Methanosarcina barkeri accepts electrons directly from G. metallireducens via DIET and uses them to reduce CO2 to methane. Unlike traditional hydrogen-mediated syntrophy, this process involves direct biological electrical connections between cells rather than diffusible intermediates. M. barkeri is unique as a methanogen capable of using either H2 or electrons from DIET for CO2 reduction, demonstrating metabolic flexibility. The electron transfer enables stoichiometric conversion of ethanol to methane in the coculture.
-
M. barkeri accepts DIET electrons for CO2 reduction to methane. Bulk ethanol-to-methane conversion also includes acetate metabolism; its stoichiometry is not an isotope measurement assigning every methane molecule to a route. The 2014 first-report wording is historical, not timeless uniqueness. Whether DIET-driven CO2 reduction alone supports methanogen growth, without acetate metabolism, was proposed for future testing rather than established here.
-
Geobacter metallireducens expresses a type VI secretion system (T6SS) during the initiation of DIET cocultures, and this is associated with a long delay before the partnership becomes productive. Cocultures started with wild-type G. metallireducens showed a lag of more than 30 days before methane production, whereas cocultures started with an Hcp-deficient (T6SS structural protein) mutant had very little lag and established DIET with M. barkeri faster. The sign of this edge is NEGATIVE: the wild-type T6SS-expressing state suppresses the rate at which the DIET partnership is established. The molecular attribution is confounded and must not be curated as demonstrated antagonism toward the archaeon - the same mutant also reduced Fe(III) oxide faster than wild type, a phenotype not expected from loss of the T6SS, and the authors state that the effect of T6SSs on archaeal cells still requires study. Encoded as a delay of establishment, not as predation, killing, or toxin delivery to M. barkeri.
-
+
In the G. metallireducens-M. barkeri comparison, wild-type Geobacter cocultures had a methane-production lag exceeding 30 days, while hcp-deficient cocultures had little lag. This is a measured genotype-associated establishment phenotype, not niche partitioning or demonstrated toxin delivery. Discovery RNA-seq and GAC/AQDS comparisons used the G. sulfurreducens partner, not M. barkeri. Altered extracellular-electron-transfer transcripts and the mutant Fe(III)-oxide phenotype expose pleiotropy. T6SS-specific inhibition of the archaeon remains HYPOTHESIZED; protein secretion or killing was not measured by the lag comparison.
-
Source Taxon: Geobacter metallireducens
-
Participating Taxa:
@@ -778,17 +771,6 @@
T6SS-Associated Delay of DIET Establishment
-
Biological Processes:
-
-
- -
- protein secretion by the type VI secretion system
- (GO:0033103)
-
-
-
-
@@ -796,7 +778,7 @@
T6SS-Associated Delay of DIET Establishment
→ Ethanol Oxidation and Direct Electron Transfer
-
NEGATIVE edge - the wild-type T6SS-expressing state of G. metallireducens delays establishment of the DIET partnership (>30 d lag vs very little lag for the Hcp-deficient mutant). Demonstrated by knockout phenotype in this exact coculture, but the mutant is pleiotropic, so the causal attribution to the T6SS specifically is HYPOTHESIZED rather than proven.
+
HYPOTHESIZED NEGATIVE: The wild-type Hcp/T6SS-associated state may delay DIET establishment relative to the hcp deletion strain. The exact coculture demonstrates a lag difference, but altered electron-transfer physiology prevents assigning the delay selectively to T6SS antagonism. The sign refers to establishment timing, not proven archaeal killing.
@@ -867,6 +849,40 @@
Evidence
+
+ Knowledge gaps & discussions (2)
+
+
+
+ KNOWLEDGE_GAP
+ OPEN
+ Which electron-entry components and hcp-dependent changes govern this DIET partnership?
+
+
Preserve the positive DIET and mutant-lag observations while separating genotype effects from secretion-specific antagonism. Partner-specific perturbations and complementation in the methanogenic coculture would distinguish proposed mechanisms. The Pelobacter/H2 comparator used a different medium and is not a selective same-medium H2 switch. Methanosaeta radiotracer results must not be imported into this system. Non-graph uniqueness/aggregation claims remain preserved, not certified.
+
+
Attaches to: ecological_interactions#Ethanol Oxidation and Direct Electron Transfer, ecological_interactions#DIET-Linked Carbon Dioxide Reduction to Methane, ecological_interactions#Hcp-Associated Delay of DIET Establishment
+
+
+
+
+
+
+ CURATION_TODO
+ OPEN
+ Complete the separately supported acetate branch after Edison review.
+
+
The primary paper supports an acetate contribution, but the graph still lacks that branch. A separate one-community Edison dry run completed without API calls or credits; specific authorization and report inspection remain pending under #1483. Add source-backed structure with its own evidence, without promoting ideal stoichiometry to an isotope-measured fraction or claiming DIET-only growth. This repair remains needs_research.
+
+
Attaches to: ecological_interactions#Ethanol Oxidation and Direct Electron Transfer, ecological_interactions#DIET-Linked Carbon Dioxide Reduction to Methane, ecological_interactions#Hcp-Associated Delay of DIET Establishment
+
+
+
+
+
@@ -1305,7 +1321,7 @@
Evidence
(function() {
var intId = "interaction:1";
- var intType = "SYNTROPHY";
+ var intType = "UNKNOWN";
var metabolites = [];
@@ -1324,7 +1340,7 @@
Evidence
nodes.push({
id: intId,
- label: "Direct Electron Acceptance and Methanogenesis",
+ label: "DIET-Linked Carbon Dioxide Reduction to Methane",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1352,20 +1368,16 @@
Evidence
(function() {
var intId = "interaction:2";
- var intType = "NICHE_PARTITIONING";
+ var intType = "UNKNOWN";
var metabolites = [];
var processes = [];
-
- processes.push("protein secretion by the type VI secretion system");
-
-
var evidenceCount = 4;
nodes.push({
id: intId,
- label: "T6SS-Associated Delay of DIET Establishment",
+ label: "Hcp-Associated Delay of DIET Establishment",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
@@ -1374,12 +1386,20 @@
Evidence
});
- var srcKey = "Geobacter metallireducens";
- if (taxonNodeIds[srcKey]) {
- links.push({ source: taxonNodeIds[srcKey], target: intId });
- }
+ var participantKeys = [
+
+ "Geobacter metallireducens",
+
+ "Methanosarcina barkeri"
+
+ ];
+ participantKeys.forEach(function(key) {
+ if (taxonNodeIds[key]) {
+ links.push({ source: taxonNodeIds[key], target: intId });
+ }
+ });
})();
diff --git a/history/records/Geobacter_Methanosaeta_DIET/2026-10-06T124951Z-codex-b6123c.yaml b/history/records/Geobacter_Methanosaeta_DIET/2026-10-06T124951Z-codex-b6123c.yaml
new file mode 100644
index 000000000..8924352c7
--- /dev/null
+++ b/history/records/Geobacter_Methanosaeta_DIET/2026-10-06T124951Z-codex-b6123c.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Geobacter_Methanosaeta_DIET.yaml
+ slug: Geobacter_Methanosaeta_DIET
+session:
+ id: 2026-10-06T124951Z-codex-b6123c
+ timestamp: '2026-10-06T12:49:51Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1480
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Separate the donor reaction from aggregate formation and methane carbon allocation.;
+ Retain positive defined-coculture DIET while bounding aggregation and electron-entry claims.;
+ Retain only the CO2 methane route, explicitly not the missing acetate branch.
+ details: 'Existing graph repair; acetate extension #1482 remains incomplete. reports/causal_graph_review/decisions/20261006-methanogens-batch46.yaml'
diff --git a/history/records/Geobacter_Methanosarcina_DIET/2026-10-06T124951Z-codex-59a839.yaml b/history/records/Geobacter_Methanosarcina_DIET/2026-10-06T124951Z-codex-59a839.yaml
new file mode 100644
index 000000000..e1d9cff79
--- /dev/null
+++ b/history/records/Geobacter_Methanosarcina_DIET/2026-10-06T124951Z-codex-59a839.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Geobacter_Methanosarcina_DIET.yaml
+ slug: Geobacter_Methanosarcina_DIET
+session:
+ id: 2026-10-06T124951Z-codex-59a839
+ timestamp: '2026-10-06T12:49:51Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1481
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ summary: Retain donor-to-partner DIET and condition-dependent pili/GAC evidence; correct
+ the donor carbon reaction.; Bound the existing methane node to CO2 reduction without universal
+ uniqueness or DIET-only growth.; Retain the exact hcp-lag phenotype and hypothetical negative
+ arrow without niche partitioning, secretion or killing claims.
+ details: 'Existing graph repair; acetate extension #1483 remains incomplete. reports/causal_graph_review/decisions/20261006-methanogens-batch46.yaml'
diff --git a/kb/communities/Geobacter_Methanosaeta_DIET.yaml b/kb/communities/Geobacter_Methanosaeta_DIET.yaml
index 630e24726..c304e4d0f 100644
--- a/kb/communities/Geobacter_Methanosaeta_DIET.yaml
+++ b/kb/communities/Geobacter_Methanosaeta_DIET.yaml
@@ -103,17 +103,11 @@ taxonomy:
ethanol to methane
explanation: Establishes M. harundinacea as a DIET-capable acetoclastic methanogen
ecological_interactions:
-- name: Ethanol Oxidation and Direct Electron Transfer
- description: 'Geobacter metallireducens oxidizes ethanol to acetate and CO2, transferring
- electrons directly to Methanosaeta harundinacea via electrically conductive aggregates.
- This direct interspecies electron transfer (DIET) bypasses the need for diffusible
- electron carriers like H2 or formate. The conductive aggregates serve as biological
- electrical conduits for long-range electron transfer between cells. Aggregate
- formation is essential for DIET, providing the physical and electrical connection
- necessary for electron flow from G. metallireducens to M. harundinacea.
-
- '
- interaction_type: SYNTROPHY
+- name: Geobacter Ethanol Oxidation
+ description: In the defined Geobacter metallireducens-Methanosaeta harundinacea coculture, Geobacter oxidizes
+ ethanol to acetate and releases electrons for DIET. This is the donor reaction, not a claim that ethanol carbon
+ is directly oxidized to CO2 at this step. The acetate coproduct also contributes to bulk methane through a separate
+ route, not yet represented as its own graph branch.
scope: PAIRWISE
source_taxon:
preferred_term: Geobacter metallireducens
@@ -137,27 +131,24 @@ ecological_interactions:
id: GO:0006068
label: ethanol catabolic process
downstream:
- - target: Conductive Aggregate-Mediated DIET
- description: Ethanol metabolism and extracellular electron transfer by
- aggregate-associated Geobacter feed the conductive aggregates where
- Geobacter and Methanosaeta exchange electrons by DIET.
+ - target: DIET in Defined Coculture Aggregates
+ description: Ethanol oxidation releases reducing equivalents that Geobacter supplies to the defined partner
+ through DIET. This arrow routes electron supply, not acetate carbon, and does not assert that ethanol oxidation
+ selectively causes aggregate formation.
evidence:
- reference: doi:10.1039/C3EE42189A
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Furthermore, Geobacter species, the most abundant bacteria in the aggregates,
- highly expressed genes for ethanol metabolism and for extracellular electron
- transfer via electrically conductive pili, suggesting that Geobacter and Methanosaeta
- species were exchanging electrons via direct interspecies electron transfer
- (DIET)
- explanation: Demonstrates ethanol oxidation coupled to direct electron transfer
- in conductive aggregates
-- name: Conductive Aggregate-Mediated DIET
- description: >
- G. metallireducens and M. harundinacea cells in conductive aggregates
- exchange electrons by direct interspecies electron transfer through
- electrically conductive pili, replacing diffusible H2 or formate as the
- interspecies electron carrier.
+ snippet: stoichiometrically converted ethanol to methane
+ explanation: Abstract support for coupled conversion; primary defined-coculture Results and Figure 4 locate
+ the donor reaction. Not environmental gene-expression proof.
+- name: DIET in Defined Coculture Aggregates
+ description: Defined G. metallireducens-M. harundinacea cocultures form mixed aggregates and support DIET; the
+ pilA-deficient Geobacter comparison supports a requirement for its pili-associated machinery under these conditions.
+ This evidence is distinct from Geobacter-species and Methanosaeta concilii expression in brewery-digester aggregates.
+ Aggregate formation itself was not selectively perturbed, and the methanogen electron-entry components remain
+ unresolved. Do not transfer measured conductivity of environmental aggregates to these defined aggregates as
+ a separately measured property.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -176,32 +167,24 @@ ecological_interactions:
id: GO:0022900
label: electron transport chain
downstream:
- - target: Direct Electron Acceptance and Methanogenesis
- description: Conductive-aggregate electron transfer delivers electrons to
- M. harundinacea for carbon dioxide reduction to methane.
