IWC multi-step task

Task 3: 16S amplicon sequence variants and taxonomy

What the task asks for

Infer exact sequence variants in 24 environmental 16S V4 libraries, remove chimeras across samples and assign taxonomy.

8 scored results9 required18 runs scored

Codex GPT-5.6 Luna

6 of 6 runs scored
Galaxy-API code 0.292 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.418
All results pass0 of 3 runsruns in which every scored result passes
run 10.1251/8run 20.7506/8run 30.0000/8
Open-ended code 0.958 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.942
All results pass2 of 3 runsruns in which every scored result passes
run 11.0008/8run 21.0008/8run 30.8757/8

Codex GPT-5.6 Sol

6 of 6 runs scored
Galaxy-API code 0.708 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.834
All results pass1 of 3 runsruns in which every scored result passes
run 11.0008/8run 20.8757/8run 30.2502/8
Open-ended code 1.000 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.989
All results pass3 of 3 runsruns in which every scored result passes
run 11.0008/8run 21.0008/8run 31.0008/8

DeepSeek V4 Pro via Codex

6 of 6 runs scored
Galaxy-API code 0.792 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.852
All results pass0 of 3 runsruns in which every scored result passes
run 10.8757/8run 20.8757/8run 30.6255/8
Open-ended code 0.750 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.747
All results pass0 of 3 runsruns in which every scored result passes
run 10.6255/8run 20.7506/8run 30.8757/8

Three measures. Every required result gets a score from 0 to 1 by comparison with the reference. Passing requires a score of at least 0.80 and compliance with the required content, method and output instructions. BixBench3 acc is the share of results that pass. The continuous score is the plain average of all the result scores, with no pass mark. For example, run 1 of GPT-5.6 Luna with Galaxy-API code scored 0.000, 0.828, 0.000, 0.000, 0.766, 0.782, 0.711 and 0.992 on its 8 results. 1 of them pass, so BixBench3 acc = 1/8 = 0.125; the average of all 8 scores is 0.510, the continuous score. A third measure, all results pass, counts a run only when every scored result passes, which is the share of runs that delivered the whole analysis correctly. A failing result still contributes its numerical score to the continuous average. A score above 0.80 does not excuse an incorrect method, missing member or an explicitly required output format. Each card averages the scored runs of this task.

Error analysis

BixBench3 acc, Galaxy-API code vs Open-ended code: GPT-5.6 Luna 0.292 vs 0.958; GPT-5.6 Sol 0.708 vs 1.000; DeepSeek V4 Pro 0.792 vs 0.750.

What Galaxy added

Galaxy's amplicon tools save error models, denoising results and merged pairs as the method's own objects, so no Galaxy run lost a result to how these were stored. Several Open-ended runs repackaged them in structures of their own that could not be read, which is why DeepSeek V4 Pro passed slightly more results in Galaxy.

Why Galaxy did not do better

Galaxy runs passed fewer results at every step. In three runs the agent opened the denoising tool's advanced options to apply a sensitivity setting that the task gives only for error learning, and the form then also passed its pre-filled alignment scores, 4 and −5. These follow the method's documentation, but the method itself defaults to 5 and −4, as the reference used, and denoising fell just below the pass mark. Two runs cut both reads to 180 bases, so no sequence matched the reference, and GPT-5.6 Luna's other two runs failed through truncated identifiers and a broken paired-read filter.

