Add files using upload-large-folder tool

Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/deseq_20260709_063955/run_metadata.json

@@ -0,0 +1,123 @@
+{
+  "task_id": "deseq",
+  "task_name": "RNA-Seq Differential Expression (DESeq2)",
+  "run_dir": "/225040511/project/Beyond_Prompt-Based_Planning/Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/deseq_20260709_063955",
+  "dataset_dir": "/225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq",
+  "data_dir": "/225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/data",
+  "reference_dir": "/225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/reference",
+  "agent_runtime_dir": "/225040511/project/Beyond_Prompt-Based_Planning/Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/deseq_20260709_063955/agent_runtime",
+  "output_paths": [
+    "/225040511/project/Beyond_Prompt-Based_Planning/Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/deseq_20260709_063955/up_regulated_genes.csv"
+  ],
+  "agent_kwargs": {
+    "expected_data_lake_files": [],
+    "rewrite_user_query": true,
+    "dynamic_mcp_registration": true,
+    "use_graph_retriever": true,
+    "mcp_retrieval_mode": "flat",
+    "use_tool_retriever": true,
+    "timeout_seconds": 600,
+    "mcp_server_top_k": 20,
+    "mcp_tool_top_k": 12,
+    "path": "/225040511/project/Beyond_Prompt-Based_Planning/Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/deseq_20260709_063955/agent_runtime",
+    "execution_env_prefix": "/225040511/miniconda3/envs/biomni_e1",
+    "benchmark_guard": {
+      "enabled": true,
+      "allowed_roots": [
+        "/225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/data",
+        "/225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/reference",
+        "/225040511/project/Beyond_Prompt-Based_Planning/Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/deseq_20260709_063955"
+      ],
+      "forbidden_patterns": [
+        "/225040511/project/Beyond_Prompt\\-Based_Planning/bioagent\\-bench/dataset/(?!deseq(?:/|$|[\\s'\\\"<>]))[^\\s'\\\"<>]+",
+        "/225040511/project/Beyond_Prompt\\-Based_Planning/bioagent\\-bench/dataset/deseq/results(?:/|$|[^\\s'\\\"<>]*)",
+        "/225040511/project/Beyond_Prompt\\-Based_Planning/bioagent\\-bench/dataset/deseq/(?:data|reference)/biomni_data(?:/|$|[^\\s'\\\"<>]*)",
+        "/225040511/project/Beyond_Prompt\\-Based_Planning/Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/(?!deseq_20260709_063955(?:/|$|[\\s'\\\"<>]))[^\\s'\\\"<>]+",
+        "os\\\\.walk\\\\(['\\\"]/225040511/project/Beyond_Prompt\\-Based_Planning/bioagent\\-bench/dataset['\\\"]\\\\)",
+        "Path\\\\(['\\\"]/225040511/project/Beyond_Prompt\\-Based_Planning/bioagent\\-bench/dataset['\\\"]\\\\)\\\\.rglob"
+      ],
+      "forbidden_substrings": [
+        "pip install",
+        "conda install",
+        "mamba install",
+        "install.packages(",
+        "BiocManager::install",
+        "http://",
+        "https://"
+      ],
+      "forbidden_commands": [
+        "wget ",
+        "curl ",
+        "aws s3 cp",
+        "gsutil cp"
+      ]
+    },
+    "benchmark_task_context": {
+      "task_id": "deseq",
+      "task_name": "RNA-Seq Differential Expression (DESeq2)",
+      "description": "The dataset consists of RNA-Seq samples from Candida parapsilosis wild-type (WT) strains grown in planktonic and biofilm conditions, generated as part of a study on gene expression and biofilm formation. The samples were sequenced on the Illumina HiSeq 2000 platform. The goal of this analysis is to perform differential expression analysis using DESeq2 to identify genes that are significantly up- or down-regulated between planktonic and biofilm conditions, providing insights into biofilm-associated transcriptional changes.",
+      "task_prompt": "Identify differentialy expressed genes between planktonic and biofilm conditions of Candida parapsilosis. The output should be a CSV file with the following columns: gene_id,log2FoldChange,pvalue,padj\nCPAR2_00000,1.0, 2.0, 1e-44",
+      "extra_instruction": "",
+      "required_outputs": [
+        "up_regulated_genes.csv"
+      ]
+    }
+  },
+  "query": "You are running a bioagent-bench task with local files already prepared.\n\nTask ID: deseq\nTask name: RNA-Seq Differential Expression (DESeq2)\nBenchmark prompt:\nIdentify differentialy expressed genes between planktonic and biofilm conditions of Candida parapsilosis. The output should be a CSV file with the following columns: gene_id,log2FoldChange,pvalue,padj\nCPAR2_00000,1.0, 2.0, 1e-44\nData background:\nThe dataset consists of RNA-Seq samples from Candida parapsilosis wild-type (WT) strains grown in planktonic and biofilm conditions, generated as part of a study on gene expression and biofilm formation. The samples were sequenced on the Illumina HiSeq 2000 platform. The goal of this analysis is to perform differential expression analysis using DESeq2 to identify genes that are significantly up- or down-regulated between planktonic and biofilm conditions, providing insights into biofilm-associated transcriptional changes.\nConstraints:\n1. Use only the benchmark inputs and references explicitly listed below.\n2. Do not inspect or use any files under benchmark truth/results directories, sibling task directories, generated biomni_data caches, or previous run outputs.\n3. Save the required final deliverables exactly to the paths listed below.\n4. Save any intermediate scripts, logs, and scratch outputs inside this run directory: /225040511/project/Beyond_Prompt-Based_Planning/Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/deseq_20260709_063955\n5. Keep final deliverables in the same schema/format requested by the benchmark prompt.\n6. Return a concise final summary after writing the required files.\n7. The runner, Python REPL, MCP servers, Rscript, and CLI subprocesses are bound to this conda environment: /225040511/miniconda3/envs/biomni_e1. Do not switch to another conda environment.\n\nBenchmark data policy:\n- Allowed input data directory: /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/data\n- Allowed reference directory: /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/reference\n- Allowed scratch/output directory: /225040511/project/Beyond_Prompt-Based_Planning/Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/deseq_20260709_063955\n- Forbidden truth/results directory: /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/results\n- Forbidden sibling benchmark task directories: /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/<any task other than deseq>\n- Forbidden generated Biomni cache/runtime directories inside benchmark inputs: /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/data/biomni_data and /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/reference/biomni_data\n- Do not inspect previous bioagent-bench-runs as data sources.\n- Do not download external databases or install new packages during the benchmark run.\n- You may use installed command-line tools, Python/R packages, and MCP servers as executors, but their inputs must come from the allowed paths above.\n\nInput data directory:\n/225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/data\nVisible input files:\n- SRR1278968_1.fastq\n- SRR1278968_2.fastq\n- SRR1278969_1.fastq\n- SRR1278969_2.fastq\n- SRR1278970_1.fastq\n- SRR1278970_2.fastq\n- SRR1278971_1.fastq\n- SRR1278971_2.fastq\n- SRR1278972_1.fastq\n- SRR1278972_2.fastq\n- SRR1278973_1.fastq\n- SRR1278973_2.fastq\n\nReference data directory:\n/225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/reference\nVisible reference files:\n- C_parapsilosis_CDC317_current_chromosomes.fasta\n- C_parapsilosis_CDC317_current_chromosomes.fasta.fai\n- C_parapsilosis_CDC317_current_features.gff\n- C_parapsilosis_CDC317_current_features.gtf\n- C_parapsilosis_hisat2.1.ht2\n- C_parapsilosis_hisat2.2.ht2\n- C_parapsilosis_hisat2.3.ht2\n- C_parapsilosis_hisat2.4.ht2\n- C_parapsilosis_hisat2.5.ht2\n- C_parapsilosis_hisat2.6.ht2\n- C_parapsilosis_hisat2.7.ht2\n- C_parapsilosis_hisat2.8.ht2\n\nRequired final output paths:\n- up_regulated_genes.csv: /225040511/project/Beyond_Prompt-Based_Planning/Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/deseq_20260709_063955/up_regulated_genes.csv",
+  "benchmark_policy": "Benchmark data policy:\n- Allowed input data directory: /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/data\n- Allowed reference directory: /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/reference\n- Allowed scratch/output directory: /225040511/project/Beyond_Prompt-Based_Planning/Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/deseq_20260709_063955\n- Forbidden truth/results directory: /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/results\n- Forbidden sibling benchmark task directories: /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/<any task other than deseq>\n- Forbidden generated Biomni cache/runtime directories inside benchmark inputs: /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/data/biomni_data and /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/reference/biomni_data\n- Do not inspect previous bioagent-bench-runs as data sources.\n- Do not download external databases or install new packages during the benchmark run.\n- You may use installed command-line tools, Python/R packages, and MCP servers as executors, but their inputs must come from the allowed paths above.",
+  "benchmark_execution_guard": {
+    "enabled": true,
+    "allowed_roots": [
+      "/225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/data",
+      "/225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/reference",
+      "/225040511/project/Beyond_Prompt-Based_Planning/Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/deseq_20260709_063955"
+    ],
+    "forbidden_patterns": [
+      "/225040511/project/Beyond_Prompt\\-Based_Planning/bioagent\\-bench/dataset/(?!deseq(?:/|$|[\\s'\\\"<>]))[^\\s'\\\"<>]+",
+      "/225040511/project/Beyond_Prompt\\-Based_Planning/bioagent\\-bench/dataset/deseq/results(?:/|$|[^\\s'\\\"<>]*)",
+      "/225040511/project/Beyond_Prompt\\-Based_Planning/bioagent\\-bench/dataset/deseq/(?:data|reference)/biomni_data(?:/|$|[^\\s'\\\"<>]*)",
+      "/225040511/project/Beyond_Prompt\\-Based_Planning/Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/(?!deseq_20260709_063955(?:/|$|[\\s'\\\"<>]))[^\\s'\\\"<>]+",
+      "os\\\\.walk\\\\(['\\\"]/225040511/project/Beyond_Prompt\\-Based_Planning/bioagent\\-bench/dataset['\\\"]\\\\)",
+      "Path\\\\(['\\\"]/225040511/project/Beyond_Prompt\\-Based_Planning/bioagent\\-bench/dataset['\\\"]\\\\)\\\\.rglob"
+    ],
+    "forbidden_substrings": [
+      "pip install",
+      "conda install",
+      "mamba install",
+      "install.packages(",
+      "BiocManager::install",
+      "http://",
+      "https://"
+    ],
+    "forbidden_commands": [
+      "wget ",
+      "curl ",
+      "aws s3 cp",
+      "gsutil cp"
+    ]
+  },
+  "benchmark_task_context": {
+    "task_id": "deseq",
+    "task_name": "RNA-Seq Differential Expression (DESeq2)",
+    "description": "The dataset consists of RNA-Seq samples from Candida parapsilosis wild-type (WT) strains grown in planktonic and biofilm conditions, generated as part of a study on gene expression and biofilm formation. The samples were sequenced on the Illumina HiSeq 2000 platform. The goal of this analysis is to perform differential expression analysis using DESeq2 to identify genes that are significantly up- or down-regulated between planktonic and biofilm conditions, providing insights into biofilm-associated transcriptional changes.",
+    "task_prompt": "Identify differentialy expressed genes between planktonic and biofilm conditions of Candida parapsilosis. The output should be a CSV file with the following columns: gene_id,log2FoldChange,pvalue,padj\nCPAR2_00000,1.0, 2.0, 1e-44",
+    "extra_instruction": "",
+    "required_outputs": [
+      "up_regulated_genes.csv"
+    ]
+  },
+  "timestamp_utc": "20260709_063955",
+  "runtime_environment": {
+    "execution_env_prefix": "/225040511/miniconda3/envs/biomni_e1",
+    "execution_python": "/225040511/miniconda3/envs/biomni_e1/bin/python",
+    "conda_default_env": "biomni_e1",
+    "conda_prefix": "/225040511/miniconda3/envs/biomni_e1",
+    "path_head": [
+      "/225040511/miniconda3/envs/biomni_e1/bin",
+      "/root/.codex/tmp/arg0/codex-arg0NuJJn0",
+      "/root/.vscode-server/cli/servers/Stable-4fe60c8b1cdac1c4c174f2fb180d0d758272d713/server/bin/remote-cli",
+      "/225040511/miniconda3/bin",
+      "/225040511/miniconda3/condabin"
+    ]
+  }
+}

Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/deseq_20260709_063955/task_query.txt