+ - target: DIET-Linked Carbon Dioxide Reduction to Methane
+ description: DIET supplies electrons for M. harundinacea CO2 reduction to methane, supported by the defined-coculture
+ radiotracer and pilA comparison. This direction does not allocate acetate-derived methane to the CO2 branch
+ or establish a particular methanogen entry protein.
evidence:
- reference: doi:10.1039/C3EE42189A
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Furthermore, Geobacter species, the most abundant bacteria in the aggregates,
- highly expressed genes for ethanol metabolism and for extracellular electron
- transfer via electrically conductive pili, suggesting that Geobacter and Methanosaeta
- species were exchanging electrons via direct interspecies electron transfer
- (DIET)
- explanation: Supports conductive aggregate-mediated electron transfer
- between Geobacter and Methanosaeta cells.
-- name: Direct Electron Acceptance and Methanogenesis
- description: 'Methanosaeta harundinacea accepts electrons directly from G. metallireducens
- via DIET and uses them to reduce CO2 to methane. Unlike traditional hydrogen-mediated
- syntrophy, this process involves direct biological electrical connections through
- conductive aggregates rather than diffusible intermediates. M. harundinacea''s
- ability to accept electrons via DIET is particularly significant as it is an obligate
- acetoclastic methanogen, expanding our understanding of electron transfer mechanisms
- beyond the more metabolically versatile Methanosarcina species. The electron transfer
- enables stoichiometric conversion of ethanol to methane in the coculture.
-
- '
- interaction_type: MUTUALISM
+ snippet: Transcriptomic, radiotracer, and genetic analysis demonstrated that M. harundinacea accepted electrons
+ via DIET
+ explanation: The abstract identifies experimental DIET evidence in the defined coculture; Figures 4-5 bound
+ aggregate and mutant interpretation.
+- name: DIET-Linked Carbon Dioxide Reduction to Methane
+ description: M. harundinacea accepts DIET electrons for CO2 reduction to methane in the defined coculture, supported
+ by transcript, radiotracer and genetic analyses. Bulk methane also includes acetate conversion. The reported
+ stoichiometry and bicarbonate radiolabel are consistent with roughly one-third of methane arising through CO2
+ reduction, not all methane. This node represents that CO2 route; it does not replace the missing acetate branch
+ or identify the methanogen surface electron receptor.
scope: PAIRWISE
source_taxon:
preferred_term: Methanosaeta harundinacea
@@ -228,13 +211,9 @@ ecological_interactions:
- reference: doi:10.1039/C3EE42189A
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Furthermore, Geobacter species, the most abundant bacteria in the aggregates,
- highly expressed genes for ethanol metabolism and for extracellular electron
- transfer via electrically conductive pili, suggesting that Geobacter and Methanosaeta
- species were exchanging electrons via direct interspecies electron transfer
- (DIET)
- explanation: Establishes M. harundinacea's ability to use DIET-derived electrons
- for methanogenesis
+ snippet: reduction of carbon dioxide to methane
+ explanation: Supports the CO2-reduction route, not an assertion that every methane carbon follows it. Primary
+ Figures 4c and 5 distinguish the routes.
environmental_factors:
- name: Anaerobic Conditions
value: Strict anaerobic
@@ -411,35 +390,62 @@ metal_notes: Metal/REE detected via environmental factor measurements; Metal/REE
via keyword matching in description (context-validated)
discussions:
- discussion_id: kg-geobacter-methanosaeta-acetate-route-unresolved
- prompt: >
- Alongside DIET-driven CO2 reduction, does M. harundinacea also cross-feed on the
- acetate generated by G. metallireducens ethanol oxidation, and what fraction of
- methane comes from each route in this defined coculture?
+ prompt: 'Alongside DIET-driven CO2 reduction, does M. harundinacea also cross-feed on the acetate generated by
+ G. metallireducens ethanol oxidation, and what fraction of methane comes from each route in this defined coculture?
+
+ '
kind: KNOWLEDGE_GAP
- status: OPEN
+ status: RESOLVED
attaches_to:
- - ecological_interactions#Ethanol Oxidation and Direct Electron Transfer
- - ecological_interactions#Direct Electron Acceptance and Methanogenesis
- rationale: >
- A causal-graph pass on this record proposed an additional acetate cross-feeding node
- and an acetate -> methanogenesis edge, on the reasoning that Methanosaeta is
- classically an acetoclastic genus and that ethanol oxidation by G. metallireducens
- yields acetate, giving an overall stoichiometry near 1.5 mol CH4 per mol ethanol.
- That claim is NOT curated here as an interaction: the primary source
- (doi:10.1039/C3EE42189A) is cached abstract-only and its full text was not
- retrievable, and the abstract states only that M. harundinacea "accepted electrons
- via DIET for the reduction of carbon dioxide to methane" - it does not report acetate
- cross-feeding, the acetate/DIET split, or the per-route methane stoichiometry. The
- supporting quotations offered for the acetate route came from secondary reviews
- attributing findings to this study, which per this repo's conservative-curation rule
- (see CommunityMech:000176) is not a sufficient basis for an exact-system causal edge.
- Resolving this needs the primary full text or a radiotracer/isotope partition
- experiment in this exact coculture.
+ - ecological_interactions#Geobacter Ethanol Oxidation
+ - ecological_interactions#DIET-Linked Carbon Dioxide Reduction to Methane
+ rationale: The earlier discussion deferred an acetate branch because only the abstract was accessible and secondary
+ attributions were insufficient. The primary full paper is now available and has been read; its defined-coculture
+ evidence resolves the biological/source-access question, while graph implementation remains a separate open
+ curation task.
evidence:
- reference: doi:10.1039/C3EE42189A
- supports: PARTIAL
+ supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Transcriptomic, radiotracer, and genetic analysis demonstrated that M. harundinacea
- accepted electrons via DIET for the reduction of carbon dioxide to methane
- explanation: The abstract demonstrates only the DIET/CO2-reduction route; it is silent on an
- acetate cross-feeding route, which is why that edge is filed as a gap rather than curated.
+ explanation: Primary defined-coculture Results and Figures 4c/5, reviewed directly rather than inferred from
+ the environmental expression excerpt or secondary reviews.
+ resolved_date: '2026-10-06'
+ resolution_note: 'Primary Figure 4c separates acetate conversion from DIET-dependent CO2 reduction, and Figure
+ 5 supports the route distinction by bicarbonate radiolabel. See the source hash and inspection scope in the
+ batch46 decision ledger. The missing branch remains open under #1482; resolving this discussion does not mark
+ the graph complete.'
+- discussion_id: methanosaeta_entry_and_aggregation_scope
+ prompt: Which methanogen surface components receive DIET electrons?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Geobacter Ethanol Oxidation
+ - ecological_interactions#DIET in Defined Coculture Aggregates
+ - ecological_interactions#DIET-Linked Carbon Dioxide Reduction to Methane
+ rationale: The positive DIET result does not identify the receiver proteins or selectively establish aggregate
+ formation itself as necessary. Targeted perturbations would distinguish these mechanisms. Canonical Methanosaeta/Methanothrix
+ naming is preserved; stronger non-graph aggregate and uniqueness wording is not certified by this graph-only
+ review.
+ posed_by: codex
+ posed_date: '2026-10-06'
+- discussion_id: methanosaeta_acetate_branch_curation
+ prompt: Complete the separately supported acetate branch after Edison review.
+ kind: CURATION_TODO
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Geobacter Ethanol Oxidation
+ - ecological_interactions#DIET in Defined Coculture Aggregates
+ - ecological_interactions#DIET-Linked Carbon Dioxide Reduction to Methane
+ rationale: 'The primary evidence is now available, but an acetate-transfer/conversion branch is new causal structure.
+ A one-community Edison dry run completed without API calls or cost; specific credit authorization and report
+ inspection remain pending under #1482. Do not count the bounded CO2 route as completion of the whole graph.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T12:49:50Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Separate the donor reaction from aggregate formation and methane carbon allocation.; Retain positive
+ defined-coculture DIET while bounding aggregation and electron-entry claims.; Retain only the CO2 methane route,
+ explicitly not the missing acetate branch. Repair #1480; extension remains #1482; reports/causal_graph_review/decisions/20261006-methanogens-batch46.yaml'
+ llm_assisted: true
diff --git a/kb/communities/Geobacter_Methanosarcina_DIET.yaml b/kb/communities/Geobacter_Methanosarcina_DIET.yaml
index f2dee7121..9e12f2edf 100644
--- a/kb/communities/Geobacter_Methanosarcina_DIET.yaml
+++ b/kb/communities/Geobacter_Methanosarcina_DIET.yaml
@@ -97,16 +97,11 @@ taxonomy:
transfer capabilities
ecological_interactions:
- name: Ethanol Oxidation and Direct Electron Transfer
- description: 'Geobacter metallireducens oxidizes ethanol to acetate and CO2, transferring
- electrons directly to Methanosarcina barkeri via electrically conductive pili
- (e-pili). This direct interspecies electron transfer (DIET) bypasses the need
- for diffusible electron carriers like H2 or formate. The pili serve as biological
- electrical conduits for long-range electron transfer between cells. Pilin-deficient
- G. metallireducens mutants cannot initiate cocultures, demonstrating the essential
- role of pili in DIET. However, conductive materials like granular activated carbon
- can substitute for pili, showing that DIET can be mediated by abiotic conductors.
-
- '
+ description: G. metallireducens oxidizes ethanol to acetate and supplies electrons to M. barkeri through DIET.
+ Pilin-deficient cocultures did not establish ethanol-to-methane conversion without amendment, whereas granular
+ activated carbon enabled the tested mutant cocultures. Thus the pili-associated requirement is condition-dependent,
+ not universal in conductive-material-amended cultures. The methanogen entry proteins remain unresolved; the
+ donor reaction should not be described as direct ethanol-carbon oxidation to CO2.
interaction_type: SYNTROPHY
scope: PAIRWISE
source_taxon:
@@ -136,42 +131,39 @@ ecological_interactions:
id: GO:0006068
label: ethanol catabolic process
downstream:
- - target: Direct Electron Acceptance and Methanogenesis
- description: Electrons transferred via DIET are accepted by M. barkeri for methanogenesis
+ - target: DIET-Linked Carbon Dioxide Reduction to Methane
+ description: DIET delivers ethanol-derived electrons to M. barkeri for CO2 reduction. This electron-supply arrow
+ supports the CO2 route, not an attribution of all bulk methane to that route; acetate conversion is a separate
+ missing branch.
evidence:
- reference: PMID:24837373
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Cocultures formed aggregates that shared electrons via DIET during the
- stoichiometric conversion of ethanol to methane
- explanation: Demonstrates that the G. metallireducens-M. barkeri coculture coupled
- ethanol conversion to aggregate-mediated DIET.
+ snippet: Cocultures formed aggregates that shared electrons via DIET during the stoichiometric conversion of
+ ethanol to methane
+ explanation: Demonstrates that the G. metallireducens-M. barkeri coculture coupled ethanol conversion to aggregate-mediated
+ DIET.
- reference: PMID:24837373
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Cocultures could not be initiated with a pilin-deficient G. metallireducens
- strain, suggesting that long-range electron transfer along pili was important
- for DIET
- explanation: Establishes the essential role of conductive pili in mediating DIET
+ snippet: Cocultures could not be initiated with a pilin-deficient G. metallireducens strain, suggesting that
+ long-range electron transfer along pili was important for DIET
+ explanation: Supports the pilin-deficient initiation phenotype under the tested unamended conditions, not a
+ universal requirement in GAC-amended cocultures or identification of the methanogen entry machinery.
- reference: PMID:24837373
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: Amendments of granular activated carbon permitted the pilin-deficient
- G. metallireducens isolates to share electrons with M. barkeri
- explanation: Demonstrates that conductive materials can substitute for pili in
- DIET
-- name: Direct Electron Acceptance and Methanogenesis
- description: 'Methanosarcina barkeri accepts electrons directly from G. metallireducens
- via DIET and uses them to reduce CO2 to methane. Unlike traditional hydrogen-mediated
- syntrophy, this process involves direct biological electrical connections between
- cells rather than diffusible intermediates. M. barkeri is unique as a methanogen
- capable of using either H2 or electrons from DIET for CO2 reduction, demonstrating
- metabolic flexibility. The electron transfer enables stoichiometric conversion
- of ethanol to methane in the coculture.
-
- '
+ snippet: Amendments of granular activated carbon permitted the pilin-deficient G. metallireducens isolates to
+ share electrons with M. barkeri
+ explanation: Supports conductive-material rescue of the tested pilin-deficient cocultures; it does not prove
+ direct physical contact is required under this amendment.
