Protocol

Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge)

Each submission's list of taxa and predicted causal pathogen, compared with CCHFV.

Overview

Each submission's list of taxa and predicted causal pathogen, compared with CCHFV.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

8 recorded evaluations, 16 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

8 evaluations · 16 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CCMetagen v1.1.3 (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	yes success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source CCMetagen v1.1.3: CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell B12, row 'CCMetagen v1.1.3', column 'Causal pathogen in submitted list of taxa'
Configuration: CCMetagen v1.1.3 (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	yes success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source CCMetagen v1.1.3: CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell C12, row 'CCMetagen v1.1.3', column 'Predicted causal pathogen'
Configuration: LSHVec (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	no success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source LSHVec: CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell B5, row 'LSHVec', column 'Causal pathogen in submitted list of taxa'
Configuration: LSHVec (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	no success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source LSHVec: CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell C5, row 'LSHVec', column 'Predicted causal pathogen'
Configuration: MetaPhlAn v2.2.0 (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	yes success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source MetaPhlAn v2.2.0: CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell B6, row 'MetaPhlAn v2.2.0', column 'Causal pathogen in submitted list of taxa'
Configuration: MetaPhlAn v2.2.0 (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	yes success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source MetaPhlAn v2.2.0: CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell C6, row 'MetaPhlAn v2.2.0', column 'Predicted causal pathogen'
Configuration: MetaPhlAn v2.9.14 (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	no success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source MetaPhlAn v2.9.14: CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell B7, row 'MetaPhlAn v2.9.14', column 'Causal pathogen in submitted list of taxa'
Configuration: MetaPhlAn v2.9.14 (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	no success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source MetaPhlAn v2.9.14: CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell C7, row 'MetaPhlAn v2.9.14', column 'Predicted causal pathogen'
Configuration: MetaPhyler v1.25 (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	no success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source MetaPhyler v1.25: CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell B8, row 'MetaPhyler v1.25', column 'Causal pathogen in submitted list of taxa'
Configuration: MetaPhyler v1.25 (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	no success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source MetaPhyler v1.25: CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell C8, row 'MetaPhyler v1.25', column 'Predicted causal pathogen'
Configuration: NSSAC (assembly) (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	no success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source NSSAC (assembly): CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell B10, row 'NSSAC (assembly)', column 'Causal pathogen in submitted list of taxa'
Configuration: NSSAC (assembly) (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	no success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source NSSAC (assembly): CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell C10, row 'NSSAC (assembly)', column 'Predicted causal pathogen'
Configuration: NSSAC (full genome) (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	no success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source NSSAC (full genome): CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell B9, row 'NSSAC (full genome)', column 'Causal pathogen in submitted list of taxa'
Configuration: NSSAC (full genome) (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	no success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source NSSAC (full genome): CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell C9, row 'NSSAC (full genome)', column 'Predicted causal pathogen'
Configuration: Pathoscope v2.0.7 (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	no success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source Pathoscope v2.0.7: CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell B11, row 'Pathoscope v2.0.7', column 'Causal pathogen in submitted list of taxa'
Configuration: Pathoscope v2.0.7 (CAMI II pathogen challenge submission)	Protocol: Identify all pathogens and the causal pathogen in one clinical blood metagenome (CAMI II clinical pathogen challenge) Dataset: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever	no success-rate unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source Pathoscope v2.0.7: CAMI II clinical pathogen challenge rna-pathogen-20261009-protocol-meyer2022-causal-pathogen Aggregation: Not reported Meyer et al. 2022, Supplementary Tables 1-40 · Supplementary Table 39 cell C11, row 'Pathoscope v2.0.7', column 'Predicted causal pathogen'

Source checking is not independent reproduction. Release 2026-10-09-8cc1db47c7f9.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

unreported: 8

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Protocol-valid abundance or assignment control

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Conventional reference-database method with pinned taxonomy/database

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This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-09-8cc1db47c7f9. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

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Strengths, limitations and unresolved questions

Evidence

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Evidence table

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Sources and history

Release 2026-10-09-8cc1db47c7f9 · Record review: source checked

2 source records and release history

Critical Assessment of Metagenome Interpretation: the second round of challenges · Original source · Nature Methods 19(4):429, published 2022-04-08; PMC9007738 full-text XML
Meyer et al. 2022, Supplementary Tables 1-40 · Original source · 41592_2022_1431_MOESM3_ESM.xlsx (Supplementary Tables), as linked from the article XML <supplementary-material id="MOESM3">

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Technical metadata and extraction receipts

Stable ID: rna-pathogen-20261009-protocol-meyer2022-causal-pathogen

areas: microbes-communities
contexts: clinical_research
protocol: Participants received the metagenome and a case description and submitted all pathogens found and the one most likely to cause the symptoms. Scored as whether CCHFV appears in the submitted taxa and whether it is the predicted causal pathogen.
version: Supplementary Table 39
denominator: 1
source locator: Results 'Clinical pathogen prediction: a concept challenge'; Methods 'Challenge datasets' paragraph 5 and 'Challenge organization'
limitations: One sample; the causal role of CCHFV is the most plausible explanation, not clinically proven (Methods).; Submissions were manually curated and not reproducible.; No false-positive or contamination scoring is printed; the number of taxa per submission is in Supplementary Fig. 16 only.
missing metadata: uncertainty: reason: inapplicable; note: Single categorical outcome per submission

Related records

uses data: CAMI II clinical pathogen challenge: blood metagenome from a patient with haemorrhagic fever
assessment: CCMetagen v1.1.3: CAMI II clinical pathogen challenge
assessment: LSHVec: CAMI II clinical pathogen challenge
assessment: MetaPhlAn v2.2.0: CAMI II clinical pathogen challenge
assessment: MetaPhlAn v2.9.14: CAMI II clinical pathogen challenge
assessment: MetaPhyler v1.25: CAMI II clinical pathogen challenge
assessment: NSSAC (assembly): CAMI II clinical pathogen challenge
assessment: NSSAC (full genome): CAMI II clinical pathogen challenge
assessment: Pathoscope v2.0.7: CAMI II clinical pathogen challenge
assessed by: Select an RNA pathogen-detection workflow for diagnostic testing

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