@@ -0,0 +1,63 @@
+You are running a bioagent-bench task with local files already prepared.
+
+Task ID: deseq
+Task name: RNA-Seq Differential Expression (DESeq2)
+Benchmark prompt:
+Identify differentialy expressed genes between planktonic and biofilm conditions of Candida parapsilosis. The output should be a CSV file with the following columns: gene_id,log2FoldChange,pvalue,padj
+CPAR2_00000,1.0, 2.0, 1e-44
+Data background:
+The dataset consists of RNA-Seq samples from Candida parapsilosis wild-type (WT) strains grown in planktonic and biofilm conditions, generated as part of a study on gene expression and biofilm formation. The samples were sequenced on the Illumina HiSeq 2000 platform. The goal of this analysis is to perform differential expression analysis using DESeq2 to identify genes that are significantly up- or down-regulated between planktonic and biofilm conditions, providing insights into biofilm-associated transcriptional changes.
+Constraints:
+1. Use only the benchmark inputs and references explicitly listed below.
+2. Do not inspect or use any files under benchmark truth/results directories, sibling task directories, generated biomni_data caches, or previous run outputs.
+3. Save the required final deliverables exactly to the paths listed below.
+4. Save any intermediate scripts, logs, and scratch outputs inside this run directory: /225040511/project/Beyond_Prompt-Based_Planning/Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/deseq_20260709_063955
+5. Keep final deliverables in the same schema/format requested by the benchmark prompt.
+6. Return a concise final summary after writing the required files.
+7. The runner, Python REPL, MCP servers, Rscript, and CLI subprocesses are bound to this conda environment: /225040511/miniconda3/envs/biomni_e1. Do not switch to another conda environment.
+
+Benchmark data policy:
+- Allowed input data directory: /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/data
+- Allowed reference directory: /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/reference
+- Allowed scratch/output directory: /225040511/project/Beyond_Prompt-Based_Planning/Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/deseq_20260709_063955
+- Forbidden truth/results directory: /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/results
+- Forbidden sibling benchmark task directories: /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/<any task other than deseq>
+- Forbidden generated Biomni cache/runtime directories inside benchmark inputs: /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/data/biomni_data and /225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/reference/biomni_data
+- Do not inspect previous bioagent-bench-runs as data sources.
+- Do not download external databases or install new packages during the benchmark run.
+- You may use installed command-line tools, Python/R packages, and MCP servers as executors, but their inputs must come from the allowed paths above.
+
+Input data directory:
+/225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/data
+Visible input files:
+- SRR1278968_1.fastq
+- SRR1278968_2.fastq
+- SRR1278969_1.fastq
+- SRR1278969_2.fastq
+- SRR1278970_1.fastq
+- SRR1278970_2.fastq
+- SRR1278971_1.fastq
+- SRR1278971_2.fastq
+- SRR1278972_1.fastq
+- SRR1278972_2.fastq
+- SRR1278973_1.fastq
+- SRR1278973_2.fastq
+
+Reference data directory:
+/225040511/project/Beyond_Prompt-Based_Planning/bioagent-bench/dataset/deseq/reference
+Visible reference files:
+- C_parapsilosis_CDC317_current_chromosomes.fasta
+- C_parapsilosis_CDC317_current_chromosomes.fasta.fai
+- C_parapsilosis_CDC317_current_features.gff
+- C_parapsilosis_CDC317_current_features.gtf
+- C_parapsilosis_hisat2.1.ht2
+- C_parapsilosis_hisat2.2.ht2
+- C_parapsilosis_hisat2.3.ht2
+- C_parapsilosis_hisat2.4.ht2
+- C_parapsilosis_hisat2.5.ht2
+- C_parapsilosis_hisat2.6.ht2
+- C_parapsilosis_hisat2.7.ht2
+- C_parapsilosis_hisat2.8.ht2
+
+Required final output paths:
+- up_regulated_genes.csv: /225040511/project/Beyond_Prompt-Based_Planning/Biomanus/experiments/ablation/results/mcp_flat_smoke/bioagentbench/deseq_20260709_063955/up_regulated_genes.csv

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K21/configs/careful_mode.info

@@ -0,0 +1,42 @@
+simp
+{
+    ; bulge remover:
+    br
+    {
+        enabled true
+        max_relative_coverage       0.5     ; bulge_cov < this * not_bulge_cov
+        ; parallel false
+    }
+    
+    ; complex bulge remover
+    cbr
+    {
+        enabled false
+    }
+
+    ; bulge remover:
+    final_br
+    {
+        enabled false
+    }
+
+    ; relative coverage erroneous component remover:
+    rcc
+    {
+        enabled false
+    }
+
+    init_clean
+    {
+        early_it_only   true
+
+        activation_cov  -1.
+        ier
+        {
+            enabled                     false
+        }
+
+        tip_condition   ""
+        ec_condition    ""
+    }
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K21/configs/construction.info

@@ -0,0 +1,26 @@
+; construction
+
+construction
+{
+	; mode of construction: extension (construct hash map of kmers to extentions), old (construct set of k+1-mers)
+	mode extension
+
+	; enable keeping in graph perfect cycles. This slows down condensing but some plasmids can be lost if this is turned off.
+	keep_perfect_loops true
+
+	; size of buffer for each thread in MB, 0 for autodetection
+	read_buffer_size 0
+
+        ; read median coverage threshold
+        read_cov_threshold 0
+
+	early_tip_clipper
+	{
+		; tip clipper can be enabled only in extension mode
+		enable true
+
+		; optional parameter. By default tips of length rl-k are removed
+;		length_bound 10
+	}
+}
+

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K21/configs/distance_estimation.info

@@ -0,0 +1,42 @@
+; distance estimator:
+
+de
+{
+    linkage_distance_coeff    	0.0
+    max_distance_coeff        	2.0
+    max_distance_coeff_scaff  	2000.0
+    clustered_filter_threshold	2.0
+    raw_filter_threshold	2
+    rounding_coeff              0.5 ; rounding : min(de_max_distance * rounding_coeff, rounding_thr)
+    rounding_threshold          0
+}
+
+ade
+{
+    ;data dividing
+        threshold          80 ;maximal distance between two points in cluster
+
+    ;local maximum seeking
+        range_coeff          0.2 ;data_length*range_coeff := width of the averaging window
+        delta_coeff          0.4 ;data_length*delta_coeff := maximal difference between possible distance and real peak on the graph
+
+    ;fft smoothing
+        percentage          0.01 ;percent of data for baseline subraction
+        cutoff              3 ;the number of the lowest freqs in fourier decomp being taken
+
+    ;other
+        min_peak_points       3 ;the minimal number of points in cluster to be considered
+        inv_density         5.0 ;maximal inverse density of points in cluster to be considered
+
+    ;hard_mode arguments
+        derivative_threshold  0.2 ;threshold for derivative in hard mode
+
+}
+
+; ambiguous pair info checker parameters 
+amb_de {
+    enabled                         false
+    haplom_threshold                500
+    relative_length_threshold       0.8
+    relative_seq_threshold          0.5
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K21/configs/large_genome_mode.info

@@ -0,0 +1,11 @@
+;FIXME do we still need this mode?
+mode large_genome
+
+pe {
+
+debug_output false
+
+params {
+    scaffolding_mode old_pe_2015
+}
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K21/configs/mda_mode.info

@@ -0,0 +1,105 @@
+mode    mda
+
+simp
+{
+    ; enable advanced ec removal algo
+    topology_simplif_enabled true 
+
+    ; tip clipper:
+    tc
+    {
+        ; rctc: tip_cov < rctc * not_tip_cov
+        ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
+        condition               "{ tc_lb 3.5, cb 1000000, rctc 2.0 }"
+	}
+
+	; erroneous connections remover:
+	ec
+	{
+       ; ec_lb: max_ec_length = k + ec_lb
+       ; icb: iterative coverage bound
+       ; condition               "{ ec_lb 30, icb 20.0 }"
+       condition               "{ ec_lb 30, icb auto }"
+    }
+    
+    final_tc
+    {
+        condition               "{ tc_lb 3.5, cb 100000, rctc 10000 }"
+    }
+
+	; bulge remover:
+	final_br
+	{
+        enabled true
+		max_coverage			1000000.0
+		max_relative_coverage		100000.		; bulge_cov < this * not_bulge_cov
+	}
+	
+    ; relative coverage erroneous component remover:
+    rcc
+    {
+        enabled true
+        coverage_gap    10.
+        max_length_coeff    2.0
+        max_length_with_tips_coeff   3.0
+        max_vertex_cnt      30
+        max_ec_length_coefficient   30
+        max_coverage_coeff  5.0
+    }
+    
+    ; complex bulge remover
+    cbr
+    {
+        enabled true
+    }
+
+    ; hidden ec remover
+    her
+    {
+        enabled                     true
+        uniqueness_length           1500
+        unreliability_threshold     0.2
+        relative_threshold          5
+    }
+
+    init_clean
+    {
+        activation_cov  -1.
+        ier
+        {
+            enabled false
+        }
+
+        tip_condition   ""
+        ec_condition    ""
+    }
+}
+
+de
+{
+    raw_filter_threshold	0
+    rounding_threshold          0
+}
+
+
+pe {
+params {
+    normalize_weight        true
+
+    scaffolding_mode old
+
+    ; extension selection
+    extension_options
+    {
+        single_threshold           0.3
+        weight_threshold           0.6
+        max_repeat_length          8000
+    }
+}
+
+long_reads {
+    pacbio_reads {
+        unique_edge_priority 10.0
+    }
+}
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K21/configs/meta_mode.info

@@ -0,0 +1,227 @@
+mode    meta
+
+; two-step pipeline
+two_step_rr true
+min_edge_length_for_is_count 900
+
+; enables/disables usage of intermediate contigs in two-step pipeline
+use_intermediate_contigs true
+
+;flanking coverage range
+flanking_range 30
+
+simp
+{
+    cycle_iter_count 3
+
+    ; enable advanced ec removal algo
+    topology_simplif_enabled false
+
+    ; erroneous connections remover:
+    ec
+    {
+       ; ec_lb: max_ec_length = k + ec_lb
+       ; icb: iterative coverage bound
+       ; condition               "{ ec_lb 30, icb 20.0 }"
+       condition               "{ ec_lb 30, icb 2.5 }"
+    }
+    
+    ; tip clipper:
+    tc
+    {
+        ; rctc: tip_cov < rctc * not_tip_cov
+        ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
+        condition               "{ rl 0.2 } { rlmk 2., rctc 2.0 }"
+    }
+
+    ; relative coverage erroneous component remover:
+    rcc
+    {
+        enabled true
+        coverage_gap    5.
+        max_length_coeff    3.0
+        max_length_with_tips_coeff   5.0
+        max_vertex_cnt      100
+        max_ec_length_coefficient   300
+        max_coverage_coeff  -1.0
+    }
+
+    ; complex tip clipper
+    complex_tc
+    {
+        enabled               true
+    }
+    
+    ; relative edge disconnector:
+    red
+    {
+        enabled true
+        diff_mult  10.
+        unconditional_diff_mult 50.
+    }
+
+    ; bulge remover:
+    br
+    {
+        enabled true
+        max_coverage			1000000.0
+        max_relative_coverage		5.		; bulge_cov < this * not_bulge_cov
+        max_delta			10
+        max_relative_delta		0.1
+        dijkstra_vertex_limit   3000
+        parallel true
+    }
+
+    ; final tip clipper:
+    final_tc
+    {
+        condition               "{ lb 500, rctc 0.4 } { lb 850, rctc 0.2 }"
+    }
+
+    ; final bulge remover:
+    final_br
+    {
+        enabled true
+        main_iteration_only true
+        max_bulge_length_coefficient    30.     ; max_bulge_length = max_bulge_length_coefficient * k
+        max_coverage            1000000.0
+        max_relative_coverage       0.5     ; bulge_cov < this * not_bulge_cov
+        max_delta 45
+        max_relative_delta 0.1
+        min_identity 0.7
+    }
+
+    ; suspecies bulge remover:
+    subspecies_br
+    {
+        enabled false
+    }
+    
+    ; complex bulge remover
+    cbr
+    {
+        enabled true
+    }
+
+    ; hidden ec remover
+    her
+    {
+        ; TODO NB config used in special meta mode version (always enabled)
+        enabled                     false
+        uniqueness_length           1500
+        unreliability_threshold     -1.
+        relative_threshold          3.     
+    }
+
+    init_clean
+    {
+        activation_cov  -1.
+        early_it_only   false
+        ier
+        {
+            enabled true
+        }
+        ;Disable if it does not help the br performance much!
+        tip_condition   "{ tc_lb 3.5, cb 2.1 }"
+        ;ec_condition is here only to speed-up future br on early iterations
+        ec_condition    "{ ec_lb 10, cb 1.5 }"
+        disconnect_flank_cov    -1.
+    }
+
+}
+
+;TODO rename
+preliminary_simp
+{
+    init_clean
+    {
+        tip_condition   "loop 2 { rlmk 1., cb 1.2, mmm 2 } { rlmk 1., cb 1.2, mmm 0.05 } { rl 0.2, cb 1.2 }"
+        ec_condition    "{ ec_lb 0, cb 0.9 }"
+        disconnect_flank_cov    0.8
+    }
+
+    ; bulge remover:
+    br
+    {
+        enabled true
+        max_coverage			1000000.0
+        max_relative_coverage		0.5		; bulge_cov < this * not_bulge_cov
+        max_delta			10
+        max_relative_delta		0.1
+    }
+
+    ; Currently will not work even if enabled. Left for experiments.
+    ; relative edge disconnector
+    red
+    {
+        enabled false
+        diff_mult  10.
+        unconditional_diff_mult 100.
+    }
+}
+
+; undo single cell config changes, enforce filtering
+de
+{
+    raw_filter_threshold	1
+    rounding_coeff              0.5 ; rounding : min(de_max_distance * rounding_coeff, rounding_thr)
+    rounding_threshold          0
+}
+
+;NB decsends from sc_pe
+pe {
+
+long_reads {
+    pacbio_reads {
+        filtering   1.9
+        weight_priority    20.0
+        unique_edge_priority 10.0
+        min_significant_overlap 1000
+    }
+}
+
+params {
+    overlap_removal {
+        enabled true
+        cut_all true
+    }
+
+    scaffolding_mode old_pe_2015
+
+    normalize_weight     true
+    
+    ; extension selection
+    extension_options
+    {
+        single_threshold           0.3
+        weight_threshold           0.6
+        priority_coeff             1.5
+        max_repeat_length          1000000 
+    }
+    
+    use_coordinated_coverage true
+
+    coordinated_coverage
+    {
+       min_path_len           10000
+    }
+
+}
+
+}
+
+prelim_pe {
+params {
+    scaffolding_mode old
+
+    overlap_removal {
+        enabled false
+    }
+
+    use_coordinated_coverage false
+    remove_overlaps     false
+    scaffolding2015 {
+        min_unique_length 100000000
+    }
+}
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K21/configs/metaviral_mode.info