+- name: DIET-Linked Carbon Dioxide Reduction to Methane
+ description: M. barkeri accepts DIET electrons for CO2 reduction to methane. Bulk ethanol-to-methane conversion
+ also includes acetate metabolism; its stoichiometry is not an isotope measurement assigning every methane molecule
+ to a route. The 2014 first-report wording is historical, not timeless uniqueness. Whether DIET-driven CO2 reduction
+ alone supports methanogen growth, without acetate metabolism, was proposed for future testing rather than established
+ here.
scope: COMMUNITY_LEVEL
- interaction_type: SYNTROPHY
participating_taxa:
- preferred_term: Geobacter metallireducens
term:
@@ -201,28 +193,18 @@ ecological_interactions:
- reference: PMID:24837373
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: M. barkeri is the second methanogen found to accept electrons via DIET
- and the first methanogen known to be capable of using either H2 or electrons
- derived from DIET for CO2 reduction
- explanation: Establishes M. barkeri's ability to use DIET-derived electrons for
- methanogenesis
-- name: T6SS-Associated Delay of DIET Establishment
- description: 'Geobacter metallireducens expresses a type VI secretion system (T6SS) during
- the initiation of DIET cocultures, and this is associated with a long delay before the
- partnership becomes productive. Cocultures started with wild-type G. metallireducens showed
- a lag of more than 30 days before methane production, whereas cocultures started with an
- Hcp-deficient (T6SS structural protein) mutant had very little lag and established DIET
- with M. barkeri faster. The sign of this edge is NEGATIVE: the wild-type T6SS-expressing
- state suppresses the rate at which the DIET partnership is established. The molecular
- attribution is confounded and must not be curated as demonstrated antagonism toward the
- archaeon - the same mutant also reduced Fe(III) oxide faster than wild type, a phenotype
- not expected from loss of the T6SS, and the authors state that the effect of T6SSs on
- archaeal cells still requires study. Encoded as a delay of establishment, not as
- predation, killing, or toxin delivery to M. barkeri.
-
- '
+ snippet: M. barkeri is the second methanogen found to accept electrons via DIET and the first methanogen known
+ to be capable of using either H2 or electrons derived from DIET for CO2 reduction
+ explanation: Supports the reported DIET capability and historical dual H2/DIET context, not present-day uniqueness,
+ all-methane CO2 attribution or DIET-only growth.
+- name: Hcp-Associated Delay of DIET Establishment
+ description: In the G. metallireducens-M. barkeri comparison, wild-type Geobacter cocultures had a methane-production
+ lag exceeding 30 days, while hcp-deficient cocultures had little lag. This is a measured genotype-associated
+ establishment phenotype, not niche partitioning or demonstrated toxin delivery. Discovery RNA-seq and GAC/AQDS
+ comparisons used the G. sulfurreducens partner, not M. barkeri. Altered extracellular-electron-transfer transcripts
+ and the mutant Fe(III)-oxide phenotype expose pleiotropy. T6SS-specific inhibition of the archaeon remains HYPOTHESIZED;
+ protein secretion or killing was not measured by the lag comparison.
scope: COMMUNITY_LEVEL
- interaction_type: NICHE_PARTITIONING
participating_taxa:
- preferred_term: Geobacter metallireducens
term:
@@ -232,38 +214,26 @@ ecological_interactions:
term:
id: NCBITaxon:2208
label: Methanosarcina barkeri
- source_taxon:
- preferred_term: Geobacter metallireducens
- term:
- id: NCBITaxon:28232
- label: Geobacter metallireducens
- biological_processes:
- - preferred_term: protein secretion by the type VI secretion system
- term:
- id: GO:0033103
- label: protein secretion by the type VI secretion system
downstream:
- target: Ethanol Oxidation and Direct Electron Transfer
- description: NEGATIVE edge - the wild-type T6SS-expressing state of G. metallireducens
- delays establishment of the DIET partnership (>30 d lag vs very little lag for the
- Hcp-deficient mutant). Demonstrated by knockout phenotype in this exact coculture, but
- the mutant is pleiotropic, so the causal attribution to the T6SS specifically is
- HYPOTHESIZED rather than proven.
+ description: 'HYPOTHESIZED NEGATIVE: The wild-type Hcp/T6SS-associated state may delay DIET establishment relative
+ to the hcp deletion strain. The exact coculture demonstrates a lag difference, but altered electron-transfer
+ physiology prevents assigning the delay selectively to T6SS antagonism. The sign refers to establishment timing,
+ not proven archaeal killing.'
evidence:
- reference: PMID:37650614
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: there was a lag period of more than 30 d in co-cultures initiated with wild-type
- G. metallireducens
- explanation: Wild-type baseline for the delay, measured in the G. metallireducens-M. barkeri
- ethanol coculture that this record describes.
+ snippet: there was a lag period of more than 30 d in co-cultures initiated with wild-type G. metallireducens
+ explanation: Wild-type baseline for the delay, measured in the G. metallireducens-M. barkeri ethanol coculture
+ that this record describes.
- reference: PMID:37650614
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: In contrast, there was very little lag in co-cultures initiated with the Hcp-deficient
- G. metallireducens strain
- explanation: Knockout arm of the perturbation - removing the T6SS structural protein Hcp
- largely removes the lag, which is the basis for the negative causal edge.
+ snippet: In contrast, there was very little lag in co-cultures initiated with the Hcp-deficient G. metallireducens
+ strain
+ explanation: Supports the hcp-deletion lag phenotype in the exact pair. Deletion changes more than the presence
+ of T6SS machinery, so the phenotype does not isolate a secretion-specific mechanism.
- reference: PMID:37650614
supports: SUPPORT
evidence_source: IN_VITRO
@@ -272,10 +242,10 @@ ecological_interactions:
- reference: PMID:37650614
supports: PARTIAL
evidence_source: IN_VITRO
- snippet: the mutant also reduced Fe(III) oxide faster than the wild-type strain, a phenotype
- not expected from the loss of the T6SS
- explanation: Records the pleiotropy confounder - the reason this edge is curated as
- T6SS-associated rather than T6SS-caused.
+ snippet: the mutant also reduced Fe(III) oxide faster than the wild-type strain, a phenotype not expected from
+ the loss of the T6SS
+ explanation: Records the pleiotropy confounder - the reason this edge is curated as T6SS-associated rather than
+ T6SS-caused.
environmental_factors:
- name: Anaerobic Conditions
value: Strict anaerobic
@@ -499,3 +469,42 @@ metals_present: []
metal_relevance: SIGNIFICANT
metal_notes: Metal/REE detected via environmental factor measurements; Metal/REE detected
via keyword matching in description (context-validated)
+discussions:
+- discussion_id: methanosarcina_entry_and_hcp_pleiotropy
+ prompt: Which electron-entry components and hcp-dependent changes govern this DIET partnership?
+ kind: KNOWLEDGE_GAP
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Ethanol Oxidation and Direct Electron Transfer
+ - ecological_interactions#DIET-Linked Carbon Dioxide Reduction to Methane
+ - ecological_interactions#Hcp-Associated Delay of DIET Establishment
+ rationale: Preserve the positive DIET and mutant-lag observations while separating genotype effects from secretion-specific
+ antagonism. Partner-specific perturbations and complementation in the methanogenic coculture would distinguish
+ proposed mechanisms. The Pelobacter/H2 comparator used a different medium and is not a selective same-medium
+ H2 switch. Methanosaeta radiotracer results must not be imported into this system. Non-graph uniqueness/aggregation
+ claims remain preserved, not certified.
+ posed_by: codex
+ posed_date: '2026-10-06'
+- discussion_id: methanosarcina_acetate_branch_curation
+ prompt: Complete the separately supported acetate branch after Edison review.
+ kind: CURATION_TODO
+ status: OPEN
+ attaches_to:
+ - ecological_interactions#Ethanol Oxidation and Direct Electron Transfer
+ - ecological_interactions#DIET-Linked Carbon Dioxide Reduction to Methane
+ - ecological_interactions#Hcp-Associated Delay of DIET Establishment
+ rationale: 'The primary paper supports an acetate contribution, but the graph still lacks that branch. A separate
+ one-community Edison dry run completed without API calls or credits; specific authorization and report inspection
+ remain pending under #1483. Add source-backed structure with its own evidence, without promoting ideal stoichiometry
+ to an isotope-measured fraction or claiming DIET-only growth. This repair remains needs_research.'
+ posed_by: codex
+ posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T12:49:51Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: 'Retain donor-to-partner DIET and condition-dependent pili/GAC evidence; correct the donor carbon reaction.;
+ Bound the existing methane node to CO2 reduction without universal uniqueness or DIET-only growth.; Retain the
+ exact hcp-lag phenotype and hypothetical negative arrow without niche partitioning, secretion or killing claims.
+ Repair #1481; extension remains #1483; reports/causal_graph_review/decisions/20261006-methanogens-batch46.yaml'
+ llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 850aab5b1..a9e34f6eb 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,17 @@ source-based self-adversarial review. These records are not independent approval
or proof that every graph is complete. The current inventory and summary distinguish
`reviewed`, `pending` and `needs_research`.
+## Batch46: Methanogen DIET Pairs
+
+[Decisions](decisions/20261006-methanogens-batch46.yaml),
+[validation](validation-20261006-batch46.json) and
+[self-adversarial review](adversarial-review-20261006-batch46.yaml) distinguish
+defined-coculture DIET evidence from environmental inference, bulk methane from
+its CO2 route, and the hcp mutant phenotype from T6SS-specific antagonism.
+Both records remain `needs_research`: the source-supported acetate branches
+are still missing under #1482 and #1483. Separate Edison dry runs spent no
+credits; paid research and report inspection remain pending.
+
## Batch45: Geobacter-Clostridium
[Decisions](decisions/20261006-clostridium-batch45.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261006-batch46.yaml b/reports/causal_graph_review/adversarial-review-20261006-batch46.yaml
new file mode 100644
index 000000000..f98e245cd
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261006-batch46.yaml
@@ -0,0 +1,184 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 038ac9ce75c9922efa357610386a34da7a313305
+scope:
+- kb/communities/Geobacter_Methanosaeta_DIET.yaml
+- kb/communities/Geobacter_Methanosarcina_DIET.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261006-methanogens-batch46.yaml
+validation_report: reports/causal_graph_review/validation-20261006-batch46.json
+findings:
+- issue: 1480
+ severity: P2
+ status: addressed_in_this_change
+ finding: Separate the donor reaction from aggregate formation and methane carbon allocation.; Retain
+ positive defined-coculture DIET while bounding aggregation and electron-entry claims.; Retain only
+ the CO2 methane route, explicitly not the missing acetate branch.
+ disposition: Close after protected main merge.
+- issue: 1482
+ severity: P2
+ status: open_incomplete_extension
+ finding: Source-supported acetate branch remains missing.
+ disposition: Keep open; complete authorized one-community Edison/report review and independently verified
+ curation before declaring the graph reviewed.
+- issue: 1481
+ severity: P2
+ status: addressed_in_this_change
+ finding: Retain donor-to-partner DIET and condition-dependent pili/GAC evidence; correct the donor carbon
+ reaction.; Bound the existing methane node to CO2 reduction without universal uniqueness or DIET-only
+ growth.; Retain the exact hcp-lag phenotype and hypothetical negative arrow without niche partitioning,
+ secretion or killing claims.
+ disposition: Close after protected main merge.
+- issue: 1483
+ severity: P2
+ status: open_incomplete_extension
+ finding: Source-supported acetate branch remains missing.
+ disposition: Keep open; complete authorized one-community Edison/report review and independently verified
+ curation before declaring the graph reviewed.
+adversarial_checks:
+- Both whole records, all six original nodes and all four arrows reviewed. Complete primary main bodies/Methods/captions
+ read for the two2014 studies and2023 T6SS study. Selected2014 figures inspected as specified in the
+ ledger; no2023 figure images, supplements, raw data or code audited.
+- 'Methanosaeta: replace environmental Geobacter/Methanosaeta concilii expression excerpts with independently
+ checked primary abstract excerpts about the defined G. metallireducens/M. harundinacea coculture. Preserve
+ positive DIET rather than demote demonstrated electron transfer to a generic hypothesis.'
+- 'Methanosaeta: distinguish the donor reaction, interspecies transfer and CO2 reduction. Pili-associated
+ initiation evidence is not a selective test of aggregate formation or direct measurement of conductivity
+ in these defined aggregates. Receiver proteins remain unresolved; both retained directions are bounded
+ to electron supply, not acetate-carbon routing.'
+- 'Methanosaeta: resolve the obsolete primary-access biological question using the primary figures, while
+ separately keeping the missing acetate graph branch OPEN under#1482. Roughly one-third CO2-derived methane
+ is a bounded stoichiometric/radiotracer interpretation, not an all-methane claim or an exact universal
+ fraction.'
