5 tool steps across 3 unique tools, including tools inside nested subworkflows. A plus sign denotes parallel branches.
Workflow
Compose text parameter value + MitoHiFi→MitoHiFi→Compress file(s)
Complete query
The full task shown to the agent, excluding execution-condition instructions.
Assemble the complete mitochondrial genome of `Eutresis hypereia` from the provided PacBio HiFi reads.
Write the assembled mitochondrial nucleotide sequence to `final_answer/mitogenome.fasta.gz` as a gzip-compressed FASTA containing exactly one non-empty, nonredundant sequence record.
acc evaluator
acc compares the final output files with the reference outputs.
Metric
canonical_kmer_f1
Definition
Compare the 31-base DNA fragments in the submitted assembly with the reference, treating opposite DNA strands as equivalent and counting repeated fragments by their number of occurrences. Precision measures how much of the submitted sequence matches; recall measures how much of the reference is covered. F1 combines the two. Missing or extra sequence lowers the score.
Formula
Final scoreS = F1(M, C, R)
Canonical 31-mer multiplicities are the matching units.
Multiset matchM = Σ_k min(n_C(k), n_R(k)); C = Σ_k n_C(k); R = Σ_k n_R(k)
Each k is the lexicographically canonical form of a 31-mer and its reverse complement.
Record constraintnumber of nonempty FASTA records = 1
This is a validity requirement evaluated before the k-mer score.
Analysis stages
The run records show the assembly, candidate-selection and final-file stages. The reported acc score evaluates the submitted mitochondrial sequence.
Step 1Use the PacBio HiFi reads to produce one or more mitochondrial assembly candidates.
A successful assembly or equivalent read-derived reconstruction used the provided PacBio HiFi reads.
One or more mitochondrial candidate contigs/sequences were produced from that execution.
Step 2Identify and resolve one complete, nonredundant mitochondrial sequence, including checks for competing contigs, redundant ends, and completeness.
Competing mitochondrial candidate contigs were compared or ruled out.
Circular/redundant terminal overlap was checked and removed without duplicating sequence.
Completeness was assessed using length, expected mitochondrial features, read support, or an equivalently defensible check.
Exactly one complete nonredundant sequence was selected from the read-derived candidates.
Step 3Write exactly one nonempty mitochondrial FASTA record and gzip it.
The gzip file is readable and contains exactly one nonempty FASTA record.
The record is the sequence selected in step 2 and passes final-answer checks.
Model results and score explanations
17 assemblies differed from the reference under the original scoring rule. Their explanations below report the measured DNA-fragment differences. Each replicate shows its recorded workflow, acc and Hugging Face trace. Galaxy histories can be imported by link but are not published in Galaxy's public history listing.
GPT-5.5
Open-ended code
R1acc
0.989
Recorded workflow
Input read qc→Deterministic read subsample 5pct→Candidate seed support screen→Candidate seed high identity rerank→Mitochondrial read cloud selection→Mitochondrial read cloud extraction→8 more steps
All 14 recorded steps
Input read qc
Deterministic read subsample 5pct
Candidate seed support screen
Candidate seed high identity rerank
Mitochondrial read cloud selection
Mitochondrial read cloud extraction
Mitochondrial read cloud downsample 3000
Draft tandem repeat circularization
Draft self alignment for circularity
Extract circular period candidate
Read cloud mapping and consensus polish — SAMtools
Final circular consensus validation — SAMtools
Final deliverable write
Final deliverable validation
Score explanation
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 15,045 matching fragment occurrences; 15,210 in the submitted assembly and 15,206 in the reference. Precision=0.989152, recall=0.989412.
High copy read selection→Strict high copy read selection→Top scoring read subset→Mitochondrial like read filter — Filter rows→Candidate consensus and subset validation — SAMtools→Full input validation — SAMtools→Final packaging and acceptance validation
All 7 recorded steps
High copy read selection
Strict high copy read selection
Top scoring read subset
Mitochondrial like read filter — Filter rows
Candidate consensus and subset validation — SAMtools
Full input validation — SAMtools
Final packaging and acceptance validation
Score explanation
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 15,041 matching fragment occurrences; 15,206 in the submitted assembly and 15,206 in the reference. Precision=0.989149, recall=0.989149.
Unmatched mitochondrial sequenceThe submitted sequence shares no 31-base DNA fragments with the reference mitochondrial assembly.Evidence. 0 matching fragment occurrences; 16,556 in the submitted assembly and 15,206 in the reference. Precision=0.000000, recall=0.000000.
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 14,046 matching fragment occurrences; 15,187 in the submitted assembly and 15,206 in the reference. Precision=0.924870, recall=0.923714.
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 15,034 matching fragment occurrences; 15,209 in the submitted assembly and 15,206 in the reference. Precision=0.988494, recall=0.988689.
