IWC benchmark item

wf_003_host_contamination_removal

Host or Contamination Removal on Short-Reads

Host-reference filtering of paired reads (SRR12665180)

Open source IWC workflowGround-truth Galaxy history

Reference workflow

2 tool steps across 2 unique tools, including tools inside nested subworkflows. A plus sign denotes parallel branches.

Workflow
Bowtie2MultiQC

Complete query

The full task shown to the agent, excluding execution-condition instructions.

Filter the provided paired-end reads against the hg38 human reference assembly using a suitable paired-end short-read aligner.
Remove read pairs that the selected aligner classifies as valid paired-end alignments to the human reference under its standard paired-end criteria, and retain all other pairs. Do not trim or otherwise modify the retained reads, and keep the two output files synchronized.
Write the synchronized retained mates to `final_answer/filtered_forward.fastqsanger.gz` and `final_answer/filtered_reverse.fastqsanger.gz`.
Write `final_answer/method.json` as a JSON object with a single key `aligner` whose value is the common name of the aligner you used.

acc evaluator

acc compares the final output files with the reference outputs.

Metric
paired_fastq_f1
Definition

Transformation-aware paired FASTQ score emphasizing host-read removal while checking retained read identities.

Formula
Final scoreS = √(F1(M_T, C_T, R_T) × F1(M_ID, C_ID, R_ID))

Geometric mean of transformation agreement and retained-read-ID agreement.

F1F1(M,C,R) = 2M/(C+R)

Equivalent to 2PR/(P+R), where P=M/C and recall=M/R; if C=R=0, F1=1.

Transform matchM_T = Σᵢ tᵢ; tᵢ = 1 if both remove the pair, √(J_F J_R) if both retain a changed pair, otherwise 0

C_T and R_T are the numbers of input pairs changed or removed by the candidate and reference.

Mate similarityJ_m = max |I_C ∩ I_R| / |I_C ∪ I_R|

I_C and I_R are candidate and reference contiguous sequence-and-quality slices of the same input mate.

Retained IDsM_ID = |ID_C ∩ ID_R|; C_ID = |ID_C|; R_ID = |ID_R|

Read-pair IDs are the matching units.

Step-score requirements

A step passes when the trace directly shows that it ran. Parameter correctness and output quality are measured separately by acc.

  1. Step 1Align the paired reads to hg38 using a suitable paired-end short-read aligner.
    • A successful paired-end short-read alignment execution used hg38, not another human assembly.
    • Both mates from the provided input pairs entered the alignment/classification chain.
  2. Step 2Remove pairs classified by the selected aligner as valid paired-end human alignments; preserve all retained reads unchanged and keep mates synchronized.
    • Pair removal used the selected aligner's valid/proper paired-end human-alignment classification.
    • If either mate belonged to a removed valid human pair, the whole pair was removed.
    • Retained sequences and qualities are byte-for-byte unchanged apart from FASTQ container compression and ordering allowed by the contract.
    • Forward and reverse retained outputs contain the same synchronized read identifiers and pass final-answer checks.

Model results and score explanations

The 3 results below acc 1.000 each include a score explanation and quantitative evidence. A score below 1.000 is not automatically an error. Each replicate shows its recorded workflow, acc, step score, 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 · step score 1.000
1.000
Recorded workflow
Align paired reads to hg38 with Bowtie2Align paired reads to hg38 with BWAClassify alignments and retain non-human read pairsWrite and validate synchronized retained FASTQ mates
All 4 recorded steps
  1. Align paired reads to hg38 with Bowtie2
  2. Align paired reads to hg38 with BWA
  3. Classify alignments and retain non-human read pairs
  4. Write and validate synchronized retained FASTQ mates
Hugging Face trace
R2acc · step score 1.000
0.996
Recorded workflow
Validate inputs and reference — Table transformationSplit hg38 reference into contig chunksAlign minimap2 hg38 contig chunksFilter original fastq pairs — Filter rowsValidate final outputs — Table transformation
All 5 recorded steps
  1. Validate inputs and reference — Table transformation
  2. Split hg38 reference into contig chunks
  3. Align minimap2 hg38 contig chunks
  4. Filter original fastq pairs — Filter rows
  5. Validate final outputs — Table transformation

