Outputs and quality control

Outputs and quality control#

BASALT writes final and intermediate outputs into the current working directory. The exact intermediate set depends on input read types, selected modules, quality-control backend, optional binners, and whether stages were skipped or resumed.

Final output#

For a normal CheckM2 run, -o names the final directory:

<value supplied to -o>/

With the default, this is:

Final_binset/

The directory contains final bin FASTA files, generally with a .fa suffix, and a final quality report when CheckM2 completes successfully.

Warning

Earlier documentation referred to Final_binset_final_binset/ or Final_bestbinset/. Those names do not describe the current -o behaviour in the default CheckM2 orchestration.

Run-level provenance#

File

Role

Retain?

BASALT_command.txt

Recorded input and parameter summary

yes

Basalt_log.txt

Runtime events and warnings

yes

Basalt_checkpoint.txt

Textual stage completion markers

yes

Autobinner_checkpoint.txt

Candidate-generation progress

recommended

captured stdout and stderr

External-tool messages not always duplicated in the BASALT log

yes

Archive these files with the final MAGs. They are required to distinguish a completed result from a partially successful run.

Principal intermediate groups#

Names can vary, but the following patterns reflect the current workflow.

Candidate generation#

Pattern

Contents

*_metabat_genomes/

MetaBAT 2 candidate bins

*_maxbin2_genomes/

MaxBin 2.0 candidates in more-sensitive mode

*_concoct_genomes/

CONCOCT candidates in non-quick modes

*_semibin_genomes/

SemiBin 2 candidates

*_checkm2/ or *_checkm/

Stage-specific quality estimates

Coverage_matrix_*.txt

Coverage matrices used by downstream stages

condense_connections_*.txt

Summarized paired-end connectivity

Selection and refinement#

Pattern

Contents

*BestBinsSet* or BestBinset*

Selected or dereplicated binsets at successive stages

*outlier_refined*

Bins after model-based contig screening

*filtrated_retrieved*

Bins after thresholding and contig retrieval

Predicted_potential_outlier.txt

Contig-level model predictions where produced

Reassembly and polishing#

Pattern

Contents

*_re-assembly*

Reassembled bin candidates

*_OLC*

Bins processed by OLC comparison or extension

Remained_seq.tar.gz

Unassigned or remaining reads from compatible polishing paths

Cleanup can archive or remove intermediate groups after a full run. Copy required audit artifacts before manual cleanup.

Quality reports#

CheckM2 commonly writes quality_report.tsv. BASALT may copy the final report to Final_bestbinset_quality_report.tsv inside the output directory when a final report is generated after selection.

CheckM2 columns and their precise meaning are defined by the installed CheckM2 version. Do not assume a fixed column order in downstream scripts without inspecting the header.

For the legacy CheckM path, stage outputs include CheckM lineage-workflow files such as bin_stats_ext.tsv.

Interpreting quality estimates#

Completeness and contamination are model- or marker-based estimates. They are not direct measurements of genome truth. Interpret them together with:

  • genome size and sequence count;

  • N50 or other contiguity summaries;

  • taxonomic assignment and marker consistency;

  • read support and coverage distribution;

  • unexpected composition or duplicated regions;

  • the biological and environmental context.

State the software version, database, and threshold logic whenever quality classes are reported.

Completion audit#

Before accepting the result:

test -d study_01_basalt
test -s Basalt_log.txt
test -s Basalt_checkpoint.txt

find study_01_basalt -maxdepth 1 -type f -name '*.fa' -size +0c | wc -l
tail -n 20 Basalt_checkpoint.txt
tail -n 50 Basalt_log.txt

Then verify that:

  1. the expected final stage completed or was intentionally skipped;

  2. optional-binner failures were understood;

  3. each retained FASTA is non-empty and parseable;

  4. a matching final quality report exists;

  5. all post-processing filters are scripted and recorded;

  6. final files have checksums.

find study_01_basalt -maxdepth 1 -type f -print0 \
  | sort -z \
  | xargs -0 sha256sum \
  > study_01_basalt.sha256

Do not infer from directory names#

Intermediate names encode program stages, not validated biological categories. A folder containing MAGs, refined, polished, retrieved, or Best is not evidence that every contained genome passes a publication-specific standard. Apply and report explicit acceptance criteria.

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