+- 'Methanosarcina: retain the positive DIET and pilin/GAC evidence. Correct direct ethanol-carbon-to-CO2
+ wording; distinguish bulk methane from its CO2 route. Historical first-report wording does not mean
+ timeless uniqueness, and DIET-only growth without acetate was not established.'
+- 'Methanosarcina: preserve the exact hcp genotype/lag comparison but remove NICHE_PARTITIONING and unmeasured
+ secretion annotations. Discovery RNA-seq and GAC/AQDS controls involve G. sulfurreducens. Pleiotropic
+ EET changes prevent a selective T6SS-antagonism attribution; the retained negative arrow is explicitly
+ HYPOTHESIZED and refers to establishment timing, not killing.'
+- Do not import Methanosaeta radiotracer evidence into Methanosarcina. The Pelobacter/H2 comparator uses
+ a different medium, not a selective same-medium H2 switch. The inspected Gmet1868 curve has residual
+ methane; no new absolute zero-activity claim is added.
+- Both acetate branches remain incomplete, not silently absorbed into a CO2 node or declared unnecessary
+ for an easier passing graph. Both records remain needs_research under#1482/#1483. Separate dry runs
+ are hash-bound and cost0; no provider report, paid-job execution or authorization is fabricated.
+- Both graph diffs inspected. Two guarded records, two append-only histories and two regenerated pages.
+ All458 other records, all920 caches, taxonomy, non-graph raw blocks and prior histories preserved. Stronger
+ non-graph claims and the composite cached Methanosaeta Content are not certified.
+- All per-record gates passed;31 snippets match unchanged caches. Reference canaries included, but DOI
+ case-sensitivity and SupportingReference/provenance limitations remain explicit. Zero structural errors
+ and all34 prior network findings unchanged. Repeat renders deterministic and descriptions parser-checked
+ across456 pages without a browser screenshot claim.
+- Six focused tests plus historical/shared regressions passed. Canonical endpoints and explicit participants
+ preserved; registry and corrected connectivity census unchanged. No production auditor, ranker or census-bound
+ changes.
+- Dedup includes794 all-state issue titles/bodies and ignored/hidden local files;#1091/#751/#306 bodies
+ read. No duplication of existing cache/validator issues. Not every comment or PR review inspected.
+- Pre-source batch45 baseline and fresh pre-edit batch46 baseline distinguished. Selected record and all
+ cache hashes match across them. Self-adversarial review is not independent approval, graph expansion
+ completion or full-corpus completion. Exact-head COMMENT and actual post-commit docs-current remain
+ separate publication gates.
+verification:
+ combined_regressions: 461 passed in 211.31s (0:03:31)
+ new_regression_tests: 6
+ schema_strict_terms_history: Passed with actual outputs and digests
+ references: CLI Total checks counts reported issues, not executed checks. Both local runs exited0; this
+ does not certify Linux DOI-cache lookup (#1091), SupportingReference coverage (#476), independent
+ cache provenance (#1362) or scientific support.
+ snippet_counts_by_record:
+ kb/communities/Geobacter_Methanosaeta_DIET.yaml:
+ MATCH: 12
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ kb/communities/Geobacter_Methanosarcina_DIET.yaml:
+ MATCH: 19
+ RENDERING: 0
+ ASSEMBLED: 0
+ WEAK: 0
+ MISMATCH: 0
+ NOCONTENT: 0
+ network:
+ existing_findings_preserved: 34
+ added_findings: {}
+ removed_findings: {}
+ black_ruff_diff: passed
+ tested_file_sha256:
+ reports/causal_graph_review/decisions/20261006-methanogens-batch46.yaml: 655c8cf5bb1a6c8810c2afad82fb0083fe651ed4a72642857547fbe9483a2272
+ tests/test_causal_review_batch46.py: 83a759a575d1d3eaec5043dd25f2fd74a69939cbacf5cd32c7b1b3eff6b264cc
+ kb/communities/Geobacter_Methanosaeta_DIET.yaml: 8e194a9177b013c6db3e2dd9b4ed9744f06ca0379116f41a0f4ed62cf1d4fde1
+ kb/communities/Geobacter_Methanosarcina_DIET.yaml: b6b5f1714e6692936ca408e74dba44df4cbb9518a258c7c7203425998c2979e0
+ reports/causal_graph_review/README.md: 5ff428c05ffa0e218a58ab54d3551d32176e41a127fe0681fc19438d71f30ff2
+ post_commit_docs_current: Separate publication gate, not asserted before commit.
+participant_census:
+ measurements:
+ baseline:
+ records: 460
+ with_community_level: 388
+ mixed: 125
+ community_level_only: 263
+ taxa: 1496
+ credited_solely_by_the_rule: 1223
+ current:
+ records: 460
+ with_community_level: 388
+ mixed: 125
+ community_level_only: 263
+ taxa: 1496
+ credited_solely_by_the_rule: 1223
+ interpretation: Canonical endpoints and participants preserved; registry remains 194. No census bounds
+ or production matching logic changed.
+corpus:
+ records: 460
+ nodes: 1465
+ edges: 681
+ review_status_counts:
+ needs_research: 14
+ pending: 278
+ reviewed: 168
+edison:
+- community: Geobacter_Methanosaeta_DIET
+ issue: 1482
+ meta_path: /private/tmp/communitymech-batch45/edison/Geobacter_Methanosaeta_DIET-edison-literature-causal-meta.yaml
+ meta_sha256: 4a99808b7cd4b5ac10be8a8b63dfccb1f4c9e17d315966d3b38d31640867bb1d
+ query_sha256: e1f4b922bfcf60f8b40c0148c22b31e04c767f7ae8355be74783937c9a074b81
+ query_chars: 13233
+ job: LITERATURE
+ status: dry-run
+ provider_calls: 0
+ provider_credits_spent: 0
+ authorization: Specific async request pending; no paid run or report.
+- community: Geobacter_Methanosarcina_DIET
+ issue: 1483
+ meta_path: /private/tmp/communitymech-batch46/edison/Geobacter_Methanosarcina_DIET-edison-literature-causal-meta.yaml
+ meta_sha256: 14f5ea6d34fd2772d4721a607cc7321a4a981addce7ae479fa427c5973fe735d
+ query_sha256: 04978828f6bc783e3d6655b40e8ddc62d7f0eb9b50d1b777e6f770805442996c
+ query_chars: 13853
+ job: LITERATURE
+ status: dry-run
+ provider_calls: 0
+ provider_credits_spent: 0
+ authorization: Specific async request pending; no paid run or report.
+limitations:
+- Whole 445-line Methanosaeta and 501-line Methanosarcina records and all six nodes/four arrows reviewed.
+ Complete primary main bodies/Methods/captions read for both 2014 papers and the 2023 T6SS paper. Selected
+ 2014 Figures 2-5 (Methanosaeta) and 1-3 (Methanosarcina) inspected; no 2023 figure images, separate
+ supplements, raw data or analysis code audited.
+- 'Existing-node/edge repairs only. Both acetate branches remain unimplemented new causal structure under
+ #1482/#1483; both records remain needs_research. Two separate dry runs spent no credits and produced
+ no provider reports; specific paid-job authorization remains pending.'
+- Canonical taxonomy, all non-graph raw blocks, prior history and all 920 caches are preserved, not certified.
+ Selected updated Methanosaeta excerpts were independently checked in the actual primary abstract; its
+ cached composite Content is not certified as a faithful complete abstract. Full copyrighted PDFs remain
+ temporary, not committed.
+- Research began after the batch45 pre-source baseline at batch44 head. Both selected records and caches
+ are unchanged at the fresh batch46 pre-edit baseline; the latter is not falsely described as preceding
+ all source reading.
+- Reference CLI Total checks counts reported issues, not executed checks. SupportingReference coverage
+ remains incomplete (#476); DOI cache casing remains a cross-platform limitation (#1091), and textual
+ matching is not provenance or scientific support (#1362).
+- Source-based self-adversarial review is not independent approval; protected-main merge and full-corpus
+ completion remain pending.
diff --git a/reports/causal_graph_review/decisions/20261006-methanogens-batch46.yaml b/reports/causal_graph_review/decisions/20261006-methanogens-batch46.yaml
new file mode 100644
index 000000000..a88b8b558
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261006-methanogens-batch46.yaml
@@ -0,0 +1,256 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 038ac9ce75c9922efa357610386a34da7a313305
+baseline_commit: 038ac9ce75c9922efa357610386a34da7a313305
+base_tree: 3c84057a0efa0f1ca56f874dd8a7c7fab3ba0b8a
+issues:
+- 1480
+- 1481
+- 1482
+- 1483
+repair_issues:
+- 1480
+- 1481
+open_research_issues:
+- 1482
+- 1483
+issue_deduplication:
+ all_state_issue_titles_and_bodies: 794
+ ignored_hidden_local_search: true
+ relevant_bodies_read:
+ - 1091
+ - 751
+ - 306
+ local_matching_files: 12
+ limitations: Matches include prior render/audit logs and current inventory, not completed source-specific reviews.
+ Not every comment or PR review inspected.
+reference_cache_original_hashes:
+ references_cache/doi_10.1039_C3EE42189A.md: 49d5dd97f9a4ae9a613f4cee1fb126c322d0bed9ae41ec15715e6b00baf13462
+ references_cache/doi_10.1039_C3EE42189A.txt: 3ae93752c8660aa7755dbfe95d4e943228ed4a7226049f30c5a92bfe9e41e4b4
+ references_cache/doi_10.1039_C3EE42189A.json: 114f83f2081e7586b73b29531ed2de8fa8eda05cd101fa3a306a54bcb157f9c8
+ references_cache/PMID_24837373.txt: 51a1f3c88ee49aba3f391b6341f1d05b5f59c4ffbe3b249237c1b77ae0a28e7c
+ references_cache/PMID_37650614.txt: f8a5276dd4ad1447a6f1e912e5ef4033039a05c845c1be2bec0dc9a1444f1a87
+pre_source_baseline:
+ path: /private/tmp/communitymech-batch45/baseline.json
+ sha256: 1fbc4cd6eac3bc1409a8b8a9111c512119db46daee9d493e26474f74968ba58a
+ base_commit: 7bdc93828cb9585f0711253d58d7382037207010
+ selected_record_and_cache_hashes_match_current: true
+edison:
+- community: Geobacter_Methanosaeta_DIET
+ issue: 1482
+ meta_path: /private/tmp/communitymech-batch45/edison/Geobacter_Methanosaeta_DIET-edison-literature-causal-meta.yaml
+ meta_sha256: 4a99808b7cd4b5ac10be8a8b63dfccb1f4c9e17d315966d3b38d31640867bb1d
+ query_sha256: e1f4b922bfcf60f8b40c0148c22b31e04c767f7ae8355be74783937c9a074b81
+ query_chars: 13233
+ job: LITERATURE
+ status: dry-run
+ provider_calls: 0
+ provider_credits_spent: 0
+ authorization: Specific async request pending; no paid run or report.
+- community: Geobacter_Methanosarcina_DIET
+ issue: 1483
+ meta_path: /private/tmp/communitymech-batch46/edison/Geobacter_Methanosarcina_DIET-edison-literature-causal-meta.yaml
+ meta_sha256: 14f5ea6d34fd2772d4721a607cc7321a4a981addce7ae479fa427c5973fe735d
+ query_sha256: 04978828f6bc783e3d6655b40e8ddc62d7f0eb9b50d1b777e6f770805442996c
+ query_chars: 13853
+ job: LITERATURE
+ status: dry-run
+ provider_calls: 0
+ provider_credits_spent: 0
+ authorization: Specific async request pending; no paid run or report.
+limitations:
+- Whole 445-line Methanosaeta and 501-line Methanosarcina records and all six nodes/four arrows reviewed. Complete
+ primary main bodies/Methods/captions read for both 2014 papers and the 2023 T6SS paper. Selected 2014 Figures
+ 2-5 (Methanosaeta) and 1-3 (Methanosarcina) inspected; no 2023 figure images, separate supplements, raw data or
+ analysis code audited.
+- 'Existing-node/edge repairs only. Both acetate branches remain unimplemented new causal structure under #1482/#1483;
+ both records remain needs_research. Two separate dry runs spent no credits and produced no provider reports; specific
+ paid-job authorization remains pending.'
+- Canonical taxonomy, all non-graph raw blocks, prior history and all 920 caches are preserved, not certified. Selected
+ updated Methanosaeta excerpts were independently checked in the actual primary abstract; its cached composite
+ Content is not certified as a faithful complete abstract. Full copyrighted PDFs remain temporary, not committed.
+- Research began after the batch45 pre-source baseline at batch44 head. Both selected records and caches are unchanged
+ at the fresh batch46 pre-edit baseline; the latter is not falsely described as preceding all source reading.