@@ -0,0 +1,40 @@
+mode metaextrachromosomal
+two_step_rr false
+
+simp
+{
+
+    ; suspecies bulge remover:
+    subspecies_br
+    {
+        enabled true
+        main_iteration_only true
+        max_bulge_length_coefficient    30.     ; max_bulge_length = max_bulge_length_coefficient * k
+        max_coverage            1000000.0
+        max_relative_coverage       15     ; bulge_cov < this * not_bulge_cov
+        max_delta 45
+        max_relative_delta 0.2
+        min_identity 0.7
+    }
+
+}
+plasmid
+{
+;isolated
+    long_edge_length 1000
+    edge_length_for_median 10000
+    relative_coverage 0.3
+    small_component_size 10000
+    small_component_relative_coverage 1.5
+    min_component_length 10000
+    min_isolated_length 1000
+;   reference_removal replace this with path to reference and uncomment for reference based filtration
+;meta                          
+    iterative_coverage_elimination true
+    additive_step 5
+    relative_step 1.3
+    max_length 1000000
+    output_linear true
+    min_circular_length 1000
+    min_linear_length 500
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K21/configs/pe_params.info

@@ -0,0 +1,179 @@
+pe {
+
+; output options
+
+debug_output    false
+
+output {
+    write_overlaped_paths   true
+    write_paths             true
+}
+
+visualize {
+    print_overlaped_paths   true
+    print_paths             true
+}
+
+params {
+    multi_path_extend   false
+    ; old | 2015 | combined | old_pe_2015
+    scaffolding_mode old_pe_2015
+    
+    overlap_removal {
+        enabled true
+        end_start_only  false
+        cut_all false
+    }
+
+    normalize_weight     true
+    
+    ; extension selection
+    extension_options
+    {
+        single_threshold           0.1
+        weight_threshold           0.5
+        priority_coeff             1.5
+        ;TODO remove from here
+        max_repeat_length          8000
+    }    
+
+    mate_pair_options
+    {
+        single_threshold           30
+        weight_threshold           0.5
+        priority_coeff             1.5
+        ;TODO remove from here
+        max_repeat_length          8000
+    }
+
+    scaffolder {
+        enabled       true
+        cutoff        2
+        hard_cutoff   0
+        rel_cov_cutoff    0.0
+        sum_threshold 3  
+
+        cluster_info  true
+        cl_threshold  0
+
+        fix_gaps       true
+        use_la_gap_joiner true
+        ;next param should be 0.51 - 1.0 if use_old_score = true and 3.0 otherwise
+        min_gap_score   0.7
+
+        max_can_overlap   1.
+        short_overlap     6
+        artificial_gap    10
+
+        min_overlap_length 10
+        flank_multiplication_coefficient .5
+        flank_addition_coefficient 5
+
+        var_coeff 3.0
+        basic_overlap_coeff 2.0
+    }
+
+    path_cleaning_presets ""
+
+    use_coordinated_coverage false
+    coordinated_coverage
+    {
+       max_edge_length_repeat 300
+       delta                  0.5
+       min_path_len           1000
+    }
+
+
+    simple_coverage_resolver {
+        enabled false
+        coverage_margin 2
+        min_upper_coverage 5
+        max_coverage_variation 5
+    }
+
+
+    scaffolding2015 {
+        ; (median * (1+variation) > unique > median * (1 - variation))
+        relative_weight_cutoff 2.0
+
+        unique_length_upper_bound 2000   ; max(unique_length_upper_bound, max_is(all libs))
+        unique_length_lower_bound 500    ; max(unique_length_lower_bound, unique_length_step)
+        unique_length_step 300
+
+        graph_connectivity_max_edges 200000
+    }
+
+    scaffold_graph {
+        construct    false
+        output       false
+        always_add   40         ; connection with read count >= always_add are always added to the graph
+        never_add     5         ; connection with read count < never_add are never added to the graph
+        relative_threshold 0.25 ; connection with read count >= max_read_count * relative_threshod are added to the graph if satisfy condition above, max_read_count is calculated amond all alternatives
+        use_graph_connectivity false
+        max_path_length 10000
+    }
+
+    genome_consistency_checker {
+        max_gap 1000
+        relative_max_gap 0.2
+        use_main_storage true ; if set to true, next two parameters are set to min_unique_length
+        unresolvable_jump 1000 ; length of unresolvable repeats
+        unique_length 500  ; spelling genome in the alphabet of edges longer than this          
+    }
+
+    uniqueness_analyser {
+        enabled        true
+        unique_coverage_variation 0.5
+
+        nonuniform_coverage_variation 50
+        uniformity_fraction_threshold 0.8
+    }
+
+    loop_traversal
+    {
+        min_edge_length         1000
+        max_component_size      10
+        max_path_length         1000
+    }
+}
+
+
+long_reads {
+    pacbio_reads {
+        filtering   2.5
+        weight_priority    1.2
+        unique_edge_priority 5.0
+        min_significant_overlap 0
+    }
+
+    single_reads {
+        filtering  1.25 
+        weight_priority    5.0
+        unique_edge_priority 10000.0
+        min_significant_overlap 0
+    }
+
+    contigs {
+        filtering   0.0
+        weight_priority    1.5
+        unique_edge_priority 2.0
+        min_significant_overlap 0
+    }
+
+    meta_untrusted_contigs {
+        filtering   0.0
+        weight_priority    10000.0
+        unique_edge_priority 10000.0
+        min_significant_overlap 200
+    }
+
+    rna_long_reads {
+        filtering   0.1
+        weight_priority    1.1
+        unique_edge_priority 2.0
+        min_significant_overlap 0
+    }
+
+
+}
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K21/configs/rna_mode.info

@@ -0,0 +1,213 @@
+mode rna
+
+preserve_raw_paired_index true
+min_edge_length_for_is_count 500
+
+calculate_coverage_for_each_lib true
+strand_specificity {
+    ss_enabled false
+    antisense false
+}
+
+ss_coverage_splitter {
+    enabled           true
+    bin_size          50   
+    min_edge_len      200
+    min_edge_coverage 5
+    min_flanking_coverage 2
+    coverage_margin   5
+}
+
+pacbio_processor
+{
+    internal_length_cutoff 100
+;align and traverse.
+;    compression_cutoff 0.6
+;    path_limit_stretching 1.3
+;    path_limit_pressing 0.7
+    max_path_in_dijkstra 5000
+    max_vertex_in_dijkstra 1000
+    rna_filtering   true
+
+;gap_closer
+    long_seq_limit 100
+    enable_gap_closing false
+    enable_fl_gap_closing true
+    pacbio_min_gap_quantity 2
+    contigs_min_gap_quantity 1
+    max_contigs_gap_length 10000
+}
+
+contig_output {
+    scaffolds_name  transcripts
+    ; none  --- do not output broken scaffolds | break_gaps --- break only by N steches | break_all --- break all with overlap < k
+    output_broken_scaffolds     none
+}
+
+simp
+{
+    ;all topology based erroneous connection removers are off
+    topology_simplif_enabled false
+
+    tc
+    {
+        ; rctc: tip_cov < rctc * not_tip_cov
+        ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
+        condition  "{ mmm 3 tc_lb 4, cb 100000, rctc 0.5 } { tc_lb 2, cb 1, rctc 10000 }"
+    }
+
+    dead_end
+    {
+        enabled true
+        condition  "{ tc_lb 3.5, cb 2 }"
+    }
+
+    ; bulge remover:
+    br
+    {
+        enabled true
+        max_additive_length_coefficient 100
+        max_coverage            1000000.0
+        max_relative_coverage       100000.0 ; bulge_cov < this * not_bulge_cov
+    }
+
+    ; erroneous connections remover:
+    ec
+    { 
+       ; ec_lb: max_ec_length = k + ec_lb
+       ; icb: iterative coverage bound
+       ; to_ec_lb: max_ec_length = 2*tip_length(to_ec_lb) - 1
+       ; nbr: use not bulge erroneous connections remover 
+       ; condition               "{ ec_lb 9, icb 40.0, nbr }"
+       condition               "{ ec_lb 30, icb 200, rcec_cb 1.0 }"
+    }
+
+    ; relative coverage erroneous connections remover:
+    rcec
+    {
+        rcec_lb 30
+        rcec_cb 1.0
+        enabled true
+    }
+
+    rcc
+    {
+        enabled true
+        coverage_gap    20.
+    }
+
+    ; hidden ec remover
+    her
+    {
+        ; TODO NB config also used in special rna mode version (always enabled)
+        enabled                     false
+        uniqueness_length           1500
+        unreliability_threshold     0.2
+        relative_threshold          5
+    }
+
+    ier
+    {
+        enabled                       true
+        use_rl_for_max_length         true ; max_length will be taken max with read_length
+        use_rl_for_max_length_any_cov false ; use_rl_for_max_length_any_cov will be taken max with read_length
+        max_length                    80
+        max_coverage                  2
+        max_length_any_cov            0
+        rl_threshold_increase         2 ; add this value to read length if used, i.e. flags above are set
+    }
+
+}
+
+; disable filtering in rna mode
+de
+{
+    raw_filter_threshold	0
+}
+
+pe {
+debug_output    true
+
+params {
+    multi_path_extend   true
+
+    scaffolding_mode old
+
+    overlap_removal {
+        enabled false
+        end_start_only  true
+        cut_all true
+    }
+
+    extension_options
+    {
+        single_threshold           0.05
+    }
+
+    scaffolder {
+        cutoff        1
+        hard_cutoff   5
+        rel_cov_cutoff    0.1
+        cluster_info false
+        min_overlap_for_rna_scaffolding 8
+    }
+
+    path_cleaning_presets "default soft hard"
+    ; All length cutoffs presented in nucleotides
+    ; So edges less than or equal to (relative cutoff * RL - K) or (absolute cutoff - K) will be deleted
+    path_cleaning
+    {
+        enabled true
+        min_length  110
+        isolated_min_length 130
+        isolated_min_cov 4
+        min_length_for_low_covered 140
+        rel_cutoff 1.3
+        rel_isolated_cutoff 1.5
+        rel_low_covered_cutoff 1.6
+        min_coverage 2
+    }
+
+    ; All length cutoffs presented in nucleotides
+    hard_path_cleaning
+    {
+        enabled true
+        min_length  130
+        isolated_min_length 180
+        isolated_min_cov 8
+        min_length_for_low_covered 180
+        rel_cutoff 1.5
+        rel_isolated_cutoff 2.0
+        rel_low_covered_cutoff 2.0
+        min_coverage 3
+    }
+
+    ; All length cutoffs presented in nucleotides
+    soft_path_cleaning
+    {
+        enabled true
+        min_length  85
+        isolated_min_length 100
+        isolated_min_cov 2
+        min_length_for_low_covered 130
+        rel_cutoff 1.05
+        rel_isolated_cutoff 1.2
+        rel_low_covered_cutoff 1.5
+        min_coverage 1
+    }
+
+    use_coordinated_coverage false
+    coordinated_coverage {
+       max_edge_length_repeat 1000
+       delta                  0.5
+       min_path_len           300
+    }
+
+    simple_coverage_resolver {
+        enabled true
+        coverage_margin 2  
+        min_upper_coverage 2
+        max_coverage_variation 10
+    }
+}
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K21/configs/rnaviral_mode.info

