| { |
| "counts": { |
| "descendant_taxid_count": 3464, |
| "n_enterococcus_link_rows_used": 7937, |
| "n_host_assemblies_in_sequence_db": 1497, |
| "n_host_assemblies_linked": 1497, |
| "n_host_assemblies_with_non_plasmid_contigs": 1497, |
| "n_host_assembly_evidence_accessions_linked": 2382, |
| "n_host_assembly_evidence_accessions_resolved": 2376, |
| "n_host_assembly_evidence_accessions_unresolved": 6, |
| "n_host_contigs": 4530, |
| "n_host_non_plasmid_bp": 4266416394, |
| "n_host_parquet_parts": 168, |
| "n_host_sampling_failure_rows": 0, |
| "n_host_segment_rows": 728720, |
| "n_link_rows_after_taxon_filter": 8152, |
| "n_link_rows_before_taxon_filter": 220095, |
| "n_plasmid_segment_rows": 182180, |
| "n_representatives_after_taxon_filter": 2613, |
| "n_representatives_before_clean_filter": 2613, |
| "n_representatives_excluded_by_clean_filter": 94, |
| "n_representatives_sampled": 2519, |
| "target_host_rows": 728720, |
| "taxonomy_evidence_columns": [ |
| "taxid" |
| ] |
| }, |
| "created_at": "2026-07-07T11:55:32.195788+00:00", |
| "inputs": { |
| "assembly_metadata": [ |
| "/project/c_evolm/training_datasets/phage_db/NCBI/sequence_reports/full/analysis_high_confidence/high_confidence_plasmid_assembly_links.tsv", |
| "/project/c_evolm/training_datasets/phage_db/NCBI/sequence_reports/full/analysis/high_confidence_plasmid_assembly_links.tsv" |
| ], |
| "nr_links": "/project/c_evolm/training_datasets/phage_db/NCBI/plasmid_nr/clean_v2_len2k_4mb_nochrom_broadhq20/nr/tables/nr_plasmid_to_assembly_links.feather", |
| "nr_reps": "/project/c_evolm/training_datasets/phage_db/NCBI/plasmid_nr/clean_v2_len2k_4mb_nochrom_broadhq20/nr/tables/all_nr_plasmids.feather", |
| "sequence_db_chunks": "/scratch/c_evolm/plasmids/genome_downloads/high_confidence_plasmid_assemblies/sequence_db/parquet/chunks", |
| "sequence_db_manifest": "/scratch/c_evolm/plasmids/genome_downloads/high_confidence_plasmid_assemblies/sequence_db/metadata/assembly_manifest.parquet", |
| "taxonomy_dir": "/project/c_evolm/training_datasets/phage_db/ncbi_taxonomy" |
| }, |
| "outputs": { |
| "excluded_representatives": "/project/c_evolm/training_datasets/phage_db/NCBI/TrainingSamples/ncbi_enterococcus_clean_v2_nr_reps_len1k_400k_nochr_cov2_h4_actL4000/selected/excluded_plasmid_representatives.tsv", |
| "host_assemblies": "/project/c_evolm/training_datasets/phage_db/NCBI/TrainingSamples/ncbi_enterococcus_clean_v2_nr_reps_len1k_400k_nochr_cov2_h4_actL4000/selected/enterococcus_host_assemblies.tsv", |
| "host_sampling_failures": "/project/c_evolm/training_datasets/phage_db/NCBI/TrainingSamples/ncbi_enterococcus_clean_v2_nr_reps_len1k_400k_nochr_cov2_h4_actL4000/qc/host_sampling_failures.tsv", |
| "host_sampling_stats": "/project/c_evolm/training_datasets/phage_db/NCBI/TrainingSamples/ncbi_enterococcus_clean_v2_nr_reps_len1k_400k_nochr_cov2_h4_actL4000/qc/host_sampling_stats.tsv", |
| "host_segments_manifest": "/project/c_evolm/training_datasets/phage_db/NCBI/TrainingSamples/ncbi_enterococcus_clean_v2_nr_reps_len1k_400k_nochr_cov2_h4_actL4000/segments/actL4000/host_segments_candidates_manifest.tsv", |
| "host_segments_parquet_dir": "/project/c_evolm/training_datasets/phage_db/NCBI/TrainingSamples/ncbi_enterococcus_clean_v2_nr_reps_len1k_400k_nochr_cov2_h4_actL4000/segments/actL4000/host_segments_candidates_parquet", |
| "plasmid_filter_summary": "/project/c_evolm/training_datasets/phage_db/NCBI/TrainingSamples/ncbi_enterococcus_clean_v2_nr_reps_len1k_400k_nochr_cov2_h4_actL4000/qc/plasmid_filter_summary.tsv", |
| "plasmid_segments": "/project/c_evolm/training_datasets/phage_db/NCBI/TrainingSamples/ncbi_enterococcus_clean_v2_nr_reps_len1k_400k_nochr_cov2_h4_actL4000/segments/actL4000/plasmid_segments_fullmeta.feather", |
| "reference_fasta": "/project/c_evolm/training_datasets/phage_db/NCBI/TrainingSamples/ncbi_enterococcus_clean_v2_nr_reps_len1k_400k_nochr_cov2_h4_actL4000/fasta/enterococcus_clean_v2_nr_plasmids.fasta", |
| "reference_metadata": "/project/c_evolm/training_datasets/phage_db/NCBI/TrainingSamples/ncbi_enterococcus_clean_v2_nr_reps_len1k_400k_nochr_cov2_h4_actL4000/fasta/enterococcus_clean_v2_nr_plasmids_metadata.tsv", |
| "selected_links": "/project/c_evolm/training_datasets/phage_db/NCBI/TrainingSamples/ncbi_enterococcus_clean_v2_nr_reps_len1k_400k_nochr_cov2_h4_actL4000/selected/enterococcus_clean_v2_nr_assembly_links.tsv", |
| "selected_representatives": "/project/c_evolm/training_datasets/phage_db/NCBI/TrainingSamples/ncbi_enterococcus_clean_v2_nr_reps_len1k_400k_nochr_cov2_h4_actL4000/selected/enterococcus_clean_v2_nr_representatives.tsv" |
| }, |
| "parameters": { |
| "allow_sequence_db_version_fallback": false, |
| "chrom_hq_hit_threshold": 5, |
| "genus_taxid": 1350, |
| "host_ratio": 4, |
| "host_workers": 16, |
| "limit_assemblies": null, |
| "limit_representatives": null, |
| "max_plasmid_length": 400000, |
| "min_length": 200, |
| "min_plasmid_length": 1000, |
| "near_complete_hit_threshold": 2, |
| "plasmid_coverage": 2.0, |
| "plasmid_jobs": 16, |
| "seed": 42, |
| "segment_length": 4000, |
| "small_chrom_qc": "/project/c_evolm/training_datasets/phage_db/NCBI/chromosome_containment_qc/small_nr_plasmids_1kb_10kb_vs_complete_genome_chromosomes/tables/small_nr_plasmid_chromosome_hit_summary.tsv", |
| "small_cluster_max_size": 5 |
| } |
| } |
|
|