+- Reference CLI Total checks counts reported issues, not executed checks. SupportingReference coverage remains incomplete
+ (#476); DOI cache casing remains a cross-platform limitation (#1091), and textual matching is not provenance or
+ scientific support (#1362).
+- Source-based self-adversarial review is not independent approval; protected-main merge and full-corpus completion
+ remain pending.
+records:
+- path: kb/communities/Geobacter_Methanosaeta_DIET.yaml
+ id: CommunityMech:000032
+ original_sha256: 3fc22ecba6b448dd63c54896e119773338b3e331d88be489b54bb1c58277fc6a
+ record_sha256: 8e194a9177b013c6db3e2dd9b4ed9744f06ca0379116f41a0f4ed62cf1d4fde1
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-methanogens-batch46.yaml
+ scope: Every original node/arrow assessed and repaired; source-supported missing acetate branch explicitly incomplete.
+ summary: Separate the donor reaction from aggregate formation and methane carbon allocation.; Retain positive
+ defined-coculture DIET while bounding aggregation and electron-entry claims.; Retain only the CO2 methane route,
+ explicitly not the missing acetate branch.
+ renamed_nodes:
+ Ethanol Oxidation and Direct Electron Transfer: Geobacter Ethanol Oxidation
+ Conductive Aggregate-Mediated DIET: DIET in Defined Coculture Aggregates
+ Direct Electron Acceptance and Methanogenesis: DIET-Linked Carbon Dioxide Reduction to Methane
+ node_decisions:
+ - node: Geobacter Ethanol Oxidation
+ rationale: Separate the donor reaction from aggregate formation and methane carbon allocation.
+ - node: DIET in Defined Coculture Aggregates
+ rationale: Retain positive defined-coculture DIET while bounding aggregation and electron-entry claims.
+ - node: DIET-Linked Carbon Dioxide Reduction to Methane
+ rationale: Retain only the CO2 methane route, explicitly not the missing acetate branch.
+ removed_node_decisions: []
+ edges_before:
+ - source: Ethanol Oxidation and Direct Electron Transfer
+ target: Conductive Aggregate-Mediated DIET
+ description: Ethanol metabolism and extracellular electron transfer by aggregate-associated Geobacter feed the
+ conductive aggregates where Geobacter and Methanosaeta exchange electrons by DIET.
+ - source: Conductive Aggregate-Mediated DIET
+ target: Direct Electron Acceptance and Methanogenesis
+ description: Conductive-aggregate electron transfer delivers electrons to M. harundinacea for carbon dioxide
+ reduction to methane.
+ edges_after:
+ - source: Geobacter Ethanol Oxidation
+ target: DIET in Defined Coculture Aggregates
+ description: Ethanol oxidation releases reducing equivalents that Geobacter supplies to the defined partner
+ through DIET. This arrow routes electron supply, not acetate carbon, and does not assert that ethanol oxidation
+ selectively causes aggregate formation.
+ - source: DIET in Defined Coculture Aggregates
+ target: DIET-Linked Carbon Dioxide Reduction to Methane
+ description: DIET supplies electrons for M. harundinacea CO2 reduction to methane, supported by the defined-coculture
+ radiotracer and pilA comparison. This direction does not allocate acetate-derived methane to the CO2 branch
+ or establish a particular methanogen entry protein.
+ retained_edge_decisions:
+ - source: Geobacter Ethanol Oxidation
+ target: DIET in Defined Coculture Aggregates
+ description: Ethanol oxidation releases reducing equivalents that Geobacter supplies to the defined partner
+ through DIET. This arrow routes electron supply, not acetate carbon, and does not assert that ethanol oxidation
+ selectively causes aggregate formation.
+ rationale: Retain defined-coculture electron supply and CO2 reduction, not selective aggregate necessity or
+ an acetate-carbon route.
+ - source: DIET in Defined Coculture Aggregates
+ target: DIET-Linked Carbon Dioxide Reduction to Methane
+ description: DIET supplies electrons for M. harundinacea CO2 reduction to methane, supported by the defined-coculture
+ radiotracer and pilA comparison. This direction does not allocate acetate-derived methane to the CO2 branch
+ or establish a particular methanogen entry protein.
+ rationale: Retain defined-coculture electron supply and CO2 reduction, not selective aggregate necessity or
+ an acetate-carbon route.
+ removed_edge_decisions: []
+ references:
+ - doi:10.1039/C3EE42189A
+ issues:
+ - 1480
+ - 1482
+ repair_issue: 1480
+ research_issue: 1482
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Geobacter_Methanosaeta_DIET/2026-10-06T124951Z-codex-b6123c.yaml
+ source_review:
+ doi:10.1039/C3EE42189A:
+ cache: references_cache/doi_10.1039_C3EE42189A.md
+ url: https://pdfs.semanticscholar.org/d55d/65d23dd2fac1ff913e959526f40f2d7ee5d0.pdf
+ primary_pdf: /private/tmp/communitymech-batch45/methanosaeta-primary.pdf
+ primary_sha256: 6932b5512bace814ae2ed86f9cb481ec11fa7f9411659aa02d03759cdb8b72cc
+ scope: Complete body/Methods/captions; Figures 2-5 inspected from PDF pages4/5. Transparent PNG background
+ limited body visibility, so body text was separately read. No separate supplements or raw data. Actual abstract
+ excerpts independently checked.
+ cache_sha256: 49d5dd97f9a4ae9a613f4cee1fb126c322d0bed9ae41ec15715e6b00baf13462
+- path: kb/communities/Geobacter_Methanosarcina_DIET.yaml
+ id: CommunityMech:000033
+ original_sha256: 3c1a692277d402834b3acc3d529d8abe87a2afe7a0ae03027aae66eff187a543
+ record_sha256: b6b5f1714e6692936ca408e74dba44df4cbb9518a258c7c7203425998c2979e0
+ status: needs_research
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261006-methanogens-batch46.yaml
+ scope: Every original node/arrow assessed and repaired; source-supported missing acetate branch explicitly incomplete.
+ summary: Retain donor-to-partner DIET and condition-dependent pili/GAC evidence; correct the donor carbon reaction.;
+ Bound the existing methane node to CO2 reduction without universal uniqueness or DIET-only growth.; Retain the
+ exact hcp-lag phenotype and hypothetical negative arrow without niche partitioning, secretion or killing claims.
+ renamed_nodes:
+ Direct Electron Acceptance and Methanogenesis: DIET-Linked Carbon Dioxide Reduction to Methane
+ T6SS-Associated Delay of DIET Establishment: Hcp-Associated Delay of DIET Establishment
+ node_decisions:
+ - node: Ethanol Oxidation and Direct Electron Transfer
+ rationale: Retain donor-to-partner DIET and condition-dependent pili/GAC evidence; correct the donor carbon
+ reaction.
+ - node: DIET-Linked Carbon Dioxide Reduction to Methane
+ rationale: Bound the existing methane node to CO2 reduction without universal uniqueness or DIET-only growth.
+ - node: Hcp-Associated Delay of DIET Establishment
+ rationale: Retain the exact hcp-lag phenotype and hypothetical negative arrow without niche partitioning, secretion
+ or killing claims.
+ removed_node_decisions: []
+ edges_before:
+ - source: Ethanol Oxidation and Direct Electron Transfer
+ target: Direct Electron Acceptance and Methanogenesis
+ description: Electrons transferred via DIET are accepted by M. barkeri for methanogenesis
+ - source: T6SS-Associated Delay of DIET Establishment
+ target: Ethanol Oxidation and Direct Electron Transfer
+ description: NEGATIVE edge - the wild-type T6SS-expressing state of G. metallireducens delays establishment
+ of the DIET partnership (>30 d lag vs very little lag for the Hcp-deficient mutant). Demonstrated by knockout
+ phenotype in this exact coculture, but the mutant is pleiotropic, so the causal attribution to the T6SS specifically
+ is HYPOTHESIZED rather than proven.
+ edges_after:
+ - source: Ethanol Oxidation and Direct Electron Transfer
+ target: DIET-Linked Carbon Dioxide Reduction to Methane
+ description: DIET delivers ethanol-derived electrons to M. barkeri for CO2 reduction. This electron-supply arrow
+ supports the CO2 route, not an attribution of all bulk methane to that route; acetate conversion is a separate
+ missing branch.
+ - source: Hcp-Associated Delay of DIET Establishment
+ target: Ethanol Oxidation and Direct Electron Transfer
+ description: 'HYPOTHESIZED NEGATIVE: The wild-type Hcp/T6SS-associated state may delay DIET establishment relative
+ to the hcp deletion strain. The exact coculture demonstrates a lag difference, but altered electron-transfer
+ physiology prevents assigning the delay selectively to T6SS antagonism. The sign refers to establishment timing,
+ not proven archaeal killing.'
+ retained_edge_decisions:
+ - source: Ethanol Oxidation and Direct Electron Transfer
+ target: DIET-Linked Carbon Dioxide Reduction to Methane
+ description: DIET delivers ethanol-derived electrons to M. barkeri for CO2 reduction. This electron-supply arrow
+ supports the CO2 route, not an attribution of all bulk methane to that route; acetate conversion is a separate
+ missing branch.
+ rationale: Retain the bounded source-backed electron-supply direction; the hcp-associated negative direction
+ remains explicitly HYPOTHESIZED and pleiotropy-limited.
+ - source: Hcp-Associated Delay of DIET Establishment
+ target: Ethanol Oxidation and Direct Electron Transfer
+ description: 'HYPOTHESIZED NEGATIVE: The wild-type Hcp/T6SS-associated state may delay DIET establishment relative
+ to the hcp deletion strain. The exact coculture demonstrates a lag difference, but altered electron-transfer
+ physiology prevents assigning the delay selectively to T6SS antagonism. The sign refers to establishment timing,
+ not proven archaeal killing.'
+ rationale: Retain the bounded source-backed electron-supply direction; the hcp-associated negative direction
+ remains explicitly HYPOTHESIZED and pleiotropy-limited.
+ removed_edge_decisions: []
+ references:
+ - PMID:24837373
+ - PMID:37650614
+ issues:
+ - 1481
+ - 1483
+ repair_issue: 1481
+ research_issue: 1483
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ curation_events_added: 1
+ history_files:
+ - history/records/Geobacter_Methanosarcina_DIET/2026-10-06T124951Z-codex-59a839.yaml
+ source_review:
+ PMID:24837373:
+ cache: references_cache/PMID_24837373.txt
+ url: https://protocols-files.s3.amazonaws.com/public/34a1ee6658ca764b1316f8c5129dedd263745006c6d75e75787d4763edf5ff16/bt5vbabx7.pdf
+ primary_pdf: /private/tmp/communitymech-batch45/methanosarcina-primary.pdf
+ primary_sha256: d6dd4a4309296ad0a611f3eaa8689a6561c3a6a5190431db871d3eabe6d9db77
+ scope: Complete body/Methods/captions from PDF pages1-5; Figures1-3 inspected. Pypdf escaped some math glyphs;
+ page4 JPEG inspected with white background. Gmet1868 Figure3b has residual methane, so no new zero-activity
+ claim. No Figure4 image, supplement or raw-data audit.
+ cache_sha256: 51a1f3c88ee49aba3f391b6341f1d05b5f59c4ffbe3b249237c1b77ae0a28e7c
+ PMID:37650614:
+ cache: references_cache/PMID_37650614.txt
+ scope: Complete appended main body/Methods/Table1/captions read. No figure images, separate supplements, raw
+ data or code inspected.