@@ -0,0 +1,32 @@
+mode rnaviral
+two_step_rr false
+
+simp
+{
+
+    ; suspecies bulge remover:
+    subspecies_br
+    {
+        enabled true
+        main_iteration_only true
+        max_bulge_length_coefficient    30.     ; max_bulge_length = max_bulge_length_coefficient * k
+        max_coverage            1000000.0
+        max_relative_coverage       15     ; bulge_cov < this * not_bulge_cov
+        max_delta 45
+        max_relative_delta 0.2
+        min_identity 0.9
+    }
+
+     red
+     {
+         enabled true
+         diff_mult  10.
+         unconditional_diff_mult 50.
+         edge_sum 0
+     }
+
+     final_br
+     {
+         enabled false
+     }
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K21/configs/simplification.info

@@ -0,0 +1,244 @@
+; simplification
+
+simp
+{
+    ; ==== RAW SIMPLIFICATION ==== 
+    init_clean
+    {
+        self_conj_condition "{ ec_lb 100, cb 1.0 }"
+        early_it_only   false
+        ; will be enabled only if average coverage >= activate_cov
+        ; if value < 0 check not performed
+        activation_cov  10.
+
+        ; isolated edges remover
+        ier
+        {
+            enabled                     true
+            use_rl_for_max_length         false ; max_length will be taken max with read_length
+            use_rl_for_max_length_any_cov true ; use_rl_for_max_length_any_cov will be taken max with read_length
+            max_length                  0 ; will be taken max with read_length if option above is set
+            max_coverage                0
+            max_length_any_cov          0 ; will be taken max with read_length if option above is set
+            rl_threshold_increase       0 ; add this value to read length if used, i.e. flags above are set
+        }
+
+        tip_condition   "{ tc_lb 3.5, cb auto }"
+        ec_condition    "{ ec_lb 10, cb 2.0 }"
+
+        ; edges with flank cov around alternative less than value will be disconnected 
+        ; negative value to disable
+        disconnect_flank_cov    -1.0
+    }
+
+    ; ==== SIMPLIFICATION CYCLE ==== 
+
+    ; number of iterations in basic simplification cycle
+    cycle_iter_count 10
+
+    ; tip clipper:
+    tc
+    {
+        ; rctc: tip_cov < rctc * not_tip_cov
+        ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
+        ; todo think about params one more time
+        condition               "{ tc_lb 3.5, cb 1000000, rctc 2.0 } { tc_lb 10., cb auto }"
+    }
+  
+    ; bulge remover:
+    br
+    {
+        enabled				true
+        main_iteration_only false
+        max_bulge_length_coefficient	3.	; max_bulge_length = max_bulge_length_coefficient * k
+        max_additive_length_coefficient 100
+        max_coverage			1000.0
+        max_relative_coverage		1.1	; bulge_cov < this * not_bulge_cov
+        max_delta			3
+        max_relative_delta		0.1
+        max_number_edges        1000
+        dijkstra_vertex_limit   3000
+        parallel true
+        buff_size 10000
+        buff_cov_diff 2.
+        buff_cov_rel_diff 0.2
+        min_identity 0.0
+    }
+	
+	; erroneous connections remover:
+	ec
+	{
+       ; ec_lb: max_ec_length = k + ec_lb
+       ; icb: iterative coverage bound
+       ; to_ec_lb: max_ec_length = 2*tip_length(to_ec_lb) - 1
+        condition               "{ to_ec_lb 5, icb auto }"
+       ; condition               "{ ec_lb 9, icb 40.0 }"
+    }
+
+    dead_end {
+        enabled false
+        condition ""
+    }
+
+    ; ==== POST-SIMPLIFICATION ==== 
+
+    ; relative coverage erroneous connections remover:
+    rcec
+    {
+        enabled false
+        rcec_lb 30
+        rcec_cb 0.5
+    }
+    
+    ; relative coverage erroneous component remover:
+    rcc
+    {
+        enabled false
+        coverage_gap    5.
+        max_length_coeff    2.0
+        max_length_with_tips_coeff   3.0
+        max_vertex_cnt      30
+        max_ec_length_coefficient   30
+        max_coverage_coeff  2.0
+    }
+    
+    ; relative edge disconnector:
+    red
+    {
+        enabled false
+        diff_mult  20.
+        edge_sum   10000
+        unconditional_diff_mult 0. ; 0. to disable
+    }
+
+    ; final tip clipper:
+    final_tc
+    {
+        condition               ""
+    }
+
+    ; final bulge remover:
+    final_br
+    {
+        enabled				false
+        main_iteration_only false
+        max_bulge_length_coefficient	3.	; max_bulge_length = max_bulge_length_coefficient * k
+        max_additive_length_coefficient 100
+        max_coverage			1000.0
+        max_relative_coverage		1.1	; bulge_cov < this * not_bulge_cov
+        max_delta			3
+        max_relative_delta		0.1
+        max_number_edges        1000
+        dijkstra_vertex_limit   3000
+        parallel true
+        buff_size 10000
+        buff_cov_diff 2.
+        buff_cov_rel_diff 0.2
+        min_identity 0.0
+    }
+
+    ; subspecies bulge remover:
+    subspecies_br
+    {
+        enabled				false
+        main_iteration_only false
+        max_bulge_length_coefficient	3.	; max_bulge_length = max_bulge_length_coefficient * k
+        max_additive_length_coefficient 100
+        max_coverage			1000.0
+        max_relative_coverage		1.1	; bulge_cov < this * not_bulge_cov
+        max_delta			3
+        max_relative_delta		0.1
+        max_number_edges        1000
+        dijkstra_vertex_limit   3000
+        parallel true
+        buff_size 10000
+        buff_cov_diff 2.
+        buff_cov_rel_diff 0.2
+        min_identity 0.0
+    }
+
+
+    ; complex tip clipper
+    complex_tc
+    {
+        enabled               false
+        max_relative_coverage -1
+        max_edge_len          100
+        condition             "{ tc_lb 3.5 }"
+    }  
+
+    ; complex bulge remover
+    cbr
+    {
+        enabled false
+        max_relative_length 5.
+        max_length_difference   5
+    }
+ 
+    ; isolated edges remover
+    ier
+    {
+        enabled                     true
+        use_rl_for_max_length         false ; max_length will be taken max with read_length
+        use_rl_for_max_length_any_cov true ; use_rl_for_max_length_any_cov will be taken max with read_length
+        max_length                  0 ; will be taken max with read_length if option above is set
+        max_coverage                2
+        max_length_any_cov          150 ; will be taken max with read_length if option above is set
+        rl_threshold_increase       0 ; add this value to read length if used, i.e. flags above are set
+    }
+
+    ; hidden ec remover
+    her
+    {
+        enabled                     false
+        uniqueness_length           1500
+        unreliability_threshold     4
+        relative_threshold          5
+    }
+    
+    ; ==== ADVANCED EC REMOVAL ALGO ==== 
+    ; enable advanced ec removal algo
+    topology_simplif_enabled false
+    
+    ; topology based erroneous connection remover
+    tec
+    {
+        max_ec_length_coefficient   55  ; max_ec_length = k + max_ec_length_coefficient
+        uniqueness_length       1500
+        plausibility_length     200
+    }
+
+    ; topology and reliability based erroneous connection remover
+    trec
+    {
+        max_ec_length_coefficient   100 ; max_ec_length = k + max_ec_length_coefficient
+        uniqueness_length       1500
+        unreliable_coverage     2.5
+    }
+    
+    ; interstrand erroneous connection remover (thorn remover)
+    isec
+    {
+        max_ec_length_coefficient   100 ; max_ec_length = k + max_ec_length_coefficient
+        uniqueness_length       1500
+        span_distance       15000
+    }
+
+    ; max flow erroneous connection remover
+    mfec
+    {
+        enabled false
+        max_ec_length_coefficient   30  ; max_ec_length = k + max_ec_length_coefficient
+        uniqueness_length       1500
+        plausibility_length     200
+    }
+
+    ; topology tip clipper:
+    ttc
+    {
+        length_coeff    3.5
+        plausibility_length 250
+        uniqueness_length   1500
+    }
+
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K21/simplified_contigs/contigs_info

@@ -0,0 +1 @@
+14 18446744073709551615 34830 0 3402 4581952

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/careful_mda_mode.info

@@ -0,0 +1,40 @@
+simp
+{
+    ; bulge remover:
+    br
+    {
+        enabled true
+        max_relative_coverage		1.1	; bulge_cov < this * not_bulge_cov
+    }
+    
+    ; complex bulge remover
+    cbr
+    {
+        enabled false
+    }
+
+    final_tc
+    {
+        condition               ""
+    }
+
+    ; bulge remover:
+    final_br
+    {
+        enabled false
+    }
+
+    init_clean
+    {
+        early_it_only   true
+
+        activation_cov  -1.
+        ier
+        {
+            enabled                     false
+        }
+
+        tip_condition   ""
+        ec_condition    ""
+    }
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/careful_mode.info

@@ -0,0 +1,42 @@
+simp
+{
+    ; bulge remover:
+    br
+    {
+        enabled true
+        max_relative_coverage       0.5     ; bulge_cov < this * not_bulge_cov
+        ; parallel false
+    }
+    
+    ; complex bulge remover
+    cbr
+    {
+        enabled false
+    }
+
+    ; bulge remover:
+    final_br
+    {
+        enabled false
+    }
+
+    ; relative coverage erroneous component remover:
+    rcc
+    {
+        enabled false
+    }
+
+    init_clean
+    {
+        early_it_only   true
+
+        activation_cov  -1.
+        ier
+        {
+            enabled                     false
+        }
+
+        tip_condition   ""
+        ec_condition    ""
+    }
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/config.info

