are not saved in the output results.

hmmer is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others.

MMseqs2 for redundancy removal

Output files
  • mmseqs/
    • redundancy_clustering/
      • mmseqs_createtsv/
        • <samplename>.tsv: tab-separated table containing 2 columns; the first one with the cluster representative sequences, and the second with the cluster members
      • mmseqs_createdb/
        • <samplename>/
          • *: (optional) mmseqs format db of fasta sequences
      • mmseqs_linclust/
        • <samplename>/
          • *: (optional) mmseqs format clustered db
      • mmseqs_cluster/
        • <samplename>/
          • *: (optional) mmseqs format clustered db
  • remove_redundancy/
    • reps_fasta/
      • <samplename>/
        • <samplename>_reps.fa: (optional) fasta file of all family representative sequences (one sequence per family)

If --remove_sequence_redundancy is set to true, the mmseqs clustering subworkflow will be executed to very strictly cluster (--cluster_seq_identity_for_redundancy = 0.97, cluster_coverage_for_redundancy = 0.97, cluster_cov_mode_for_redundancy = 0 -meaning both strands) in-family sequences, keeping only cluster representatives before recalculating the family MSAs.

MMseqs2 clusters amino acid fasta files via either the ‘cluster’ or the ‘linclust’ algorithms.

FAMSA for redundancy removal

Output files
  • full_msa/
    • non_redundant/
      • famsa_align/
        • <samplename>/
          • <samplename>_*.aln: family full MSA (after checking for sequence redundancy)

If --remove_sequence_redundancy is set to true, then the MSAs will be recalculated after in-family sequence redundancy is removed. If the --alignment_tool is famsa, then this famsa_align folder will be created, containing the final MSA files.

FAMSA is a progressive algorithm for large-scale multiple sequence alignments.

mafft for redundancy removal

Output files
  • full_msa/
    • non_redundant/
      • mafft_align/
        • <samplename>/
          • <samplename>_*.fas: fasta files with aligned amino acid sequences (after checking for sequence redundancy)

If --remove_sequence_redundancy is set to true, then the MSAs will be recalculated after in-family sequence redundancy is removed. If the --alignment_tool is mafft, then this mafft_align folder will be created, containing the final MSA files.

mafft is a fast but not very sensitive multiple sequence alignment tool.

untar

Output files
  • untar/
    • hmm/
      • <samplename>/
        • <family_name>.{hmm.gz,hmm}: (optional) decompressed input hmm tarball
    • msa/
      • <samplename>/
        • <family_id>.{aln,fas}: (optional) decompressed input msa tarball

hmmer for updating families

Output files
  • update_families/
    • hmmer/
      • concatenated/
        • <samplename>.hmm.gz: (optional) concatenated compressed HMM models for all families in a given sample, to be used as input for hmmsearch, to determine which families will be updated with new sequences
      • hmmsearch/
        • <samplename>/
          • <samplename>.domtbl.gz: (optional) hmmsearch results of input fasta file against existing families’ HMMs
      • hmmbuild/
        • <samplename>/
          • <family_id>.hmm.gz: (optional) compressed family HMM after the update
          • <family_id>.hmmbuild.txt: (optional) hmmbuild execution log
    • branch_fasta/
      • hits/
        • <family_id>.fasta: (optional) subset of the input FASTA with hit sequences for each existing family
      • <samplename>.fasta.gz: (optional) FASTA file that contains all remaining non-hit input sequences, which will be passed to normal execution mode to create new families
    • family_reps/
      • <samplename>/
        • <samplename>_meta_mqc.csv: (optional) csv with metadata (Sample Name,Family Id,Size,Representative Length,Representative Id,Sequence)
        • <samplename>_reps.fa: (optional) fasta file of all family representative sequences (one sequence per family)

The update_families execution mode is run if paths to existing_hmms_to_update and existing_msas_to_update are provided in the input samplesheet.csv. The hmmer/hmmsearch module is used to match new incoming sequences in the existing family models. If there were hits, the new sequences are reclustered along their matching family existing ones, and new models are build with hmmer/hmmbuild in the update_families/hmmer/hmmbuild folder, from the respective new MSAs.

hmmer is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others.

SeqKit

Output files
  • seqkit/
    • <samplename>_<family_id>.fastq: (optional) fasta formatted family sequences from full MSA with gaps removed
  • update_families/
    • fasta/
      • <samplename>_<family_id>.fastq: (optional) concatenated family fasta with newly recruited sequences

The seqkit module is mainly used during the update_families mode to extract sequences from family MSA, into intermediate fasta files (seqkit output folder). The intermediate update_families/fasta folder contains the aggregation of existing family sequences along with their newly matching ones, that will together produce the updated family MSA.

SeqKit is a cross-platform and ultrafast toolkit for FASTA/Q file manipulation.