+ cache_sha256: f8a5276dd4ad1447a6f1e912e5ef4033039a05c845c1be2bec0dc9a1444f1a87
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 8372be4d8..c2dcb04f4 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -181,8 +181,8 @@ kb/communities/GLBRC_UFMP_Fermentation_Community.yaml CommunityMech:000029 0cd65
kb/communities/GOM_Oil_Degrading_Consortium.yaml CommunityMech:000030 90d4d45224abfc9829feb8fd1cabde320c410a7a843ea3410c89dda4852cc299 3 0 65.0 reports/causal_graph_review/decisions/20261006-three-records-batch44.yaml reviewed
kb/communities/Garlic_Pseudomonas_SynCom6.yaml CommunityMech:000095 0052209591a0d6d3e106ad27feaca9dde69645f9725f01ba63e41ebeb5c5c59c 1 0 65.0 reports/causal_graph_review/decisions/20261006-three-records-batch44.yaml reviewed
kb/communities/Geobacter_Clostridium_Interspecies_Electron_Transfer_Coculture.yaml CommunityMech:000031 2bfa8ffd6b7d147f3c471eb88aa26482f93b0cc8d7b23dc39838402715463329 2 1 75.0 reports/causal_graph_review/decisions/20261006-clostridium-batch45.yaml reviewed
-kb/communities/Geobacter_Methanosaeta_DIET.yaml CommunityMech:000032 3fc22ecba6b448dd63c54896e119773338b3e331d88be489b54bb1c58277fc6a 3 2 100.0 pending
-kb/communities/Geobacter_Methanosarcina_DIET.yaml CommunityMech:000033 3c1a692277d402834b3acc3d529d8abe87a2afe7a0ae03027aae66eff187a543 3 2 100.0 pending
+kb/communities/Geobacter_Methanosaeta_DIET.yaml CommunityMech:000032 8e194a9177b013c6db3e2dd9b4ed9744f06ca0379116f41a0f4ed62cf1d4fde1 3 2 93.3 reports/causal_graph_review/decisions/20261006-methanogens-batch46.yaml needs_research
+kb/communities/Geobacter_Methanosarcina_DIET.yaml CommunityMech:000033 b6b5f1714e6692936ca408e74dba44df4cbb9518a258c7c7203425998c2979e0 3 2 91.7 reports/causal_graph_review/decisions/20261006-methanogens-batch46.yaml needs_research
kb/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml CommunityMech:000201 dbef08d1731c382db77222a55e9b0ea021f739c52993a737a73b35007e328fb4 4 2 100.0 pending
kb/communities/Ginseng_CL95_Rusty_Root_Rot_Biocontrol_SynCom.yaml CommunityMech:000376 358bc325cdc09b37c2cb283713c5db68fd01c3bb70575abf798b0bd9b184e5f7 3 1 90.0 pending
kb/communities/Glutamicibacter_S11_Aquaculture_Nitrogen_Removal_SynCom.yaml CommunityMech:000411 c7f789620656b6c7973c5f27bff6b6fd11f024a978c803e45bdb17ea65c731e0 1 0 65.0 pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index f4e2527d2..04f737b35 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -7,8 +7,8 @@
"records_without_nodes": 8,
"records_without_edges": 148,
"review_status_counts": {
- "needs_research": 12,
- "pending": 280,
+ "needs_research": 14,
+ "pending": 278,
"reviewed": 168
},
"structural_defects": [],
diff --git a/reports/causal_graph_review/validation-20261006-batch46.json b/reports/causal_graph_review/validation-20261006-batch46.json
new file mode 100644
index 000000000..d56109ce0
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261006-batch46.json
@@ -0,0 +1,688 @@
+{
+ "base_commit": "038ac9ce75c9922efa357610386a34da7a313305",
+ "scope": [
+ "kb/communities/Geobacter_Methanosaeta_DIET.yaml",
+ "kb/communities/Geobacter_Methanosarcina_DIET.yaml"
+ ],
+ "reference_validator_version": "0.1.7",
+ "results": [
+ {
+ "check": "Geobacter_Methanosaeta_DIET-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Geobacter_Methanosaeta_DIET.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/Geobacter_Methanosaeta_DIET-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Geobacter_Methanosaeta_DIET-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch46/Geobacter_Methanosaeta_DIET-strict.tsv",
+ "kb/communities/Geobacter_Methanosaeta_DIET.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/Geobacter_Methanosaeta_DIET-strict.log",
+ "log_sha256": "ea47aaf30be22573c917da2e8f61334ec735cef04fd7fd080d6f433c2490e551",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch46/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch46/Geobacter_Methanosaeta_DIET-strict.tsv\n"
+ },
+ {
+ "check": "Geobacter_Methanosaeta_DIET-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Geobacter_Methanosaeta_DIET.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/Geobacter_Methanosaeta_DIET-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Geobacter_Methanosaeta_DIET-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Geobacter_Methanosaeta_DIET.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/Geobacter_Methanosaeta_DIET-references.log",
+ "log_sha256": "34506e06083e4a778c6f51e6db0c0b9313bced81ed8f85c1474f22556fb2322e",
+ "output_tail": "Validating kb/communities/Geobacter_Methanosaeta_DIET.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Geobacter_Methanosaeta_DIET.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Geobacter_Methanosaeta_DIET-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Geobacter_Methanosaeta_DIET.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/Geobacter_Methanosaeta_DIET-snippets.log",
+ "log_sha256": "389f1d2b093a1648cf407d53853e429a283f80eed2628a1a14cf1f38649ca780",
+ "output_tail": "# 12 evidence snippets scanned across 1 files\n MATCH 12\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Geobacter_Methanosaeta_DIET-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Geobacter_Methanosaeta_DIET.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/Geobacter_Methanosaeta_DIET-rank.log",
+ "log_sha256": "3989fd2e2192ecbe77f139e9d890eb1bbd203e230f4cb5963985035d9b2c3c87",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000032\",\n \"name\": \"Geobacter-Methanosaeta DIET Community\",\n \"score\": 93.3,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 3,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Geobacter_Methanosaeta_DIET.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Geobacter_Methanosaeta_DIET-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Geobacter_Methanosaeta_DIET/2026-10-06T124951Z-codex-b6123c.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/Geobacter_Methanosaeta_DIET-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Geobacter_Methanosarcina_DIET-schema",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "kb/communities/Geobacter_Methanosarcina_DIET.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/Geobacter_Methanosarcina_DIET-schema.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "Geobacter_Methanosarcina_DIET-strict",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+ "scripts/validate_strict.py",
+ "--workers",
+ "1",
+ "--out",
+ "/private/tmp/communitymech-batch46/Geobacter_Methanosarcina_DIET-strict.tsv",
+ "kb/communities/Geobacter_Methanosarcina_DIET.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/Geobacter_Methanosarcina_DIET-strict.log",
+ "log_sha256": "74655e80049b58ea02320192d17b1bb64d6126440e602b044c7f5061b8a75080",
+ "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch46/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n files scanned: 1\n files with ERROR: 0\n total ERROR rows: 0\n TSV: /private/tmp/communitymech-batch46/Geobacter_Methanosarcina_DIET-strict.tsv\n"
+ },
+ {
+ "check": "Geobacter_Methanosarcina_DIET-terms",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+ "validate-data",
+ "kb/communities/Geobacter_Methanosarcina_DIET.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--labels"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/Geobacter_Methanosarcina_DIET-terms.log",
+ "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+ "output_tail": "\u2705 Validation passed\n"
+ },
+ {
+ "check": "Geobacter_Methanosarcina_DIET-references",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+ "validate",
+ "data",
+ "kb/communities/Geobacter_Methanosarcina_DIET.yaml",
+ "-s",
+ "src/communitymech/schema/communitymech.yaml",
+ "--config",
+ "conf/reference_validator.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/Geobacter_Methanosarcina_DIET-references.log",
+ "log_sha256": "7fe4ff7fa3b6ec948d16133b9834902114e3ebd4655947ee0f54a8a34fa41297",
+ "output_tail": "Validating kb/communities/Geobacter_Methanosarcina_DIET.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n",
+ "explained_output_tail": "Validating kb/communities/Geobacter_Methanosarcina_DIET.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n Total checks: 0\n All validations passed!\n"
+ },
+ {
+ "check": "Geobacter_Methanosarcina_DIET-snippets",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/evidence_snippet_audit.py",
+ "kb/communities/Geobacter_Methanosarcina_DIET.yaml",
+ "--list-mismatch",
+ "--list-nocontent",
+ "--list-rendering",
+ "--list-assembled"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/Geobacter_Methanosarcina_DIET-snippets.log",
+ "log_sha256": "8084678f5cf248d78dd90bd74538a6320ef0dcc9940ae3e5b5f759e13588ade6",
+ "output_tail": "# 19 evidence snippets scanned across 1 files\n MATCH 19\n RENDERING 0\n ASSEMBLED 0\n WEAK 0\n MISMATCH 0\n NOCONTENT 0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+ },
+ {
+ "check": "Geobacter_Methanosarcina_DIET-rank",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "scripts/rank_causal_graph_readiness.py",
+ "kb/communities/Geobacter_Methanosarcina_DIET.yaml",
+ "--format",
+ "json"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/Geobacter_Methanosarcina_DIET-rank.log",
+ "log_sha256": "1c75003af31d8c20384e2d1c7d4083b509f6c701c77c4f2a5b606e30196d021c",
+ "output_tail": "[\n {\n \"rank\": 1,\n \"id\": \"CommunityMech:000033\",\n \"name\": \"Geobacter-Methanosarcina DIET Community\",\n \"score\": 91.7,\n \"taxonomy\": 2,\n \"connected_taxa\": 2,\n \"disconnected_taxa\": 0,\n \"ecological_interactions\": 3,\n \"downstream_edges\": 2,\n \"interaction_evidence\": 8,\n \"dangling_downstream\": 0,\n \"self_downstream\": 0,\n \"missing\": [\n \"metabolites_or_biological_processes\",\n \"interaction_type\"\n ],\n \"path\": \"kb/communities/Geobacter_Methanosarcina_DIET.yaml\"\n }\n]\n"
+ },
+ {
+ "check": "Geobacter_Methanosarcina_DIET-history-0",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+ "-s",
+ "src/communitymech/schema/history.yaml",
+ "--target-class",
+ "HistoryRecord",
+ "history/records/Geobacter_Methanosarcina_DIET/2026-10-06T124951Z-codex-59a839.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/Geobacter_Methanosarcina_DIET-history-0.log",
+ "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+ "output_tail": "No issues found\n"
+ },
+ {
+ "check": "inventory",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "reports/causal_graph_review/build_inventory.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/inventory.log",
+ "log_sha256": "096faa2cec5fe9cf77ddcc46dbdcd18764cf77e1e31faeaf7edcf83118ebbb34",
+ "output_tail": "{\n \"scope\": \"Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.\",\n \"semantic_review_rule\": \"Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.\",\n \"records\": 460,\n \"nodes\": 1465,\n \"edges\": 681,\n \"records_without_nodes\": 8,\n \"records_without_edges\": 148,\n \"review_status_counts\": {\n \"needs_research\": 14,\n \"pending\": 278,\n \"reviewed\": 168\n },\n \"structural_defects\": []\n}\n"
+ },
+ {
+ "check": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_codes": [
+ 1
+ ],
+ "log": "/private/tmp/communitymech-batch46/network.log",
+ "log_sha256": "71a1e46fdd5d7c44e1766fabc85efb996c70258e3e64018891cfa94bb22fb13e",