@@ -0,0 +1,216 @@
+; input options:
+
+#include "simplification.info"
+#include "construction.info"
+#include "distance_estimation.info"
+#include "detail_info_printer.info"
+#include "pe_params.info"
+
+K 55
+;FIXME introduce isolate mode
+mode base
+
+dataset /225040511/project/Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/dataset.info
+log_filename    log.properties
+
+output_base /225040511/project/Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly
+tmp_dir /225040511/project/Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/tmp/spades_lhfdc3lg
+
+main_iteration false
+; iterative mode switcher, activates additional contigs usage
+use_additional_contigs true
+additional_contigs /225040511/project/Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K33/simplified_contigs
+load_from /225040511/project/Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/saves
+
+; Multithreading options
+temp_bin_reads_dir	.bin_reads/
+max_threads 8
+max_memory 32
+buffer_size     512; in Megabytes
+
+entry_point read_conversion
+;entry_point construction
+;entry_point simplification
+;entry_point hybrid_aligning
+;entry_point late_pair_info_count
+;entry_point distance_estimation
+;entry_point repeat_resolving
+
+checkpoints none
+developer_mode false
+sewage false
+sewage_matrix /225040511/miniconda3/envs/biomni_e1/share/spades/sewage/usher_barcodes.csv
+
+scaffold_correction_mode false
+
+; enabled (1) or disabled (0) repeat resolution (former "paired_mode")
+rr_enable false
+; 0 for graph N50
+min_edge_length_for_is_count 0
+
+; Whether GFA v1.2 (jump links) or GFA v1.1 (scaffold segments) graphs is written
+gfa11 false
+
+;preserve raw paired index after distance estimation
+preserve_raw_paired_index false
+
+; two-step pipeline
+two_step_rr false
+; enables/disables usage of intermediate contigs in two-step pipeline
+use_intermediate_contigs false
+
+;use single reads for rr (all | only_single_libs | none )
+single_reads_rr only_single_libs
+
+; The following parameters are used ONLY if developer_mode is true
+
+; whether to output dot-files with pictures of graphs - ONLY in developer mode
+output_pictures true
+
+; whether to output resulting contigs after intermediate stages - ONLY in developer mode
+output_nonfinal_contigs true
+
+; whether to compute number of paths statistics   - ONLY in developer mode
+compute_paths_number false
+
+; End of developer_mode parameters
+
+;if true simple mismatches are corrected
+correct_mismatches false
+
+; set it true to get statistics, such as false positive/negative, perfect match, etc.
+paired_info_statistics false
+
+; set it true to get statistics for pair information (over gaps), such as false positive/negative, perfect match, etc.
+paired_info_scaffolder false
+
+;the only option left from repeat resolving
+max_repeat_length 8000
+
+; repeat resolving mode (none path_extend)
+resolving_mode path_extend
+
+use_scaffolder  true
+
+avoid_rc_connections true
+
+calculate_coverage_for_each_lib false
+strand_specificity {
+    ss_enabled false
+    antisense false
+}
+
+contig_output {
+    contigs_name    final_contigs
+    scaffolds_name  scaffolds
+    ; none  --- do not output broken scaffolds | break_gaps --- break only by N steches | break_all --- break all with overlap < k
+    output_broken_scaffolds     break_gaps
+}
+
+;position handling
+
+pos
+{
+    max_mapping_gap 0 ; in terms of K+1 mers value will be K + max_mapping_gap
+    max_gap_diff 0
+	contigs_for_threading ./data/debruijn/contigs.fasta
+    contigs_to_analyze ./data/debruijn/contigs.fasta
+	late_threading true
+	careful_labeling true
+
+}
+
+gap_closer_enable true
+
+gap_closer
+{
+    minimal_intersection	10
+
+    ;before_raw_simplify and before_simplify are mutually exclusive
+    before_raw_simplify    		true
+    before_simplify		false
+    after_simplify 		true
+    weight_threshold		2.0
+    max_dist_to_tip		5000
+}
+
+kmer_coverage_model {
+    probability_threshold 0.05
+    strong_probability_threshold 0.999
+    use_coverage_threshold false
+    coverage_threshold 10.0
+}
+
+; low covered edges remover
+lcer
+{
+    lcer_enabled                     false
+    lcer_coverage_threshold          0.0
+}
+
+pacbio_processor ;commented frozen constants default assinged in hpp
+{
+    internal_length_cutoff 200
+;align and traverse.
+;    compression_cutoff 0.6
+;    path_limit_stretching 1.3
+;    path_limit_pressing 0.7
+    max_path_in_dijkstra 15000
+    max_vertex_in_dijkstra 2000
+    rna_filtering   false
+
+;gap_closer
+    long_seq_limit 400
+    enable_gap_closing true
+    pacbio_min_gap_quantity 2
+    contigs_min_gap_quantity 1
+    max_contigs_gap_length 10000
+;spoa
+;    match 5
+;    mismatch -4
+;    gap_open -8
+;    gap_extend -6
+;    gap_open_second -10
+;    gap_extend_second -4
+}
+
+;TODO move out!
+graph_read_corr
+{
+	enable false
+	output_dir corrected_contigs/
+	binary true
+}
+
+bwa_aligner
+{
+    debug false
+    min_contig_len 0
+}
+
+;flanking coverage range
+flanking_range 55
+series_analysis ""
+save_gp false
+
+ss_coverage_splitter {
+    enabled           false
+    bin_size          50
+    min_edge_len      200
+    min_edge_coverage 5
+    min_flanking_coverage 2
+    coverage_margin   5
+}
+
+time_tracer {
+  time_tracer_enabled false
+  granularity 500
+}
+
+hybrid_aligner {
+  trusted_aligner {
+        long_read_threshold       1000
+        long_read_fuzzy_coverage  0.95
+        short_read_fuzzy_coverage 0.90
+  }
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/construction.info

@@ -0,0 +1,26 @@
+; construction
+
+construction
+{
+	; mode of construction: extension (construct hash map of kmers to extentions), old (construct set of k+1-mers)
+	mode extension
+
+	; enable keeping in graph perfect cycles. This slows down condensing but some plasmids can be lost if this is turned off.
+	keep_perfect_loops true
+
+	; size of buffer for each thread in MB, 0 for autodetection
+	read_buffer_size 0
+
+        ; read median coverage threshold
+        read_cov_threshold 0
+
+	early_tip_clipper
+	{
+		; tip clipper can be enabled only in extension mode
+		enable true
+
+		; optional parameter. By default tips of length rl-k are removed
+;		length_bound 10
+	}
+}
+

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/detail_info_printer.info

@@ -0,0 +1,46 @@
+info_printers
+{
+    default
+    {
+       basic_stats                      false
+       lib_info                         false
+       save_all                         false
+       save_full_graph                  false
+       save_graph_pack                  false
+       extended_stats                   false
+       detailed_dot_write               false
+       write_components                 false
+       components_for_genome_pos        "" ; (k+1)-mers starting on this positions will be investigated
+	   components_for_kmer              ""
+       write_components_along_genome    false
+       write_components_along_contigs   false
+       write_error_loc                  false
+       write_full_graph                 false
+       write_full_nc_graph              false
+    }
+
+	before_first_gap_closer
+    {
+    }
+
+	before_simplification
+    {
+    }
+
+    before_post_simplification    
+    {
+    }
+
+    final_simplified
+    {
+    }
+
+    final_gap_closed
+    {
+    }
+
+    before_repeat_resolution
+    {
+    }
+
+}  

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/distance_estimation.info

@@ -0,0 +1,42 @@
+; distance estimator:
+
+de
+{
+    linkage_distance_coeff    	0.0
+    max_distance_coeff        	2.0
+    max_distance_coeff_scaff  	2000.0
+    clustered_filter_threshold	2.0
+    raw_filter_threshold	2
+    rounding_coeff              0.5 ; rounding : min(de_max_distance * rounding_coeff, rounding_thr)
+    rounding_threshold          0
+}
+
+ade
+{
+    ;data dividing
+        threshold          80 ;maximal distance between two points in cluster
+
+    ;local maximum seeking
+        range_coeff          0.2 ;data_length*range_coeff := width of the averaging window
+        delta_coeff          0.4 ;data_length*delta_coeff := maximal difference between possible distance and real peak on the graph
+
+    ;fft smoothing
+        percentage          0.01 ;percent of data for baseline subraction
+        cutoff              3 ;the number of the lowest freqs in fourier decomp being taken
+
+    ;other
+        min_peak_points       3 ;the minimal number of points in cluster to be considered
+        inv_density         5.0 ;maximal inverse density of points in cluster to be considered
+
+    ;hard_mode arguments
+        derivative_threshold  0.2 ;threshold for derivative in hard mode
+
+}
+
+; ambiguous pair info checker parameters 
+amb_de {
+    enabled                         false
+    haplom_threshold                500
+    relative_length_threshold       0.8
+    relative_seq_threshold          0.5
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/hmm_mode.info

@@ -0,0 +1,6 @@
+hmm_match {
+  set_of_hmms none
+  component_size_part 10
+  start_only_from_tips false
+  set_copynumber false
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/isolate_mode.info

@@ -0,0 +1,4 @@
+mode isolate
+
+#include "careful_mode.info"
+

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/large_genome_mode.info

@@ -0,0 +1,11 @@
+;FIXME do we still need this mode?
+mode large_genome
+
+pe {
+
+debug_output false
+
+params {
+    scaffolding_mode old_pe_2015
+}
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/mda_mode.info

@@ -0,0 +1,105 @@
+mode    mda
+
+simp
+{
+    ; enable advanced ec removal algo
+    topology_simplif_enabled true 
+
+    ; tip clipper:
+    tc
+    {
+        ; rctc: tip_cov < rctc * not_tip_cov
+        ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
+        condition               "{ tc_lb 3.5, cb 1000000, rctc 2.0 }"
+	}
+
+	; erroneous connections remover:
+	ec
+	{
+       ; ec_lb: max_ec_length = k + ec_lb
+       ; icb: iterative coverage bound
+       ; condition               "{ ec_lb 30, icb 20.0 }"
+       condition               "{ ec_lb 30, icb auto }"
+    }
+    
+    final_tc
+    {
+        condition               "{ tc_lb 3.5, cb 100000, rctc 10000 }"
+    }
+
+	; bulge remover:
+	final_br
+	{
+        enabled true
+		max_coverage			1000000.0
+		max_relative_coverage		100000.		; bulge_cov < this * not_bulge_cov
+	}
+	
+    ; relative coverage erroneous component remover:
+    rcc
+    {
+        enabled true
+        coverage_gap    10.
+        max_length_coeff    2.0
+        max_length_with_tips_coeff   3.0
+        max_vertex_cnt      30
+        max_ec_length_coefficient   30
+        max_coverage_coeff  5.0
+    }
+    
+    ; complex bulge remover
+    cbr
+    {
+        enabled true
+    }
+
+    ; hidden ec remover
+    her
+    {
+        enabled                     true
+        uniqueness_length           1500
+        unreliability_threshold     0.2
+        relative_threshold          5
+    }
+
+    init_clean
+    {
+        activation_cov  -1.
+        ier
+        {
+            enabled false
+        }
+
+        tip_condition   ""
+        ec_condition    ""
+    }
+}
+
+de
+{
+    raw_filter_threshold	0
+    rounding_threshold          0
+}
+
+
+pe {
+params {
+    normalize_weight        true
+
+    scaffolding_mode old
+
+    ; extension selection
+    extension_options
+    {
+        single_threshold           0.3
+        weight_threshold           0.6
+        max_repeat_length          8000
+    }
+}
+
+long_reads {
+    pacbio_reads {
+        unique_edge_priority 10.0
+    }
+}
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/meta_mode.info