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 15,045 matching fragment occurrences; 15,210 in the submitted assembly and 15,206 in the reference. Precision=0.989152, recall=0.989412.
User environment repair→Input qc→Discovery assembly→Discovery graph parse v2→Discovery contig mapping→Candidate selection→10 more steps
All 16 recorded steps
User environment repair
Input qc
Discovery assembly
Discovery graph parse v2
Discovery contig mapping
Candidate selection
Candidate copy extraction v2
Mitochondrial orf sanity check
Full read mapping v2
Supporting read extraction
Circular junction validation
Rotated consensus validation — SAMtools
Final packaging
Final validation
Method metadata update
Final validation v2
Score explanation
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 15,045 matching fragment occurrences; 15,210 in the submitted assembly and 15,206 in the reference. Precision=0.989152, recall=0.989412.
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 15,056 matching fragment occurrences; 15,209 in the submitted assembly and 15,206 in the reference. Precision=0.989940, recall=0.990135.
Input read qc→Low gc enrichment→Low gc subsample→Low gc subsample seed42→Hifiasm primary assembly seed42→Gfa to fasta→8 more steps
All 14 recorded steps
Input read qc
Low gc enrichment
Low gc subsample
Low gc subsample seed42
Hifiasm primary assembly seed42
Gfa to fasta
Candidate self alignment
Collapse redundant circularized contig
Full sample paf validation
Full sample bam mapping and coverage — SAMtools
Samtools bayesian consensus
Independent hifiasm reassembly seed123
Independent circular sequence comparison
Final fasta validation and compression
Score explanation
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 15,045 matching fragment occurrences; 15,210 in the submitted assembly and 15,206 in the reference. Precision=0.989152, recall=0.989412.
Bait extraction→Bait mapping→Mitochondrial read alignment — SAMtools→All vs all layout→Discovery sample→Sample kmer count→12 more steps
All 18 recorded steps
Bait extraction
Bait mapping
Mitochondrial read alignment — SAMtools
All vs all layout
Discovery sample
Sample kmer count
Kmer histogram and dump
Mitochondrial component graph
Mitochondrial seed selection
Circular kmer path
Full input draft mapping
Full input read recruitment
Draft read alignment — SAMtools
Consensus polishing — SAMtools
Circular overlap trim — SAMtools
Final read backed validation — SAMtools
Final fasta generation
Methods metadata
Score explanation
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 15,045 matching fragment occurrences; 15,210 in the submitted assembly and 15,206 in the reference. Precision=0.989152, recall=0.989412.
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 15,045 matching fragment occurrences; 15,210 in the submitted assembly and 15,206 in the reference. Precision=0.989152, recall=0.989412.
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 15,034 matching fragment occurrences; 15,209 in the submitted assembly and 15,206 in the reference. Precision=0.988494, recall=0.988689.
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 14,996 matching fragment occurrences; 15,205 in the submitted assembly and 15,206 in the reference. Precision=0.986255, recall=0.986190.
Download reference bait→Select mitochondrial reads — SAMtools→Exploratory hifiasm assembly 5k reads→Patch flye managers for isolated environment→Flye assembly successful→Validate final assembly — SAMtools→Package final deliverables
All 7 recorded steps
Download reference bait
Select mitochondrial reads — SAMtools
Exploratory hifiasm assembly 5k reads
Patch flye managers for isolated environment
Flye assembly successful
Validate final assembly — SAMtools
Package final deliverables
Score explanation
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 15,045 matching fragment occurrences; 15,210 in the submitted assembly and 15,206 in the reference. Precision=0.989152, recall=0.989412.
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 15,070 matching fragment occurrences; 15,213 in the submitted assembly and 15,206 in the reference. Precision=0.990600, recall=0.991056.
Download reference sequences→Map reads to ithomiini mitogenomes→Map reads to eutresis cox1→Select mitochondrial reads→Extract mitochondrial reads→Downsample long mitochondrial reads→4 more steps
All 10 recorded steps
Download reference sequences
Map reads to ithomiini mitogenomes
Map reads to eutresis cox1
Select mitochondrial reads
Extract mitochondrial reads
Downsample long mitochondrial reads
Hifiasm assemble subset
Collapse tandem duplicate to unit
Validate unit by read mapping — SAMtools
Write final fasta gz
Score explanation
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 15,045 matching fragment occurrences; 15,210 in the submitted assembly and 15,206 in the reference. Precision=0.989152, recall=0.989412.
Sequence differences from the referenceThe submitted assembly and the reference have different 31-base DNA fragment content; this directly reduces the original F1 score.Evidence. 15,034 matching fragment occurrences; 15,209 in the submitted assembly and 15,206 in the reference. Precision=0.988494, recall=0.988689.
Three-run totals for the same input library in each condition. The ratio is Galaxy-API code tokens divided by Open-ended code tokens. Costs are API-equivalent estimates.