+ "output_tail": "{\n \"preferred_term\": \"Legionella MAGs\",\n \"term\": {\n \"id\": \"NCBITaxon:445\",\n \"label\": \"Legionella\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The study detected Legionella-affiliated MAGs and used them in a virulence-gene risk assessment; the source did not assert pathogenicity for a cultured Legionella isolate.\\n\"\n },\n \"abundance_value\": \"Lower-abundance Legionella-affiliated MAGs detected during metagenomic risk assessment.\\n\",\n \"evidence\": [\n {\n \"reference\": \"PMID:41457319\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"COMPUTATIONAL\",\n \"snippet\": \"detection of waterborne pathogens from the Legionella genus\",\n \"explanation\": \"Supports Legionella-affiliated lower-abundance bins as monitored biosafety-relevant members of the consortium.\\n\"\n }\n ]\n },\n \"message\": \"Taxon 'Legionella MAGs' has no interactions\"\n }\n ],\n \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n \"interaction_index\": 0,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n },\n {\n \"type\": \"UNKNOWN_TARGET\",\n \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n \"interaction_index\": 1,\n \"taxon\": \"Sclerotinia sclerotiorum\",\n \"severity\": \"warning\",\n \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n }\n ],\n \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Acinetobacter radioresistens 50V1\",\n \"taxon_id\": \"NCBITaxon:40216\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n \"term\": {\n \"id\": \"NCBITaxon:40216\",\n \"label\": \"Acinetobacter radioresistens\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"50V1\",\n \"genome_accession\": \"GCA_002834555.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n \"taxon_id\": \"NCBITaxon:1270\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n \"term\": {\n \"id\": \"NCBITaxon:1270\",\n \"label\": \"Micrococcus luteus\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"W4-Al-K1\",\n \"genome_accession\": \"GCA_057816565.1\"\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"taxon_id\": \"NCBITaxon:64702\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n \"term\": {\n \"id\": \"NCBITaxon:64702\",\n \"label\": \"Propionibacterium cyclohexanicum\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"TA-12T\",\n \"genome_accession\": \"GCA_900111365\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"16859\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n \"taxon_id\": \"NCBITaxon:219572\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n \"term\": {\n \"id\": \"NCBITaxon:219572\",\n \"label\": \"Pseudomonas antarctica\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"CMS 35T\",\n \"genome_accession\": \"GCA_010634845\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"15318\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n \"taxon_id\": \"NCBITaxon:29388\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n \"term\": {\n \"id\": \"NCBITaxon:29388\",\n \"label\": \"Staphylococcus capitis\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"K1-2-2-23\",\n \"genome_accession\": \"GCA_025272695\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"111179\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "check": "rank-all",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ ],
+ "log": "/private/tmp/communitymech-batch46/rank-all.log",
+ "log_sha256": "1507e9b330d05cd3b05d46a80e5e4fd68cfa7c01b2cf838fc341231a2998cc7a",
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Community\t6\t6\t0\t5\t3\t6\t\t0\t0\n441\t100.0\tkb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml\tCommunityMech:000106\tTobacco Chemotactic Biocontrol SynCom\t2\t2\t0\t3\t2\t4\t\t0\t0\n442\t100.0\tkb/communities/Tomato_Oxylipin_SynCom3.yaml\tCommunityMech:000107\tTomato Oxylipin-Protective SynCom3\t3\t3\t0\t3\t2\t4\t\t0\t0\n443\t100.0\tkb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml\tCommunityMech:000112\tTribromophenol Anaerobic Bioremediation SynCom\t3\t3\t0\t4\t3\t5\t\t0\t0\n444\t100.0\tkb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml\tCommunityMech:000188\tTrichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture\t3\t3\t0\t3\t2\t6\t\t0\t0\n445\t100.0\tkb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml\tCommunityMech:000205\tTrichoderma-E. coli Cellulosic Isobutanol 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Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "check": "render",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.render"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
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+ "log_sha256": "fb983ee0ab0886e62556c697cdb7129d52ea7939a7e257d0f11afeab9c4d3733",
+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch46/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch46/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch46/docs/index.html\n"
+ },
+ {
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+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
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+ "output_tail": "sm.html\n \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synechococcus_Bacillus_SPC.html\n \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synechococcus_Ecoli_SPC.html\n \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synechococcus_Saccharomyces_SPC.html\n \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Syntrophus_Benzoate_Degrader.html\n \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/THOR_Rhizosphere_Model_Community.html\n \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Tinto_River_Iron_Cycling_Community.html\n \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Tomato_Oxylipin_SynCom3.html\n \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Trichoderma_Lactate_Platform.html\n \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Urine_Nitrification_SynCom.html\n \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wheat_Consortium_C1.html\n \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wheat_Consortium_C6.html\n \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/hCom2_Complex_Gut_Microbiome.html\n \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch46/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch46/docs/communities\n \u2713 Generated browser at /private/tmp/communitymech-causal-batch46/docs/browser.html\n \u2713 Generated landing at /private/tmp/communitymech-causal-batch46/docs/index.html\n"
+ },
+ {
+ "check": "connectivity-survey",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-c",
+ "import json, pathlib, runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline', pathlib.Path('/private/tmp/communitymech-causal-batch45')), ('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda: paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/connectivity-survey.log",
+ "log_sha256": "b28cfbfa9c9d1c531ab7998c2146482d1b4c9b66d1d4876f30de4f7ddaeab904",
+ "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 388, \"mixed\": 125, \"community_level_only\": 263, \"taxa\": 1496, \"credited_solely_by_the_rule\": 1223}, \"current\": {\"records\": 460, \"with_community_level\": 388, \"mixed\": 125, \"community_level_only\": 263, \"taxa\": 1496, \"credited_solely_by_the_rule\": 1223}}\n"
+ },
+ {
+ "check": "regressions",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "pytest",
+ "-q",
+ "tests/test_causal_review_batch10.py",
+ "tests/test_causal_review_batch11.py",
+ "tests/test_causal_review_batch12.py",
+ "tests/test_causal_review_batch13.py",
+ "tests/test_causal_review_batch14.py",
+ "tests/test_causal_review_batch15.py",
+ "tests/test_causal_review_batch16.py",
+ "tests/test_causal_review_batch17.py",
+ "tests/test_causal_review_batch18.py",
+ "tests/test_causal_review_batch19.py",
+ "tests/test_causal_review_batch20.py",
+ "tests/test_causal_review_batch21.py",
+ "tests/test_causal_review_batch22.py",
+ "tests/test_causal_review_batch23.py",
+ "tests/test_causal_review_batch24.py",
+ "tests/test_causal_review_batch25.py",
+ "tests/test_causal_review_batch27.py",
+ "tests/test_causal_review_batch28.py",
+ "tests/test_causal_review_batch29.py",
+ "tests/test_causal_review_batch30.py",
+ "tests/test_causal_review_batch31.py",
+ "tests/test_causal_review_batch32.py",
+ "tests/test_causal_review_batch33.py",
+ "tests/test_causal_review_batch34.py",
+ "tests/test_causal_review_batch35.py",
+ "tests/test_causal_review_batch36.py",
+ "tests/test_causal_review_batch37.py",
+ "tests/test_causal_review_batch38.py",
+ "tests/test_causal_review_batch39.py",
+ "tests/test_causal_review_batch40.py",
+ "tests/test_causal_review_batch41.py",
+ "tests/test_causal_review_batch42.py",
+ "tests/test_causal_review_batch43.py",
+ "tests/test_causal_review_batch44.py",
+ "tests/test_causal_review_batch45.py",
+ "tests/test_causal_review_batch46.py",
+ "tests/test_causal_review_batch5.py",
+ "tests/test_causal_review_batch6.py",
+ "tests/test_causal_review_batch7.py",
+ "tests/test_causal_review_batch8.py",
+ "tests/test_causal_review_batch9.py",
+ "tests/test_site_audit_fixes.py",
+ "tests/test_causal_review_inventory.py",
+ "tests/test_rank_causal_graph_readiness.py",
+ "tests/test_network_auditor.py",
+ "tests/test_participating_taxa.py",
+ "tests/test_causal_descriptions_are_published.py",
+ "tests/test_published_pages_name_real_records.py",
+ "tests/test_reference_validator_actually_validates.py",
+ "tests/test_snippet_audit_artefact_classes.py",
+ "tests/test_reference_error_annotation.py",
+ "tests/test_community_level_connectivity_credit.py",
+ "tests/test_no_paywalled_text_in_repo.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/regressions.log",
+ "log_sha256": "40470c3c4377e5e721c5fd593bd1d23c10cf802c8b0a379e4e26f09f287ea1ed",
+ "output_tail": "........................................................................ [ 15%]\n........................................................................ [ 31%]\n........................................................................ [ 46%]\n........................................................................ [ 62%]\n........................................................................ [ 78%]\n........................................................................ [ 93%]\n............................. [100%]\n461 passed in 211.31s (0:03:31)\n"
+ },
+ {
+ "check": "black",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+ "--check",
+ "tests/test_causal_review_batch46.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/black.log",
+ "log_sha256": "1a56c7cd8457fd05d978cfbd139d7bfd86e86acaa9b57668e718ef8bccc0cf48",
+ "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n1 file would be left unchanged.\n"
+ },
+ {
+ "check": "ruff",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff",
+ "check",
+ "tests/test_causal_review_batch46.py"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/ruff.log",
+ "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+ "output_tail": "All checks passed!\n"
+ },
+ {
+ "check": "diff-check",
+ "command": [
+ "git",
+ "diff",
+ "--check"
+ ],
+ "exit_code": 0,
+ "expected_exit_codes": [
+ 0
+ ],
+ "log": "/private/tmp/communitymech-batch46/diff-check.log",
+ "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+ "output_tail": ""
+ }
+ ],
+ "limitations": [
+ "Whole 445-line Methanosaeta and 501-line Methanosarcina records and all six nodes/four arrows reviewed. Complete primary main bodies/Methods/captions read for both 2014 papers and the 2023 T6SS paper. Selected 2014 Figures 2-5 (Methanosaeta) and 1-3 (Methanosarcina) inspected; no 2023 figure images, separate supplements, raw data or analysis code audited.",
+ "Existing-node/edge repairs only. Both acetate branches remain unimplemented new causal structure under #1482/#1483; both records remain needs_research. Two separate dry runs spent no credits and produced no provider reports; specific paid-job authorization remains pending.",
+ "Canonical taxonomy, all non-graph raw blocks, prior history and all 920 caches are preserved, not certified. Selected updated Methanosaeta excerpts were independently checked in the actual primary abstract; its cached composite Content is not certified as a faithful complete abstract. Full copyrighted PDFs remain temporary, not committed.",
+ "Research began after the batch45 pre-source baseline at batch44 head. Both selected records and caches are unchanged at the fresh batch46 pre-edit baseline; the latter is not falsely described as preceding all source reading.",
+ "Reference CLI Total checks counts reported issues, not executed checks. SupportingReference coverage remains incomplete (#476); DOI cache casing remains a cross-platform limitation (#1091), and textual matching is not provenance or scientific support (#1362).",
+ "Source-based self-adversarial review is not independent approval; protected-main merge and full-corpus completion remain pending.",
+ "HTML descriptions checked by exact parser and repeat renders, not browser screenshots. Post-commit docs-current is a separate publication gate.",
+ "CLI Total checks counts reported issues, not executed checks. Both local runs exited0; this does not certify Linux DOI-cache lookup (#1091), SupportingReference coverage (#476), independent cache provenance (#1362) or scientific support."
+ ],
+ "snippet_counts_by_record": {
+ "kb/communities/Geobacter_Methanosaeta_DIET.yaml": {
+ "MATCH": 12,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ },
+ "kb/communities/Geobacter_Methanosarcina_DIET.yaml": {
+ "MATCH": 19,
+ "RENDERING": 0,
+ "ASSEMBLED": 0,
+ "WEAK": 0,
+ "MISMATCH": 0,
+ "NOCONTENT": 0
+ }
+ },
+ "unchanged_raw_blocks": 30,
+ "unchanged_record_files": 458,
+ "unchanged_cache_files": 920,
+ "network_delta": {
+ "existing_findings_preserved": 34,
+ "added_findings": {},
+ "removed_findings": {}
+ },
+ "render_determinism": true,
+ "published_description_coverage": {
+ "pages": 456,
+ "nodes": 1451,
+ "arrows": 673
+ },
+ "participant_census": {
+ "measurements": {
+ "baseline": {
+ "records": 460,
+ "with_community_level": 388,
+ "mixed": 125,
+ "community_level_only": 263,
+ "taxa": 1496,
+ "credited_solely_by_the_rule": 1223
+ },
+ "current": {
+ "records": 460,
+ "with_community_level": 388,
+ "mixed": 125,
+ "community_level_only": 263,
+ "taxa": 1496,
+ "credited_solely_by_the_rule": 1223
+ }
+ },
+ "interpretation": "Canonical endpoints and participants preserved; registry remains 194. No census bounds or production matching logic changed."