Score explanation

Borderline pair classification Minimap2 made a slightly different set of primary proper-pair decisions at ambiguous alignment boundaries. The retained files are complete; the deficit comes from those pair-classification differences. Evidence. This minimap2 output reached acc 0.995730 under the specified short-read preset and synchronized-pair filtering.
Hugging Face trace
R3acc · step score 1.000
1.000
Recorded workflow
Setup — SAMtoolsInput validation — Table transformationReference validationMinimap2 setup — SAMtoolsMinimap2 input validation — Table transformationMinimap2 reference validation9 more steps
All 15 recorded steps
  1. Setup — SAMtools
  2. Input validation — Table transformation
  3. Reference validation
  4. Minimap2 setup — SAMtools
  5. Minimap2 input validation — Table transformation
  6. Minimap2 reference validation
  7. Minimap2 setup — SAMtools
  8. Minimap2 input validation — Table transformation
  9. Minimap2 reference validation
  10. Minimap2 setup
  11. Minimap2 input validation — Table transformation
  12. Minimap2 reference validation
  13. Minimap2 alignment filter — Filter rows + Table transformation
  14. Minimap2 method json
  15. Minimap2 deliverable validation — Table transformation
Hugging Face trace

Galaxy-API code

GPT-5.6 Sol

Open-ended code

R1acc · step score 1.000
1.000
Recorded workflow
Align paired reads to hg38 with Bowtie2Write and validate synchronized retained FASTQ mates
All 2 recorded steps
  1. Align paired reads to hg38 with Bowtie2
  2. Write and validate synchronized retained FASTQ mates
Hugging Face trace
R2acc · step score 1.000
1.000
Recorded workflow
Align paired reads to hg38 with BWAClassify alignments and retain non-human read pairsWrite and validate synchronized retained FASTQ mates
All 3 recorded steps
  1. Align paired reads to hg38 with BWA
  2. Classify alignments and retain non-human read pairs
  3. Write and validate synchronized retained FASTQ mates
Hugging Face trace
R3acc · step score 1.000
1.000
Recorded workflow
Align paired reads to hg38 with Bowtie2Write and validate synchronized retained FASTQ mates
All 2 recorded steps
  1. Align paired reads to hg38 with Bowtie2
  2. Write and validate synchronized retained FASTQ mates
Hugging Face trace

Galaxy-API code

R1acc · step score 1.000
1.000
Recorded workflow
Bowtie2Data retrievalBwa Mem2SAMtoolsBedtools BamtofastqSAMtools2 more steps
All 9 recorded steps
  1. Bowtie2
  2. Data retrieval
  3. Bwa Mem2
  4. SAMtools
  5. Bedtools Bamtofastq
  6. SAMtools
  7. Tp Cut Tool
  8. Filter rows
  9. Filter rows
Galaxy historyHugging Face trace
R2acc · step score 1.000
1.000
Recorded workflow
Bowtie2Data retrievalBwa MemSAMtools ×5Filter rows ×2Converter Uncompressed To Gz ×2
All 12 recorded steps
  1. Bowtie2
  2. Data retrieval
  3. Bwa Mem
  4. SAMtools
  5. SAMtools
  6. SAMtools
  7. SAMtools
  8. SAMtools
  9. Filter rows
  10. Filter rows
  11. Converter Uncompressed To Gz
  12. Converter Uncompressed To Gz
Galaxy historyHugging Face trace