@@ -0,0 +1,227 @@
+mode    meta
+
+; two-step pipeline
+two_step_rr true
+min_edge_length_for_is_count 900
+
+; enables/disables usage of intermediate contigs in two-step pipeline
+use_intermediate_contigs true
+
+;flanking coverage range
+flanking_range 30
+
+simp
+{
+    cycle_iter_count 3
+
+    ; enable advanced ec removal algo
+    topology_simplif_enabled false
+
+    ; erroneous connections remover:
+    ec
+    {
+       ; ec_lb: max_ec_length = k + ec_lb
+       ; icb: iterative coverage bound
+       ; condition               "{ ec_lb 30, icb 20.0 }"
+       condition               "{ ec_lb 30, icb 2.5 }"
+    }
+    
+    ; tip clipper:
+    tc
+    {
+        ; rctc: tip_cov < rctc * not_tip_cov
+        ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
+        condition               "{ rl 0.2 } { rlmk 2., rctc 2.0 }"
+    }
+
+    ; relative coverage erroneous component remover:
+    rcc
+    {
+        enabled true
+        coverage_gap    5.
+        max_length_coeff    3.0
+        max_length_with_tips_coeff   5.0
+        max_vertex_cnt      100
+        max_ec_length_coefficient   300
+        max_coverage_coeff  -1.0
+    }
+
+    ; complex tip clipper
+    complex_tc
+    {
+        enabled               true
+    }
+    
+    ; relative edge disconnector:
+    red
+    {
+        enabled true
+        diff_mult  10.
+        unconditional_diff_mult 50.
+    }
+
+    ; bulge remover:
+    br
+    {
+        enabled true
+        max_coverage			1000000.0
+        max_relative_coverage		5.		; bulge_cov < this * not_bulge_cov
+        max_delta			10
+        max_relative_delta		0.1
+        dijkstra_vertex_limit   3000
+        parallel true
+    }
+
+    ; final tip clipper:
+    final_tc
+    {
+        condition               "{ lb 500, rctc 0.4 } { lb 850, rctc 0.2 }"
+    }
+
+    ; final bulge remover:
+    final_br
+    {
+        enabled true
+        main_iteration_only true
+        max_bulge_length_coefficient    30.     ; max_bulge_length = max_bulge_length_coefficient * k
+        max_coverage            1000000.0
+        max_relative_coverage       0.5     ; bulge_cov < this * not_bulge_cov
+        max_delta 45
+        max_relative_delta 0.1
+        min_identity 0.7
+    }
+
+    ; suspecies bulge remover:
+    subspecies_br
+    {
+        enabled false
+    }
+    
+    ; complex bulge remover
+    cbr
+    {
+        enabled true
+    }
+
+    ; hidden ec remover
+    her
+    {
+        ; TODO NB config used in special meta mode version (always enabled)
+        enabled                     false
+        uniqueness_length           1500
+        unreliability_threshold     -1.
+        relative_threshold          3.     
+    }
+
+    init_clean
+    {
+        activation_cov  -1.
+        early_it_only   false
+        ier
+        {
+            enabled true
+        }
+        ;Disable if it does not help the br performance much!
+        tip_condition   "{ tc_lb 3.5, cb 2.1 }"
+        ;ec_condition is here only to speed-up future br on early iterations
+        ec_condition    "{ ec_lb 10, cb 1.5 }"
+        disconnect_flank_cov    -1.
+    }
+
+}
+
+;TODO rename
+preliminary_simp
+{
+    init_clean
+    {
+        tip_condition   "loop 2 { rlmk 1., cb 1.2, mmm 2 } { rlmk 1., cb 1.2, mmm 0.05 } { rl 0.2, cb 1.2 }"
+        ec_condition    "{ ec_lb 0, cb 0.9 }"
+        disconnect_flank_cov    0.8
+    }
+
+    ; bulge remover:
+    br
+    {
+        enabled true
+        max_coverage			1000000.0
+        max_relative_coverage		0.5		; bulge_cov < this * not_bulge_cov
+        max_delta			10
+        max_relative_delta		0.1
+    }
+
+    ; Currently will not work even if enabled. Left for experiments.
+    ; relative edge disconnector
+    red
+    {
+        enabled false
+        diff_mult  10.
+        unconditional_diff_mult 100.
+    }
+}
+
+; undo single cell config changes, enforce filtering
+de
+{
+    raw_filter_threshold	1
+    rounding_coeff              0.5 ; rounding : min(de_max_distance * rounding_coeff, rounding_thr)
+    rounding_threshold          0
+}
+
+;NB decsends from sc_pe
+pe {
+
+long_reads {
+    pacbio_reads {
+        filtering   1.9
+        weight_priority    20.0
+        unique_edge_priority 10.0
+        min_significant_overlap 1000
+    }
+}
+
+params {
+    overlap_removal {
+        enabled true
+        cut_all true
+    }
+
+    scaffolding_mode old_pe_2015
+
+    normalize_weight     true
+    
+    ; extension selection
+    extension_options
+    {
+        single_threshold           0.3
+        weight_threshold           0.6
+        priority_coeff             1.5
+        max_repeat_length          1000000 
+    }
+    
+    use_coordinated_coverage true
+
+    coordinated_coverage
+    {
+       min_path_len           10000
+    }
+
+}
+
+}
+
+prelim_pe {
+params {
+    scaffolding_mode old
+
+    overlap_removal {
+        enabled false
+    }
+
+    use_coordinated_coverage false
+    remove_overlaps     false
+    scaffolding2015 {
+        min_unique_length 100000000
+    }
+}
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/metaplasmid_mode.info

@@ -0,0 +1,3 @@
+mode metaextrachromosomal
+two_step_rr false
+

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/metaviral_mode.info

@@ -0,0 +1,40 @@
+mode metaextrachromosomal
+two_step_rr false
+
+simp
+{
+
+    ; suspecies bulge remover:
+    subspecies_br
+    {
+        enabled true
+        main_iteration_only true
+        max_bulge_length_coefficient    30.     ; max_bulge_length = max_bulge_length_coefficient * k
+        max_coverage            1000000.0
+        max_relative_coverage       15     ; bulge_cov < this * not_bulge_cov
+        max_delta 45
+        max_relative_delta 0.2
+        min_identity 0.7
+    }
+
+}
+plasmid
+{
+;isolated
+    long_edge_length 1000
+    edge_length_for_median 10000
+    relative_coverage 0.3
+    small_component_size 10000
+    small_component_relative_coverage 1.5
+    min_component_length 10000
+    min_isolated_length 1000
+;   reference_removal replace this with path to reference and uncomment for reference based filtration
+;meta                          
+    iterative_coverage_elimination true
+    additive_step 5
+    relative_step 1.3
+    max_length 1000000
+    output_linear true
+    min_circular_length 1000
+    min_linear_length 500
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/pe_params.info

@@ -0,0 +1,179 @@
+pe {
+
+; output options
+
+debug_output    false
+
+output {
+    write_overlaped_paths   true
+    write_paths             true
+}
+
+visualize {
+    print_overlaped_paths   true
+    print_paths             true
+}
+
+params {
+    multi_path_extend   false
+    ; old | 2015 | combined | old_pe_2015
+    scaffolding_mode old_pe_2015
+    
+    overlap_removal {
+        enabled true
+        end_start_only  false
+        cut_all false
+    }
+
+    normalize_weight     true
+    
+    ; extension selection
+    extension_options
+    {
+        single_threshold           0.1
+        weight_threshold           0.5
+        priority_coeff             1.5
+        ;TODO remove from here
+        max_repeat_length          8000
+    }    
+
+    mate_pair_options
+    {
+        single_threshold           30
+        weight_threshold           0.5
+        priority_coeff             1.5
+        ;TODO remove from here
+        max_repeat_length          8000
+    }
+
+    scaffolder {
+        enabled       true
+        cutoff        2
+        hard_cutoff   0
+        rel_cov_cutoff    0.0
+        sum_threshold 3  
+
+        cluster_info  true
+        cl_threshold  0
+
+        fix_gaps       true
+        use_la_gap_joiner true
+        ;next param should be 0.51 - 1.0 if use_old_score = true and 3.0 otherwise
+        min_gap_score   0.7
+
+        max_can_overlap   1.
+        short_overlap     6
+        artificial_gap    10
+
+        min_overlap_length 10
+        flank_multiplication_coefficient .5
+        flank_addition_coefficient 5
+
+        var_coeff 3.0
+        basic_overlap_coeff 2.0
+    }
+
+    path_cleaning_presets ""
+
+    use_coordinated_coverage false
+    coordinated_coverage
+    {
+       max_edge_length_repeat 300
+       delta                  0.5
+       min_path_len           1000
+    }
+
+
+    simple_coverage_resolver {
+        enabled false
+        coverage_margin 2
+        min_upper_coverage 5
+        max_coverage_variation 5
+    }
+
+
+    scaffolding2015 {
+        ; (median * (1+variation) > unique > median * (1 - variation))
+        relative_weight_cutoff 2.0
+
+        unique_length_upper_bound 2000   ; max(unique_length_upper_bound, max_is(all libs))
+        unique_length_lower_bound 500    ; max(unique_length_lower_bound, unique_length_step)
+        unique_length_step 300
+
+        graph_connectivity_max_edges 200000
+    }
+
+    scaffold_graph {
+        construct    false
+        output       false
+        always_add   40         ; connection with read count >= always_add are always added to the graph
+        never_add     5         ; connection with read count < never_add are never added to the graph
+        relative_threshold 0.25 ; connection with read count >= max_read_count * relative_threshod are added to the graph if satisfy condition above, max_read_count is calculated amond all alternatives
+        use_graph_connectivity false
+        max_path_length 10000
+    }
+
+    genome_consistency_checker {
+        max_gap 1000
+        relative_max_gap 0.2
+        use_main_storage true ; if set to true, next two parameters are set to min_unique_length
+        unresolvable_jump 1000 ; length of unresolvable repeats
+        unique_length 500  ; spelling genome in the alphabet of edges longer than this          
+    }
+
+    uniqueness_analyser {
+        enabled        true
+        unique_coverage_variation 0.5
+
+        nonuniform_coverage_variation 50
+        uniformity_fraction_threshold 0.8
+    }
+
+    loop_traversal
+    {
+        min_edge_length         1000
+        max_component_size      10
+        max_path_length         1000
+    }
+}
+
+
+long_reads {
+    pacbio_reads {
+        filtering   2.5
+        weight_priority    1.2
+        unique_edge_priority 5.0
+        min_significant_overlap 0
+    }
+
+    single_reads {
+        filtering  1.25 
+        weight_priority    5.0
+        unique_edge_priority 10000.0
+        min_significant_overlap 0
+    }
+
+    contigs {
+        filtering   0.0
+        weight_priority    1.5
+        unique_edge_priority 2.0
+        min_significant_overlap 0
+    }
+
+    meta_untrusted_contigs {
+        filtering   0.0
+        weight_priority    10000.0
+        unique_edge_priority 10000.0
+        min_significant_overlap 200
+    }
+
+    rna_long_reads {
+        filtering   0.1
+        weight_priority    1.1
+        unique_edge_priority 2.0
+        min_significant_overlap 0
+    }
+
+
+}
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/plasmid_mode.info

@@ -0,0 +1,22 @@
+mode    plasmid
+
+plasmid 
+{
+;isolated
+    long_edge_length 1000
+    edge_length_for_median 10000
+    relative_coverage 0.3
+    small_component_size 10000
+    small_component_relative_coverage 1.5
+    min_component_length 10000
+    min_isolated_length 1000
+;   reference_removal replace this with path to reference and uncomment for reference based filtration
+;meta
+    iterative_coverage_elimination true
+    additive_step 5
+    relative_step 1.3
+    max_length 1000000
+    output_linear false
+    min_circular_length 1000
+    min_linear_length 500
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/rna_mode.info

