Output Files
All BASALT outputs are generated under the current working directory.
Final Output
The final curated MAGs are located in:
<output_prefix>_final_binset/
Default: Final_binset_final_binset/
Output Directory Structure
| Path |
Description |
Final_binset_final_binset/ |
Final curated MAGs (one FASTA per bin) |
Basalt_checkpoint.txt |
Checkpoint file used for --mode continue |
Basalt_log.txt |
Detailed runtime log |
BASALT_command.txt |
Record of the BASALT command and parameters used |
BASALT generates intermediate outputs at each stage. These can be useful for debugging or if you want to use intermediate results:
Autobinning Stage
| Path |
Description |
1_<assembly>_<param>_<binner>_genomes/ |
Raw bins from each binner/parameter combination |
*_checkm2/ or *_checkm/ |
Quality assessment for each binset |
Bins_folder.txt |
Mapping of assembly names to binset folders |
Depth_total.txt |
Coverage depth data for all assemblies |
Connections_total_dict.txt |
Paired-end connection data for all assemblies |
Assembly_MoDict.txt |
Modified assembly file mappings |
BestBins Selection
| Path |
Description |
BestBinsSet/ |
Non-redundant bins selected after within-assembly and cross-assembly dereplication |
BestBinsSet_comparison_files/ |
Comparison data used for dereplication |
Coverage_matrix_list.txt |
List of coverage matrices for each assembly |
Bestbinset_list.txt |
List of best binsets selected |
Refinement Stage
| Path |
Description |
BestBinsSet_outlier_refined/ |
Bins after DL-based contamination removal |
Predicted_potential_outlier.txt |
Per-contig contamination predictions |
BestBinsSet_outlier_refined_filtrated/ |
Bins after filtration by completeness/contamination |
BestBinsSet_outlier_refined_filtrated_retrieved/ |
Bins after PE-based and LR-based contig retrieval |
BestBinsSet_outlier_refined_filtrated_retrieved_MAGs/ |
Final MAGs after intra-group contig retrieval |
Reassembly Stage
| Path |
Description |
*_reassembly/ |
Bins reassembled with SPAdes (short-read only) |
*_hybrid_reassembly/ |
Bins reassembled with Unicycler (hybrid) |
*_reassembly_OLC/ |
Final bins after Overlap-Layout-Consensus refinement |
Quality Reports
Each binset folder contains a quality report:
| File |
Backend |
Contents |
quality_report.tsv |
CheckM2 |
Bin name, completeness, contamination, N50, genome size |
bin_stats_ext.tsv |
CheckM |
Bin name, marker lineage, completeness, contamination, genome size, mean scaffold length |
Log Files
| File |
Description |
Basalt_log.txt |
Runtime event log with timestamps |
Basalt_checkpoint.txt |
Last completed step (1st–9th) |
Cleanup
BASALT performs automatic cleanup of intermediate files (temporary BAM files, SAM files, etc.) between steps. Intermediate binsets from earlier stages are preserved on disk.