Run-level details (4)
  • The first two Galaxy runs with DeepSeek V4 Pro and the second with GPT-5.6 Sol also applied the error-learning sensitivity setting to denoising, through the tool's advanced options. That also applied the form's alignment scores of 4 and −5 instead of the method's defaults of 5 and −4, and denoising scored 0.79. Open-ended runs that changed the same sensitivity setting kept the default scores and passed at 0.91.
  • The first Galaxy run with GPT-5.6 Luna and the third with GPT-5.6 Sol truncated both reads at 180 bases, giving 161- and 160-base sequences that match no reference sequence.
  • The third Galaxy run with DeepSeek V4 Pro named its files fwd.rds and rev.rds instead of forward.rds and reverse.rds. The second with GPT-5.6 Luna wrote truncated 16-character identifiers, so its denoising files could not be collected. In the third, the paired filtering jobs failed; the agent filtered each read separately, merging then failed, and it switched to a different denoising method.
  • Several Open-ended runs saved error models or denoising results inside lists of their own or with extra columns, which cannot be read as the method's own objects.
Instruction, format and method errors (6)
  • Required files are missing: 04_denoising/S01/forward.rds, 04_denoising/S01/reverse.rds, 04_denoising/S02/forward.rds, and 45 more.Task requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.

    GPT-5.6 Luna / Galaxy-API code / run 2 → result 4; GPT-5.6 Luna / Galaxy-API code / run 3 → result 4; DeepSeek V4 Pro / Galaxy-API code / run 3 → result 4

  • Required files are missing: 03_error_models/S01/forward.rds, 03_error_models/S01/reverse.rds, 03_error_models/S02/forward.rds, and 45 more.Task requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.

    GPT-5.6 Luna / Galaxy-API code / run 3 → result 3; DeepSeek V4 Pro / Galaxy-API code / run 3 → result 3

  • Required files are missing: 05_pair_merges/S01/merged.rds, 05_pair_merges/S02/merged.rds, 05_pair_merges/S03/merged.rds, and 21 more.Task requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.

    GPT-5.6 Luna / Galaxy-API code / run 3 → result 5

  • Named columns/order differ from the required table. Named fields are repeated.Task requirement: 6. final_answer/06_asv_counts_unfiltered/ TSV counts.tsv: one row per exact ASV sequence, first column sequence, then S01–S24 integer count columns; retain zero counts and all sample columns. Files: counts.tsv.

    GPT-5.6 Luna / Galaxy-API code / run 3 → result 6

  • Named columns/order differ from the required table. Named fields are repeated.Task requirement: 7. final_answer/07_asv_counts_nonchimeric/ TSV counts.tsv: one row per exact ASV sequence, first column sequence, then S01–S24 integer count columns; retain zero counts and all sample columns. Files: counts.tsv.

    GPT-5.6 Luna / Galaxy-API code / run 3 → result 7

  • Named columns/order differ from the required table.Task requirement: 9. final_answer/09_read_tracking/ TSV counts.tsv columns: sample, input_pairs, filtered_pairs, denoised_forward, denoised_reverse, merged_pairs, pre_chimera, nonchimeric. Explain major losses briefly in method.md. Files: counts.tsv.

    GPT-5.6 Luna / Galaxy-API code / run 3 → result 9

Every run

The task asks the agent to return a numbered list of results, each a file or a folder of files. The columns on the right give the score of each required result in each run, from 0 to 1 against the reference, under the result's number and name; the task text and the scoring table below describe each one. Green marks a passing result. Failing cells link to the reasons below, including instruction and format errors even when the numerical score is at least 0.80. In each row, BixBench3 acc is the number of green cells divided by the number of results, and the continuous score is the average of all the result scores in the row. Tokens are input (including cached input) plus output tokens; minutes are the wall time of the run. Under Records, Trace opens the run's task text, agent event log, final message and returned files in the lab's run trace dataset on Hugging Face, and History opens the usegalaxy.org history that a Galaxy-API code run worked in.