MMseqs2 for updating families

Output files
  • mmseqs/
    • update_families/
      • mmseqs_createtsv/
        • <family_id>.tsv: tab-separated table containing 2 columns; the first one with the cluster representative sequences, and the second with the cluster members
      • mmseqs_createdb/
        • <family_id>/
          • *: (optional) mmseqs format db of fasta sequences
      • mmseqs_linclust/
        • <family_id>/
          • *: (optional) mmseqs format clustered db
      • mmseqs_cluster/
        • <family_id>/
          • *: (optional) mmseqs format clustered db
      • reps_fasta/
        • <samplename>/
          • <samplename>_reps.fa: (optional) fasta file of all family representative sequences (one sequence per family)

Similarly to the in-family sequence redundancy removal mechanism, the mmseqs suite is used to strictly cluster existing family sequences along newly recruited ones, keeping a non redundant set. The new family representative sequences can now be found in the intermediate mmseqs/reps_fasta folder.

MMseqs2 clusters amino acid fasta files via either the ‘cluster’ or the ‘linclust’ algorithms.

FAMSA for updating families

Output files
  • update_families/
    • full_msa/
      • famsa_align/
      • <samplename>/
        • <family_id>.aln: family full MSA (after updating with new sequences)

In the update_families mode, if new sequences are added in an existing family, and after (optionally) removing in-family sequence redundacny, if --remove_sequence_redundancy is set to true, then the family MSA is recalculated. If the --alignment_tool is famsa, then this famsa_align folder will be created, containing the updated family MSA files.

FAMSA is a progressive algorithm for large-scale multiple sequence alignments.

mafft for updating families

Output files
  • update_families/
    • full_msa/
      • mafft_align/
      • <samplename>/
        • <family_id>.fas: family full MSA (after updating with new sequences)

In the update_families mode, if new sequences are added in an existing family, and after (optionally) removing in-family sequence redundacny, if --remove_sequence_redundancy is set to true, then the family MSA is recalculated. If the --alignment_tool is mafft, then this mafft_align folder will be created, containing the updated family MSA files.

mafft is a fast but not very sensitive multiple sequence alignment tool.

ClipKIT for updating families

Output files
  • update_families/
    • full_msa/
      • clipkit/
        • <samplename>/
          • <family_id>.clipkit: gap-clipped (start, middle, end) fasta files of aligned amino acid sequences
      • clip_ends/
        • <samplename>/
          • <family_id>.clipends: gap-clipped (only start and end) fasta files of aligned amino acid sequences

If the --trim_msa parameter was set to true, then depending on the --clipping_tool, and according to the --gap_threshold either clipkit is run and gaps (above threshold) are removed throughout the alignment, or clip_ends is run and gaps (above threshold) are removed only at the ends. Results are stored in the update_families/full_msa folder.

ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others.

Extract family representatives

Output files
  • family_reps/
    • <samplename>/
      • <samplename>_meta_mqc.csv: csv with metadata to print with MultiQC (Sample Name,Family Id,Size,Representative Length,Representative Id,Sequence)
      • <samplename>_reps.fa: fasta file of all family representative sequences (one sequence per family)
  • update_families/
    • family_reps/
      • <samplename>/
        • <samplename>_meta_mqc.csv: csv with metadata to print with MultiQC (Sample Name,Family Id,Size,Representative Length,Representative Id,Sequence)
        • <samplename>_reps.fa: fasta file of all family representative sequences (one sequence per family)

The final report of the nf-core/proteinfamilies pipeline. The *_meta_mqc.csv file are used to report family metadata and statistics in the browser, via the MultiQC software. The *_reps.fa protein fasta file contains all family representative sequence in one place. This file can be further used as input in other pipelines such as nf-core/proteinfold for structural prediction or in fasta annotation pipelines.

MultiQC

Output files
  • multiqc/
    • multiqc_report.html: a standalone HTML file that can be viewed in your web browser.
    • multiqc_data/: directory containing parsed statistics from the different tools used in the pipeline.
    • multiqc_plots/: directory containing static images from the report in various formats.

MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.

Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info.

Custom output MultiQC data includes a metadata file (multiqc_data/multiqc_family_metadata.txt) with family information such as: Sample,Family Id,Size,Representative Length,Representative Id,Sequence

This custom metadata is presented as a data table in the MultiQC report file.

Pipeline information

Output files
  • pipeline_info/
    • Reports generated by Nextflow: execution_report.html, execution_timeline.html, execution_trace.txt and pipeline_dag.dot/pipeline_dag.svg.
    • Reports generated by the pipeline: pipeline_report.html, pipeline_report.txt and software_versions.yml. The pipeline_report* files will only be present if the --email / --email_on_fail parameter’s are used when running the pipeline.
    • Reformatted samplesheet files used as input to the pipeline: samplesheet.valid.csv.
    • Parameters used by the pipeline run: params.json.

Nextflow provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.