@@ -0,0 +1,213 @@
+mode rna
+
+preserve_raw_paired_index true
+min_edge_length_for_is_count 500
+
+calculate_coverage_for_each_lib true
+strand_specificity {
+    ss_enabled false
+    antisense false
+}
+
+ss_coverage_splitter {
+    enabled           true
+    bin_size          50   
+    min_edge_len      200
+    min_edge_coverage 5
+    min_flanking_coverage 2
+    coverage_margin   5
+}
+
+pacbio_processor
+{
+    internal_length_cutoff 100
+;align and traverse.
+;    compression_cutoff 0.6
+;    path_limit_stretching 1.3
+;    path_limit_pressing 0.7
+    max_path_in_dijkstra 5000
+    max_vertex_in_dijkstra 1000
+    rna_filtering   true
+
+;gap_closer
+    long_seq_limit 100
+    enable_gap_closing false
+    enable_fl_gap_closing true
+    pacbio_min_gap_quantity 2
+    contigs_min_gap_quantity 1
+    max_contigs_gap_length 10000
+}
+
+contig_output {
+    scaffolds_name  transcripts
+    ; none  --- do not output broken scaffolds | break_gaps --- break only by N steches | break_all --- break all with overlap < k
+    output_broken_scaffolds     none
+}
+
+simp
+{
+    ;all topology based erroneous connection removers are off
+    topology_simplif_enabled false
+
+    tc
+    {
+        ; rctc: tip_cov < rctc * not_tip_cov
+        ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
+        condition  "{ mmm 3 tc_lb 4, cb 100000, rctc 0.5 } { tc_lb 2, cb 1, rctc 10000 }"
+    }
+
+    dead_end
+    {
+        enabled true
+        condition  "{ tc_lb 3.5, cb 2 }"
+    }
+
+    ; bulge remover:
+    br
+    {
+        enabled true
+        max_additive_length_coefficient 100
+        max_coverage            1000000.0
+        max_relative_coverage       100000.0 ; bulge_cov < this * not_bulge_cov
+    }
+
+    ; erroneous connections remover:
+    ec
+    { 
+       ; ec_lb: max_ec_length = k + ec_lb
+       ; icb: iterative coverage bound
+       ; to_ec_lb: max_ec_length = 2*tip_length(to_ec_lb) - 1
+       ; nbr: use not bulge erroneous connections remover 
+       ; condition               "{ ec_lb 9, icb 40.0, nbr }"
+       condition               "{ ec_lb 30, icb 200, rcec_cb 1.0 }"
+    }
+
+    ; relative coverage erroneous connections remover:
+    rcec
+    {
+        rcec_lb 30
+        rcec_cb 1.0
+        enabled true
+    }
+
+    rcc
+    {
+        enabled true
+        coverage_gap    20.
+    }
+
+    ; hidden ec remover
+    her
+    {
+        ; TODO NB config also used in special rna mode version (always enabled)
+        enabled                     false
+        uniqueness_length           1500
+        unreliability_threshold     0.2
+        relative_threshold          5
+    }
+
+    ier
+    {
+        enabled                       true
+        use_rl_for_max_length         true ; max_length will be taken max with read_length
+        use_rl_for_max_length_any_cov false ; use_rl_for_max_length_any_cov will be taken max with read_length
+        max_length                    80
+        max_coverage                  2
+        max_length_any_cov            0
+        rl_threshold_increase         2 ; add this value to read length if used, i.e. flags above are set
+    }
+
+}
+
+; disable filtering in rna mode
+de
+{
+    raw_filter_threshold	0
+}
+
+pe {
+debug_output    true
+
+params {
+    multi_path_extend   true
+
+    scaffolding_mode old
+
+    overlap_removal {
+        enabled false
+        end_start_only  true
+        cut_all true
+    }
+
+    extension_options
+    {
+        single_threshold           0.05
+    }
+
+    scaffolder {
+        cutoff        1
+        hard_cutoff   5
+        rel_cov_cutoff    0.1
+        cluster_info false
+        min_overlap_for_rna_scaffolding 8
+    }
+
+    path_cleaning_presets "default soft hard"
+    ; All length cutoffs presented in nucleotides
+    ; So edges less than or equal to (relative cutoff * RL - K) or (absolute cutoff - K) will be deleted
+    path_cleaning
+    {
+        enabled true
+        min_length  110
+        isolated_min_length 130
+        isolated_min_cov 4
+        min_length_for_low_covered 140
+        rel_cutoff 1.3
+        rel_isolated_cutoff 1.5
+        rel_low_covered_cutoff 1.6
+        min_coverage 2
+    }
+
+    ; All length cutoffs presented in nucleotides
+    hard_path_cleaning
+    {
+        enabled true
+        min_length  130
+        isolated_min_length 180
+        isolated_min_cov 8
+        min_length_for_low_covered 180
+        rel_cutoff 1.5
+        rel_isolated_cutoff 2.0
+        rel_low_covered_cutoff 2.0
+        min_coverage 3
+    }
+
+    ; All length cutoffs presented in nucleotides
+    soft_path_cleaning
+    {
+        enabled true
+        min_length  85
+        isolated_min_length 100
+        isolated_min_cov 2
+        min_length_for_low_covered 130
+        rel_cutoff 1.05
+        rel_isolated_cutoff 1.2
+        rel_low_covered_cutoff 1.5
+        min_coverage 1
+    }
+
+    use_coordinated_coverage false
+    coordinated_coverage {
+       max_edge_length_repeat 1000
+       delta                  0.5
+       min_path_len           300
+    }
+
+    simple_coverage_resolver {
+        enabled true
+        coverage_margin 2  
+        min_upper_coverage 2
+        max_coverage_variation 10
+    }
+}
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/rnaviral_mode.info

@@ -0,0 +1,32 @@
+mode rnaviral
+two_step_rr false
+
+simp
+{
+
+    ; suspecies bulge remover:
+    subspecies_br
+    {
+        enabled true
+        main_iteration_only true
+        max_bulge_length_coefficient    30.     ; max_bulge_length = max_bulge_length_coefficient * k
+        max_coverage            1000000.0
+        max_relative_coverage       15     ; bulge_cov < this * not_bulge_cov
+        max_delta 45
+        max_relative_delta 0.2
+        min_identity 0.9
+    }
+
+     red
+     {
+         enabled true
+         diff_mult  10.
+         unconditional_diff_mult 50.
+         edge_sum 0
+     }
+
+     final_br
+     {
+         enabled false
+     }
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/sewage_mode.info

@@ -0,0 +1,61 @@
+simp {
+        ; bulge remover:
+        br
+        {
+            enabled true
+            max_coverage			10.0
+            max_relative_coverage		0.05		; bulge_cov < this * not_bulge_cov
+            max_delta			10
+            max_relative_delta		0.1
+            dijkstra_vertex_limit   3000
+            parallel true
+        }
+       ; final bulge remover:
+       final_br
+       {
+        	enabled false
+       }
+       ; complex bulge remover
+       cbr
+       {
+           enabled false
+       }
+    ; relative coverage erroneous component remover:
+    rcc
+    {
+        enabled true
+        coverage_gap    15.
+        max_length_coeff    3.0
+        max_length_with_tips_coeff   5.0
+        max_vertex_cnt      100
+        max_ec_length_coefficient   300
+        max_coverage_coeff  -1.0
+    }
+
+    ; tip clipper:
+    tc
+    {
+        ; rctc: tip_cov < rctc * not_tip_cov
+        ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
+        condition               "{ rl 0.2, cb 10.0 } { rlmk 1.1, rctc 2.0, cb 10.0 }"
+    }
+
+     final_tc
+     {
+     condition ""
+     }
+}
+
+preliminary_simp
+{
+    ; bulge remover:
+    br
+    {
+        enabled true
+        max_coverage			500.0
+        max_relative_coverage		0.5		; bulge_cov < this * not_bulge_cov
+        max_delta			10
+        max_relative_delta		0.1
+    }
+
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/simplification.info

@@ -0,0 +1,244 @@
+; simplification
+
+simp
+{
+    ; ==== RAW SIMPLIFICATION ==== 
+    init_clean
+    {
+        self_conj_condition "{ ec_lb 100, cb 1.0 }"
+        early_it_only   false
+        ; will be enabled only if average coverage >= activate_cov
+        ; if value < 0 check not performed
+        activation_cov  10.
+
+        ; isolated edges remover
+        ier
+        {
+            enabled                     true
+            use_rl_for_max_length         false ; max_length will be taken max with read_length
+            use_rl_for_max_length_any_cov true ; use_rl_for_max_length_any_cov will be taken max with read_length
+            max_length                  0 ; will be taken max with read_length if option above is set
+            max_coverage                0
+            max_length_any_cov          0 ; will be taken max with read_length if option above is set
+            rl_threshold_increase       0 ; add this value to read length if used, i.e. flags above are set
+        }
+
+        tip_condition   "{ tc_lb 3.5, cb auto }"
+        ec_condition    "{ ec_lb 10, cb 2.0 }"
+
+        ; edges with flank cov around alternative less than value will be disconnected 
+        ; negative value to disable
+        disconnect_flank_cov    -1.0
+    }
+
+    ; ==== SIMPLIFICATION CYCLE ==== 
+
+    ; number of iterations in basic simplification cycle
+    cycle_iter_count 10
+
+    ; tip clipper:
+    tc
+    {
+        ; rctc: tip_cov < rctc * not_tip_cov
+        ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
+        ; todo think about params one more time
+        condition               "{ tc_lb 3.5, cb 1000000, rctc 2.0 } { tc_lb 10., cb auto }"
+    }
+  
+    ; bulge remover:
+    br
+    {
+        enabled				true
+        main_iteration_only false
+        max_bulge_length_coefficient	3.	; max_bulge_length = max_bulge_length_coefficient * k
+        max_additive_length_coefficient 100
+        max_coverage			1000.0
+        max_relative_coverage		1.1	; bulge_cov < this * not_bulge_cov
+        max_delta			3
+        max_relative_delta		0.1
+        max_number_edges        1000
+        dijkstra_vertex_limit   3000
+        parallel true
+        buff_size 10000
+        buff_cov_diff 2.
+        buff_cov_rel_diff 0.2
+        min_identity 0.0
+    }
+	
+	; erroneous connections remover:
+	ec
+	{
+       ; ec_lb: max_ec_length = k + ec_lb
+       ; icb: iterative coverage bound
+       ; to_ec_lb: max_ec_length = 2*tip_length(to_ec_lb) - 1
+        condition               "{ to_ec_lb 5, icb auto }"
+       ; condition               "{ ec_lb 9, icb 40.0 }"
+    }
+
+    dead_end {
+        enabled false
+        condition ""
+    }
+
+    ; ==== POST-SIMPLIFICATION ==== 
+
+    ; relative coverage erroneous connections remover:
+    rcec
+    {
+        enabled false
+        rcec_lb 30
+        rcec_cb 0.5
+    }
+    
+    ; relative coverage erroneous component remover:
+    rcc
+    {
+        enabled false
+        coverage_gap    5.
+        max_length_coeff    2.0
+        max_length_with_tips_coeff   3.0
+        max_vertex_cnt      30
+        max_ec_length_coefficient   30
+        max_coverage_coeff  2.0
+    }
+    
+    ; relative edge disconnector:
+    red
+    {
+        enabled false
+        diff_mult  20.
+        edge_sum   10000
+        unconditional_diff_mult 0. ; 0. to disable
+    }
+
+    ; final tip clipper:
+    final_tc
+    {
+        condition               ""
+    }
+
+    ; final bulge remover:
+    final_br
+    {
+        enabled				false
+        main_iteration_only false
+        max_bulge_length_coefficient	3.	; max_bulge_length = max_bulge_length_coefficient * k
+        max_additive_length_coefficient 100
+        max_coverage			1000.0
+        max_relative_coverage		1.1	; bulge_cov < this * not_bulge_cov
+        max_delta			3
+        max_relative_delta		0.1
+        max_number_edges        1000
+        dijkstra_vertex_limit   3000
+        parallel true
+        buff_size 10000
+        buff_cov_diff 2.
+        buff_cov_rel_diff 0.2
+        min_identity 0.0
+    }
+
+    ; subspecies bulge remover:
+    subspecies_br
+    {
+        enabled				false
+        main_iteration_only false
+        max_bulge_length_coefficient	3.	; max_bulge_length = max_bulge_length_coefficient * k
+        max_additive_length_coefficient 100
+        max_coverage			1000.0
+        max_relative_coverage		1.1	; bulge_cov < this * not_bulge_cov
+        max_delta			3
+        max_relative_delta		0.1
+        max_number_edges        1000
+        dijkstra_vertex_limit   3000
+        parallel true
+        buff_size 10000
+        buff_cov_diff 2.
+        buff_cov_rel_diff 0.2
+        min_identity 0.0
+    }
+
+
+    ; complex tip clipper
+    complex_tc
+    {
+        enabled               false
+        max_relative_coverage -1
+        max_edge_len          100
+        condition             "{ tc_lb 3.5 }"
+    }  
+
+    ; complex bulge remover
+    cbr
+    {
+        enabled false
+        max_relative_length 5.
+        max_length_difference   5
+    }
+ 
+    ; isolated edges remover
+    ier
+    {
+        enabled                     true
+        use_rl_for_max_length         false ; max_length will be taken max with read_length
+        use_rl_for_max_length_any_cov true ; use_rl_for_max_length_any_cov will be taken max with read_length
+        max_length                  0 ; will be taken max with read_length if option above is set
+        max_coverage                2
+        max_length_any_cov          150 ; will be taken max with read_length if option above is set
+        rl_threshold_increase       0 ; add this value to read length if used, i.e. flags above are set
+    }
+
+    ; hidden ec remover
+    her
+    {
+        enabled                     false
+        uniqueness_length           1500
+        unreliability_threshold     4
+        relative_threshold          5
+    }
+    
+    ; ==== ADVANCED EC REMOVAL ALGO ==== 
+    ; enable advanced ec removal algo
+    topology_simplif_enabled false
+    
+    ; topology based erroneous connection remover
+    tec
+    {
+        max_ec_length_coefficient   55  ; max_ec_length = k + max_ec_length_coefficient
+        uniqueness_length       1500
+        plausibility_length     200
+    }
+
+    ; topology and reliability based erroneous connection remover
+    trec
+    {
+        max_ec_length_coefficient   100 ; max_ec_length = k + max_ec_length_coefficient
+        uniqueness_length       1500
+        unreliable_coverage     2.5
+    }
+    
+    ; interstrand erroneous connection remover (thorn remover)
+    isec
+    {
+        max_ec_length_coefficient   100 ; max_ec_length = k + max_ec_length_coefficient
+        uniqueness_length       1500
+        span_distance       15000
+    }
+
+    ; max flow erroneous connection remover
+    mfec
+    {
+        enabled false
+        max_ec_length_coefficient   30  ; max_ec_length = k + max_ec_length_coefficient
+        uniqueness_length       1500
+        plausibility_length     200
+    }
+
+    ; topology tip clipper:
+    ttc
+    {
+        length_coeff    3.5
+        plausibility_length 250
+        uniqueness_length   1500
+    }
+
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/configs/toy.info

@@ -0,0 +1,4 @@
+reads	toy.yaml
+single_cell	false
+; RL	100
+

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/final.lib_data

@@ -0,0 +1,36 @@
+�---
+max read length: 150
+nomerge max read length: 150
+average read length: 133.399
+average coverage: 8.62166
+libraries:
+  - type:            paired-end
+    number:          1
+    orientation:     fr
+    left reads:
+      - '/225040511/project/bioagent-bench/dataset/evolution/data/anc_R1.fastq.gz'
+    right reads:
+      - '/225040511/project/bioagent-bench/dataset/evolution/data/anc_R2.fastq.gz'
+    data:
+      unmerged read length: 150
+      merged read length: 0
+      insert size mean: 0
+      insert size deviation: 0
+      insert size left quantile: 0
+      insert size right quantile: 0
+      insert size median: 0
+      insert size mad: 0
+      insert size distribution: {  }
+      pi threshold:    0
+      binary reads info:
+        binary converted: true
+        bin reads info file: '/225040511/project/Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/.bin_reads/INFO_0'
+        paired read prefix: '/225040511/project/Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/.bin_reads/paired_0'
+        merged read prefix: '/225040511/project/Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/.bin_reads/merged_0'
+        single read prefix: '/225040511/project/Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/.bin_reads/single_0'
+        chunk num:       8
+      single reads mapped: false
+      library index:   0
+      number of reads: 563496
+      total nucleotides: 75169567
+...