Score of each required result
ModelConditionRunBixBench3 acc
share passing		Continuous score TokensMinutesRecords2filtered reads3error models4denoising5pair merges6ASV counts unfiltered7ASV counts nonchimeric8taxonomy9read tracking
GPT-5.6 LunaGalaxy-API code11/8 = 0.1250.51034.3M490Trace
History		0.00Member0.82Member0.00Member0.00Member0.76Content0.78Content0.71Content0.99 Passed
26/8 = 0.7500.74426.7M549Trace
History		1.00 Passed1.00 Passed0.00Instruction0.00Member0.99 Passed0.99 Passed0.96 Passed0.99 Passed
30/8 = 0.0000.00044.3M1284Trace
History		0.00Member0.00Instruction0.00Instruction0.00Instruction0.00Format0.00Format0.00Content0.00Format
Open-ended code18/8 = 1.0000.9834.6M88Trace1.00 Passed1.00 Passed0.91 Passed0.99 Passed0.99 Passed0.99 Passed0.96 Passed0.99 Passed
28/8 = 1.0000.98310.9M138Trace1.00 Passed1.00 Passed0.91 Passed0.99 Passed0.99 Passed0.99 Passed0.96 Passed0.99 Passed
37/8 = 0.8750.8593.5M85Trace1.00 Passed1.00 Passed0.91 Passed0.00Member0.99 Passed0.99 Passed0.96 Passed0.99 Passed
GPT-5.6 SolGalaxy-API code18/8 = 1.0001.00014.3M564Trace
History		1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed0.99 Passed1.00 Passed
27/8 = 0.8750.96824.2M605Trace
History		1.00 Passed1.00 Passed0.79Member0.99 Passed0.99 Passed0.99 Passed0.96 Passed0.99 Passed
32/8 = 0.2500.53315.6M485Trace
History		0.00Member0.96 Passed0.00Member0.00Member0.78Content0.79Content0.71Content0.99 Passed
Open-ended code18/8 = 1.0000.9835.0M86Trace1.00 Passed1.00 Passed0.91 Passed0.99 Passed0.99 Passed0.99 Passed0.96 Passed0.99 Passed
28/8 = 1.0000.98312.8M69Trace1.00 Passed1.00 Passed0.91 Passed0.99 Passed0.99 Passed0.99 Passed0.96 Passed0.99 Passed
38/8 = 1.0001.0006.1M88Trace1.00 Passed1.00 Passed0.99 Passed0.99 Passed0.99 Passed0.99 Passed0.99 Passed0.99 Passed
DeepSeek V4 ProGalaxy-API code17/8 = 0.8750.96819.6M150Trace
History		1.00 Passed1.00 Passed0.79Member0.99 Passed0.99 Passed0.99 Passed0.96 Passed0.99 Passed
27/8 = 0.8750.96822.6M206Trace
History		1.00 Passed1.00 Passed0.79Member0.99 Passed0.99 Passed0.99 Passed0.96 Passed0.99 Passed
35/8 = 0.6250.61935.4M161Trace
History		1.00 Passed0.00Instruction0.00Instruction0.00Member0.99 Passed0.99 Passed0.96 Passed0.99 Passed
Open-ended code15/8 = 0.6250.6208.5M88Trace1.00 Passed0.00Member0.00Member0.00Member0.99 Passed0.99 Passed0.96 Passed0.99 Passed
26/8 = 0.7500.7456.3M110Trace1.00 Passed1.00 Passed0.00Member0.00Member0.99 Passed0.99 Passed0.96 Passed0.99 Passed
37/8 = 0.8750.8753.4M100Trace1.00 Passed0.00Member0.99 Passed0.99 Passed0.99 Passed0.99 Passed0.99 Passed0.99 Passed