GPT-5.6 Luna

Open-ended code

R1acc · step score 1.000
1.000
Recorded workflow
Align paired reads to hg38 with Bowtie2Write and validate synchronized retained FASTQ mates
All 2 recorded steps
  1. Align paired reads to hg38 with Bowtie2
  2. Write and validate synchronized retained FASTQ mates
Hugging Face trace
R2acc · step score 1.000
1.000
Recorded workflow
Align paired reads to hg38 with Bowtie2Write and validate synchronized retained FASTQ mates
All 2 recorded steps
  1. Align paired reads to hg38 with Bowtie2
  2. Write and validate synchronized retained FASTQ mates
Hugging Face trace
R3acc · step score 1.000
1.000
Recorded workflow
Align paired reads to hg38 with Bowtie2Write and validate synchronized retained FASTQ mates
All 2 recorded steps
  1. Align paired reads to hg38 with Bowtie2
  2. Write and validate synchronized retained FASTQ mates
Hugging Face trace

Galaxy-API code

R1acc · step score 1.000
0.999900
Recorded workflow
Bowtie2Bwa MemSAMtools ×2
All 4 recorded steps
  1. Bowtie2
  2. Bwa Mem
  3. SAMtools
  4. SAMtools

Score explanation

Borderline pair classification BWA-MEM retained three more pairs than the BWA-MEM benchmark target. The difference is confined to borderline proper-pair classifications rather than trimming, sequence modification, or unsynchronized mates. Evidence. The output retained 20,899 pairs versus 20,896 in the target and reached acc 0.999900.
Galaxy historyHugging Face trace
R3acc · step score 1.000
1.000
Recorded workflow
Data retrievalBwa Mem2SAMtools ×3
All 5 recorded steps
  1. Data retrieval
  2. Bwa Mem2
  3. SAMtools
  4. SAMtools
  5. SAMtools
Galaxy historyHugging Face trace

Codex + DeepSeek V4 Pro

Open-ended code

R1acc · step score 1.000
1.000
Recorded workflow
Align paired reads to hg38 with BWAClassify alignments and retain non-human read pairsWrite and validate synchronized retained FASTQ mates
All 3 recorded steps
  1. Align paired reads to hg38 with BWA
  2. Classify alignments and retain non-human read pairs
  3. Write and validate synchronized retained FASTQ mates
Hugging Face trace
R2acc · step score 1.000
1.000
Recorded workflow
Align paired reads to hg38 with BWAClassify alignments and retain non-human read pairsWrite and validate synchronized retained FASTQ mates
All 3 recorded steps
  1. Align paired reads to hg38 with BWA
  2. Classify alignments and retain non-human read pairs
  3. Write and validate synchronized retained FASTQ mates
Hugging Face trace
R3acc · step score 1.000
1.000
Recorded workflow
Reference and input verificationBowtie2 indexBowtie2 paired end alignment and retain nonconcordantFinal deliverable copy and validation
All 4 recorded steps
  1. Reference and input verification
  2. Bowtie2 index
  3. Bowtie2 paired end alignment and retain nonconcordant
  4. Final deliverable copy and validation
Hugging Face trace

Galaxy-API code

R1acc · step score 1.000
0.999820
Recorded workflow
Bwa MemFilter rowsTp Cut ToolFilter rows ×2
All 5 recorded steps
  1. Bwa Mem
  2. Filter rows
  3. Tp Cut Tool
  4. Filter rows
  5. Filter rows

Score explanation

Borderline pair classification BWA-MEM classified a small number of ambiguous alignments differently at the proper-pair boundary. The output files stayed synchronized and unmodified; only the retained-versus-removed decision changed. Evidence. The output retained 20,897 pairs versus 20,896; 20,891 retained IDs matched. Of the removed-pair set, 57,188 of 57,194 target decisions matched.
Galaxy historyHugging Face trace
R2acc · step score 1.000
1.000
Recorded workflow
Bowtie2Zip CollectionBowtie2
All 3 recorded steps
  1. Bowtie2
  2. Zip Collection
  3. Bowtie2
Galaxy historyHugging Face trace