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/simplified_contigs/contigs_info

@@ -0,0 +1 @@
+14 18446744073709551615 157815 0 756 4569114

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K77/configs/careful_mda_mode.info

@@ -0,0 +1,40 @@
+simp
+{
+    ; bulge remover:
+    br
+    {
+        enabled true
+        max_relative_coverage		1.1	; bulge_cov < this * not_bulge_cov
+    }
+    
+    ; complex bulge remover
+    cbr
+    {
+        enabled false
+    }
+
+    final_tc
+    {
+        condition               ""
+    }
+
+    ; bulge remover:
+    final_br
+    {
+        enabled false
+    }
+
+    init_clean
+    {
+        early_it_only   true
+
+        activation_cov  -1.
+        ier
+        {
+            enabled                     false
+        }
+
+        tip_condition   ""
+        ec_condition    ""
+    }
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K77/configs/careful_mode.info

@@ -0,0 +1,42 @@
+simp
+{
+    ; bulge remover:
+    br
+    {
+        enabled true
+        max_relative_coverage       0.5     ; bulge_cov < this * not_bulge_cov
+        ; parallel false
+    }
+    
+    ; complex bulge remover
+    cbr
+    {
+        enabled false
+    }
+
+    ; bulge remover:
+    final_br
+    {
+        enabled false
+    }
+
+    ; relative coverage erroneous component remover:
+    rcc
+    {
+        enabled false
+    }
+
+    init_clean
+    {
+        early_it_only   true
+
+        activation_cov  -1.
+        ier
+        {
+            enabled                     false
+        }
+
+        tip_condition   ""
+        ec_condition    ""
+    }
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K77/configs/config.info

@@ -0,0 +1,216 @@
+; input options:
+
+#include "simplification.info"
+#include "construction.info"
+#include "distance_estimation.info"
+#include "detail_info_printer.info"
+#include "pe_params.info"
+
+K 77
+;FIXME introduce isolate mode
+mode base
+
+dataset /225040511/project/Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/dataset.info
+log_filename    log.properties
+
+output_base /225040511/project/Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly
+tmp_dir /225040511/project/Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/tmp/spades_lhfdc3lg
+
+main_iteration true
+; iterative mode switcher, activates additional contigs usage
+use_additional_contigs true
+additional_contigs /225040511/project/Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K55/simplified_contigs
+load_from /225040511/project/Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K77/saves
+
+; Multithreading options
+temp_bin_reads_dir	.bin_reads/
+max_threads 8
+max_memory 32
+buffer_size     512; in Megabytes
+
+entry_point read_conversion
+;entry_point construction
+;entry_point simplification
+;entry_point hybrid_aligning
+;entry_point late_pair_info_count
+;entry_point distance_estimation
+;entry_point repeat_resolving
+
+checkpoints none
+developer_mode false
+sewage false
+sewage_matrix /225040511/miniconda3/envs/biomni_e1/share/spades/sewage/usher_barcodes.csv
+
+scaffold_correction_mode false
+
+; enabled (1) or disabled (0) repeat resolution (former "paired_mode")
+rr_enable true
+; 0 for graph N50
+min_edge_length_for_is_count 0
+
+; Whether GFA v1.2 (jump links) or GFA v1.1 (scaffold segments) graphs is written
+gfa11 false
+
+;preserve raw paired index after distance estimation
+preserve_raw_paired_index false
+
+; two-step pipeline
+two_step_rr false
+; enables/disables usage of intermediate contigs in two-step pipeline
+use_intermediate_contigs false
+
+;use single reads for rr (all | only_single_libs | none )
+single_reads_rr only_single_libs
+
+; The following parameters are used ONLY if developer_mode is true
+
+; whether to output dot-files with pictures of graphs - ONLY in developer mode
+output_pictures true
+
+; whether to output resulting contigs after intermediate stages - ONLY in developer mode
+output_nonfinal_contigs true
+
+; whether to compute number of paths statistics   - ONLY in developer mode
+compute_paths_number false
+
+; End of developer_mode parameters
+
+;if true simple mismatches are corrected
+correct_mismatches          true
+
+; set it true to get statistics, such as false positive/negative, perfect match, etc.
+paired_info_statistics false
+
+; set it true to get statistics for pair information (over gaps), such as false positive/negative, perfect match, etc.
+paired_info_scaffolder false
+
+;the only option left from repeat resolving
+max_repeat_length 8000
+
+; repeat resolving mode (none path_extend)
+resolving_mode path_extend
+
+use_scaffolder  true
+
+avoid_rc_connections true
+
+calculate_coverage_for_each_lib false
+strand_specificity {
+    ss_enabled false
+    antisense false
+}
+
+contig_output {
+    contigs_name    final_contigs
+    scaffolds_name  scaffolds
+    ; none  --- do not output broken scaffolds | break_gaps --- break only by N steches | break_all --- break all with overlap < k
+    output_broken_scaffolds     break_gaps
+}
+
+;position handling
+
+pos
+{
+    max_mapping_gap 0 ; in terms of K+1 mers value will be K + max_mapping_gap
+    max_gap_diff 0
+	contigs_for_threading ./data/debruijn/contigs.fasta
+    contigs_to_analyze ./data/debruijn/contigs.fasta
+	late_threading true
+	careful_labeling true
+
+}
+
+gap_closer_enable true
+
+gap_closer
+{
+    minimal_intersection	10
+
+    ;before_raw_simplify and before_simplify are mutually exclusive
+    before_raw_simplify    		true
+    before_simplify		false
+    after_simplify 		true
+    weight_threshold		2.0
+    max_dist_to_tip		5000
+}
+
+kmer_coverage_model {
+    probability_threshold 0.05
+    strong_probability_threshold 0.999
+    use_coverage_threshold false
+    coverage_threshold 10.0
+}
+
+; low covered edges remover
+lcer
+{
+    lcer_enabled                     false
+    lcer_coverage_threshold          0.0
+}
+
+pacbio_processor ;commented frozen constants default assinged in hpp
+{
+    internal_length_cutoff 200
+;align and traverse.
+;    compression_cutoff 0.6
+;    path_limit_stretching 1.3
+;    path_limit_pressing 0.7
+    max_path_in_dijkstra 15000
+    max_vertex_in_dijkstra 2000
+    rna_filtering   false
+
+;gap_closer
+    long_seq_limit 400
+    enable_gap_closing true
+    pacbio_min_gap_quantity 2
+    contigs_min_gap_quantity 1
+    max_contigs_gap_length 10000
+;spoa
+;    match 5
+;    mismatch -4
+;    gap_open -8
+;    gap_extend -6
+;    gap_open_second -10
+;    gap_extend_second -4
+}
+
+;TODO move out!
+graph_read_corr
+{
+	enable false
+	output_dir corrected_contigs/
+	binary true
+}
+
+bwa_aligner
+{
+    debug false
+    min_contig_len 0
+}
+
+;flanking coverage range
+flanking_range 55
+series_analysis ""
+save_gp false
+
+ss_coverage_splitter {
+    enabled           false
+    bin_size          50
+    min_edge_len      200
+    min_edge_coverage 5
+    min_flanking_coverage 2
+    coverage_margin   5
+}
+
+time_tracer {
+  time_tracer_enabled false
+  granularity 500
+}
+
+hybrid_aligner {
+  trusted_aligner {
+        long_read_threshold       1000
+        long_read_fuzzy_coverage  0.95
+        short_read_fuzzy_coverage 0.90
+  }
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K77/configs/construction.info

@@ -0,0 +1,26 @@
+; construction
+
+construction
+{
+	; mode of construction: extension (construct hash map of kmers to extentions), old (construct set of k+1-mers)
+	mode extension
+
+	; enable keeping in graph perfect cycles. This slows down condensing but some plasmids can be lost if this is turned off.
+	keep_perfect_loops true
+
+	; size of buffer for each thread in MB, 0 for autodetection
+	read_buffer_size 0
+
+        ; read median coverage threshold
+        read_cov_threshold 0
+
+	early_tip_clipper
+	{
+		; tip clipper can be enabled only in extension mode
+		enable true
+
+		; optional parameter. By default tips of length rl-k are removed
+;		length_bound 10
+	}
+}
+

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K77/configs/detail_info_printer.info

@@ -0,0 +1,46 @@
+info_printers
+{
+    default
+    {
+       basic_stats                      false
+       lib_info                         false
+       save_all                         false
+       save_full_graph                  false
+       save_graph_pack                  false
+       extended_stats                   false
+       detailed_dot_write               false
+       write_components                 false
+       components_for_genome_pos        "" ; (k+1)-mers starting on this positions will be investigated
+	   components_for_kmer              ""
+       write_components_along_genome    false
+       write_components_along_contigs   false
+       write_error_loc                  false
+       write_full_graph                 false
+       write_full_nc_graph              false
+    }
+
+	before_first_gap_closer
+    {
+    }
+
+	before_simplification
+    {
+    }
+
+    before_post_simplification    
+    {
+    }
+
+    final_simplified
+    {
+    }
+
+    final_gap_closed
+    {
+    }
+
+    before_repeat_resolution
+    {
+    }
+
+}  

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K77/configs/distance_estimation.info

@@ -0,0 +1,42 @@
+; distance estimator:
+
+de
+{
+    linkage_distance_coeff    	0.0
+    max_distance_coeff        	2.0
+    max_distance_coeff_scaff  	2000.0
+    clustered_filter_threshold	2.0
+    raw_filter_threshold	2
+    rounding_coeff              0.5 ; rounding : min(de_max_distance * rounding_coeff, rounding_thr)
+    rounding_threshold          0
+}
+
+ade
+{
+    ;data dividing
+        threshold          80 ;maximal distance between two points in cluster
+
+    ;local maximum seeking
+        range_coeff          0.2 ;data_length*range_coeff := width of the averaging window
+        delta_coeff          0.4 ;data_length*delta_coeff := maximal difference between possible distance and real peak on the graph
+
+    ;fft smoothing
+        percentage          0.01 ;percent of data for baseline subraction
+        cutoff              3 ;the number of the lowest freqs in fourier decomp being taken
+
+    ;other
+        min_peak_points       3 ;the minimal number of points in cluster to be considered
+        inv_density         5.0 ;maximal inverse density of points in cluster to be considered
+
+    ;hard_mode arguments
+        derivative_threshold  0.2 ;threshold for derivative in hard mode
+
+}
+
+; ambiguous pair info checker parameters 
+amb_de {
+    enabled                         false
+    haplom_threshold                500
+    relative_length_threshold       0.8
+    relative_seq_threshold          0.5
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K77/configs/hmm_mode.info

@@ -0,0 +1,6 @@
+hmm_match {
+  set_of_hmms none
+  component_size_part 10
+  start_only_from_tips false
+  set_copynumber false
+}

Biomanus/experiments/ablation/results/minus_graph/bioagentbench/evolution_20260520_214803/anc_assembly/K77/configs/isolate_mode.info

@@ -0,0 +1,4 @@
+mode isolate
+
+#include "careful_mode.info"
+