+ },
+ "corpus": {
+ "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+ "records": 460,
+ "nodes": 1465,
+ "edges": 681,
+ "records_without_nodes": 8,
+ "records_without_edges": 148,
+ "review_status_counts": {
+ "needs_research": 14,
+ "pending": 278,
+ "reviewed": 168
+ },
+ "structural_defects": []
+ },
+ "tested_file_sha256": {
+ "reports/causal_graph_review/decisions/20261006-methanogens-batch46.yaml": "655c8cf5bb1a6c8810c2afad82fb0083fe651ed4a72642857547fbe9483a2272",
+ "tests/test_causal_review_batch46.py": "83a759a575d1d3eaec5043dd25f2fd74a69939cbacf5cd32c7b1b3eff6b264cc",
+ "kb/communities/Geobacter_Methanosaeta_DIET.yaml": "8e194a9177b013c6db3e2dd9b4ed9744f06ca0379116f41a0f4ed62cf1d4fde1",
+ "kb/communities/Geobacter_Methanosarcina_DIET.yaml": "b6b5f1714e6692936ca408e74dba44df4cbb9518a258c7c7203425998c2979e0",
+ "reports/causal_graph_review/README.md": "5ff428c05ffa0e218a58ab54d3551d32176e41a127fe0681fc19438d71f30ff2"
+ },
+ "status": "verified_methanogen_repairs_extensions_pending",
+ "reference_validator_caveat": "CLI Total checks counts reported issues, not executed checks. Both local runs exited0; this does not certify Linux DOI-cache lookup (#1091), SupportingReference coverage (#476), independent cache provenance (#1362) or scientific support.",
+ "pre_edit_baseline": {
+ "base_commit": "038ac9ce75c9922efa357610386a34da7a313305",
+ "base_tree": "3c84057a0efa0f1ca56f874dd8a7c7fab3ba0b8a",
+ "research_worktree": "/private/tmp/communitymech-causal-batch45",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch46/baseline-rank.log",
+ "sha256": "98b6e120a953c9bbac34d30ce25284de78649efdfcee03dffaf3df3e6cfffb93",
+ "output_tail": "/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch46/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "name": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_code": 1,
+ "log": "/private/tmp/communitymech-batch46/baseline-network.log",
+ "sha256": "71a1e46fdd5d7c44e1766fabc85efb996c70258e3e64018891cfa94bb22fb13e",
+ "output_tail": " \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "name": "downstream",
+ "command": [
+ "rg",
+ "--no-ignore",
+ "--hidden",
+ "-n",
+ "downstream:",
+ "kb/communities",
+ "data/isolates",
+ "--glob",
+ "*.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch46/baseline-downstream.log",
+ "sha256": "094f83f05058c6159432ce2029a3af8a578a28bc5b07a4f1784d48f29c801f12",
+ "output_tail": "um_EPS_SynCom.yaml:183: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:138: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:182: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:232: downstream:\nkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml:223: downstream:\nkb/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.yaml:157: downstream:\nkb/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.yaml:203: downstream:\nkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml:342: downstream:\nkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml:381: downstream:\nkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml:199: downstream:\nkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml:267: downstream:\nkb/communities/PMI_Variovorax_Thermotolerance_Collection.yaml:330: downstream:\nkb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml:268: downstream:\nkb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml:315: downstream:\nkb/communities/SMutans_VParvula_ASC_Biofilm.yaml:131: downstream:\nkb/communities/SMutans_VParvula_ASC_Biofilm.yaml:179: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:65: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:98: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:131: downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:155: downstream:\nkb/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml:285: downstream:\nkb/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml:324: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:207: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:249: downstream:\nkb/communities/Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession.yaml:197: downstream:\nkb/communities/Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession.yaml:241: downstream:\n"
+ }
+ ],
+ "baseline_sha256": "c305c9ea9d6339450b6bd645e7bdda56ad849857990b0a5688bf141640289945"
+ },
+ "pre_source_baseline": {
+ "base_commit": "7bdc93828cb9585f0711253d58d7382037207010",
+ "base_tree": "ae873b509fa12c69970cbafa96265ab9d55b8eb5",
+ "research_worktree": "/private/tmp/communitymech-causal-batch44",
+ "checks": [
+ {
+ "name": "rank",
+ "command": [
+ "just",
+ "rank-causal-graphs"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch45/baseline-rank.log",
+ "sha256": "ce6fef3958bc7649c0383bc1c7d39608bf5d44e524e4a22a24d7c0a287d8267b",
+ "output_tail": "/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+ },
+ {
+ "name": "just-network",
+ "command": [
+ "just",
+ "audit-network-json"
+ ],
+ "exit_code": 2,
+ "expected_exit_code": 2,
+ "log": "/private/tmp/communitymech-batch45/baseline-just-network.log",
+ "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+ "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+ },
+ {
+ "name": "network",
+ "command": [
+ "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+ "-m",
+ "communitymech.cli",
+ "audit-network",
+ "--json"
+ ],
+ "exit_code": 1,
+ "expected_exit_code": 1,
+ "log": "/private/tmp/communitymech-batch45/baseline-network.log",
+ "sha256": "71a1e46fdd5d7c44e1766fabc85efb996c70258e3e64018891cfa94bb22fb13e",
+ "output_tail": " \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n },\n {\n \"type\": \"DISCONNECTED\",\n \"taxon\": \"Streptococcus halotolerans HTS9T\",\n \"taxon_id\": \"NCBITaxon:1814128\",\n \"taxon_data\": {\n \"taxon_term\": {\n \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n \"term\": {\n \"id\": \"NCBITaxon:1814128\",\n \"label\": \"Streptococcus halotolerans\"\n },\n \"gtdb_grounding_status\": \"UNRESOLVED\",\n \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n },\n \"strain_designation\": {\n \"strain_name\": \"HTS9T\",\n \"genome_accession\": \"GCA_001598035\",\n \"culture_collections\": [\n {\n \"collection\": \"DSM\",\n \"accession\": \"101996\"\n }\n ]\n },\n \"evidence\": [\n {\n \"reference\": \"PMID:42577390\",\n \"supports\": \"SUPPORT\",\n \"evidence_source\": \"IN_VITRO\",\n \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n }\n ]\n },\n \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n }\n ]\n}\n"
+ },
+ {
+ "name": "downstream",
+ "command": [
+ "rg",
+ "--no-ignore",
+ "--hidden",
+ "-n",
+ "downstream:",
+ "kb/communities",
+ "data/isolates",
+ "--glob",
+ "*.yaml"
+ ],
+ "exit_code": 0,
+ "expected_exit_code": 0,
+ "log": "/private/tmp/communitymech-batch45/baseline-downstream.log",
+ "sha256": "0fc94c13bb307f3165477cfe9e0857808f63b133314aa5013d142ee1af1183cc",
+ "output_tail": "7: downstream:\nkb/communities/At_RSPHERE_SynCom.yaml:249: downstream:\nkb/communities/Chlamydomonas_Bacterial_H2_Consortium.yaml:311: downstream:\nkb/communities/Chlamydomonas_Bacterial_H2_Consortium.yaml:365: downstream:\nkb/communities/Shewanella_Streptococcus_Starch_Microbial_Fuel_Cell.yaml:140: downstream:\nkb/communities/Shewanella_Streptococcus_Starch_Microbial_Fuel_Cell.yaml:221: downstream:\nkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml:104: downstream:\nkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml:127: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:138: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:182: downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:232: downstream:\nkb/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml:285: downstream:\nkb/communities/Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml:324: downstream:\nkb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml:336: downstream:\nkb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml:125: downstream:\nkb/communities/KBase_ORT_Workflow_Community_Model.yaml:170: downstream:\nkb/communities/KBase_ORT_Workflow_Community_Model.yaml:261: downstream:\nkb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml:98: downstream:\nkb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml:155: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:135: downstream:\nkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml:177: downstream:\nkb/communities/Salar_Atacama_Lithium_Brine_Community.yaml:295: downstream:\nkb/communities/Salar_Atacama_Lithium_Brine_Community.yaml:339: downstream:\nkb/communities/High_Ammonia_Biogas_0B_Butyrate_Oxidizing_Enrichment.yaml:233: downstream:\nkb/communities/Groundwater_Elusimicrobia_Diverse_Metabolisms.yaml:96: downstream:\n"
+ }
+ ],
+ "baseline_sha256": "1fbc4cd6eac3bc1409a8b8a9111c512119db46daee9d493e26474f74968ba58a"
+ }
+}
diff --git a/tests/test_causal_review_batch46.py b/tests/test_causal_review_batch46.py
new file mode 100644
index 000000000..3362caf50
--- /dev/null
+++ b/tests/test_causal_review_batch46.py
@@ -0,0 +1,116 @@
+"""Keep positive DIET evidence, exact systems and unfinished acetate branches distinct."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261006-methanogens-batch46.yaml"
+
+
+def records():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ return ledger, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in ledger["records"]]
+
+
+def test_methanosaeta_uses_defined_coculture_evidence_without_aggregate_necessity():
+ _, (doc, _) = records()
+ donor, transfer, methane = doc["ecological_interactions"]
+ assert donor["name"] == "Geobacter Ethanol Oxidation"
+ assert "not a claim" in donor["description"]
+ assert "Aggregate formation itself was not selectively perturbed" in transfer["description"]
+ assert "Methanosaeta concilii" in transfer["description"]
+ assert "methanogen electron-entry components remain unresolved" in transfer["description"]
+ assert "roughly one-third" in methane["description"]
+ assert "not all methane" in methane["description"]
+ assert "missing acetate branch" in methane["description"]
+ assert donor["downstream"][0]["target"] == transfer["name"]
+ assert transfer["downstream"][0]["target"] == methane["name"]
+ assert "not acetate carbon" in donor["downstream"][0]["description"]
+ assert "interaction_type" not in donor and "interaction_type" not in methane
+ assert transfer["interaction_type"] == "SYNTROPHY"
+ for node in doc["ecological_interactions"]:
+ assert node["evidence"][0]["supports"] == "SUPPORT"
+ assert "most abundant bacteria" not in node["evidence"][0]["snippet"]
+
+
+def test_resolving_source_access_does_not_complete_the_missing_branch():
+ ledger, (doc, _) = records()
+ resolved, mechanism, todo = doc["discussions"]
+ assert resolved["discussion_id"] == "kg-geobacter-methanosaeta-acetate-route-unresolved"
+ assert resolved["status"] == "RESOLVED"
+ assert resolved["resolved_date"] == "2026-10-06"
+ assert "#1482" in resolved["resolution_note"]
+ assert "does not mark the graph complete" in resolved["resolution_note"]
+ assert mechanism["kind"] == "KNOWLEDGE_GAP" and mechanism["status"] == "OPEN"
+ assert todo["kind"] == "CURATION_TODO" and todo["status"] == "OPEN"
+ names = {n["name"] for n in doc["ecological_interactions"]}
+ for discussion in doc["discussions"]:
+ assert all(a.split("#", 1)[1] in names for a in discussion["attaches_to"])
+ assert ledger["records"][0]["status"] == "needs_research"
+
+
+def test_methanosarcina_preserves_positive_diet_without_total_methane_overclaim():
+ _, (_, doc) = records()
+ donor, methane, _ = doc["ecological_interactions"]
+ assert "oxidizes ethanol to acetate" in donor["description"]
+ assert "condition-dependent" in donor["description"]
+ assert "granular activated carbon" in donor["description"]
+ assert "not an isotope measurement" in methane["description"]
+ assert "historical, not timeless uniqueness" in methane["description"]
+ assert "proposed for future testing" in methane["description"]
+ assert donor["downstream"][0]["target"] == methane["name"]
+ assert donor["evidence"][0]["supports"] == "SUPPORT"
+ assert methane["participating_taxa"][1]["term"] == doc["taxonomy"][1]["taxon_term"]["term"]
+
+
+def test_hcp_phenotype_is_not_niche_partitioning_secretion_or_selective_antagonism():
+ _, (_, doc) = records()
+ donor, _, hcp = doc["ecological_interactions"]
+ assert hcp["name"] == "Hcp-Associated Delay of DIET Establishment"
+ for field in ["interaction_type", "source_taxon", "biological_processes"]:
+ assert field not in hcp
+ assert "G. sulfurreducens partner, not M. barkeri" in hcp["description"]
+ assert "expose pleiotropy" in hcp["description"]
+ assert "protein secretion or killing was not measured" in hcp["description"]
+ arrow = hcp["downstream"][0]
+ assert arrow["description"].startswith("HYPOTHESIZED NEGATIVE:")
+ assert arrow["target"] == donor["name"]
+ assert "establishment timing" in arrow["description"]
+ assert [e["supports"] for e in hcp["evidence"]] == ["SUPPORT"] * 3 + ["PARTIAL"]
+ assert "different medium" in doc["discussions"][0]["rationale"]
+ assert "radiotracer results must not be imported" in doc["discussions"][0]["rationale"]
+
+
+def test_every_existing_node_and_arrow_has_a_decision_but_expansion_is_open():
+ ledger, docs = records()
+ assert ledger["review_mode"] == "source_based_self_adversarial_review"
+ assert ledger["independent_approval"] is False
+ assert ledger["repair_issues"] == [1480, 1481]
+ assert ledger["open_research_issues"] == [1482, 1483]
+ assert sum(len(r["node_decisions"]) for r in ledger["records"]) == 6
+ assert sum(len(r["retained_edge_decisions"]) for r in ledger["records"]) == 4
+ for row, doc in zip(ledger["records"], docs, strict=True):
+ assert row["status"] == "needs_research"
+ assert not row["removed_node_decisions"] and not row["removed_edge_decisions"]
+ assert len(row["edges_before"]) == len(row["edges_after"]) == 2
+ assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+ assert len(row["history_files"]) == 1 and (ROOT / row["history_files"][0]).is_file()
+ assert doc["curation_history"][-1]["llm_assisted"] is True
+ assert doc["discussions"][-1]["kind"] == "CURATION_TODO"
+
+
+def test_sources_and_separate_dry_runs_do_not_claim_paid_reports():
+ ledger, _ = records()
+ assert ledger["issue_deduplication"]["ignored_hidden_local_search"] is True
+ assert ledger["pre_source_baseline"]["selected_record_and_cache_hashes_match_current"]
+ for path, digest in ledger["reference_cache_original_hashes"].items():
+ assert hashlib.sha256((ROOT / path).read_bytes()).hexdigest() == digest
+ assert [d["query_chars"] for d in ledger["edison"]] == [13233, 13853]
+ for dryrun in ledger["edison"]:
+ assert dryrun["status"] == "dry-run"
+ assert dryrun["provider_calls"] == dryrun["provider_credits_spent"] == 0
+ assert len(dryrun["meta_sha256"]) == len(dryrun["query_sha256"]) == 64
+ assert any("non-graph raw blocks" in s for s in ledger["limitations"])
+ assert any("#1091" in s for s in ledger["limitations"])