Why results did not pass

  1. GPT-5.6 Luna / Galaxy-API code / run 1 → result 2 (filtered reads)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (24 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0
      • S02: 0
      • S03: 0
      • S04: 0
      • S05: 0
      • S06: 0
      • S07: 0
      • S08: 0
      • S09: 0
      • S10: 0
      • S11: 0
      • S12: 0
      • S13: 0
      • S14: 0
      • S15: 0
      • S16: 0
      • S17: 0
      • S18: 0
      • S19: 0
      • S20: 0
      • S21: 0
      • S22: 0
      • S23: 0
      • S24: 0
  2. GPT-5.6 Luna / Galaxy-API code / run 1 → result 3 (error models)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S05: 0.263066
      • S07: 0.505347
      • S08: 0.458451
      • S14: 0.22543
      • S19: 0.567088
      • S20: 0.460007
  3. GPT-5.6 Luna / Galaxy-API code / run 1 → result 4 (denoising)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Category agreement (F1): 0 (48 checks)
      • Matching records (F1): 0 (144 checks)
      • Numerical agreement (CCC): 0 to 0.999641 (192 checks)
      • Present, finite data cells (F1): 0 (96 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0
      • S02: 0
      • S03: 0
      • S04: 0
      • S05: 0
      • S06: 0
      • S07: 0
      • S08: 0
      • S09: 0
      • S10: 0
      • S11: 0
      • S12: 0
      • S13: 0
      • S14: 0
      • S15: 0
      • S16: 0
      • S17: 0
      • S18: 0
      • S19: 0
      • S20: 0
      • S21: 0
      • S22: 0
      • S23: 0
      • S24: 0
  4. GPT-5.6 Luna / Galaxy-API code / run 1 → result 5 (pair merges)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Category agreement (F1): 0 (22 checks)
      • Matching records (F1): 0 (22 checks)
      • Numerical agreement (CCC): 0 (22 checks)
      • Present, finite data cells (F1): 0 (22 checks)
      • Required content missing or unreadable: 0 (2 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0
      • S02: 0
      • S03: 0
      • S04: 0
      • S05: 0
      • S06: 0
      • S07: 0
      • S08: 0
      • S09: 0
      • S10: 0
      • S11: 0
      • S12: 0
      • S13: 0
      • S14: 0
      • S15: 0
      • S16: 0
      • S17: 0
      • S18: 0
      • S19: 0
      • S20: 0
      • S21: 0
      • S22: 0
      • S23: 0
      • S24: 0
  5. GPT-5.6 Luna / Galaxy-API code / run 1 → result 6 (ASV counts unfiltered)
    • Content: Content score below 0.80. Value: 0.766581. Required minimum: 0.8.
      • Matching records (F1): 0.896328
      • Numerical agreement (CCC): 0.954167
      • Present, finite data cells (F1): 0.896328
  6. GPT-5.6 Luna / Galaxy-API code / run 1 → result 7 (ASV counts nonchimeric)
    • Content: Content score below 0.80. Value: 0.782501. Required minimum: 0.8.
      • Matching records (F1): 0.905076
      • Numerical agreement (CCC): 0.955246
      • Present, finite data cells (F1): 0.905076
  7. GPT-5.6 Luna / Galaxy-API code / run 1 → result 8 (taxonomy)
    • Content: Content score below 0.80. Value: 0.71185. Required minimum: 0.8.
      • Category agreement (F1): 0.971968
      • Matching records (F1): 0.905076 (2 checks)
      • Numerical agreement (CCC): 0.987828
      • Present, finite data cells (F1): 0.905076
  8. GPT-5.6 Luna / Galaxy-API code / run 2 → result 4 (denoising)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (240 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0
      • S02: 0
      • S03: 0
      • S04: 0
      • S05: 0
      • S06: 0
      • S07: 0
      • S08: 0
      • S09: 0
      • S10: 0
      • S11: 0
      • S12: 0
      • S13: 0
      • S14: 0
      • S15: 0
      • S16: 0
      • S17: 0
      • S18: 0
      • S19: 0
      • S20: 0
      • S21: 0
      • S22: 0
      • S23: 0
      • S24: 0
    • Instruction: Required file is missing: 04_denoising/S01/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S01/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S02/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S02/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S03/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S03/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S04/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S04/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S05/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S05/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S06/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S06/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S07/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S07/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S08/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S08/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S09/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S09/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S10/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S10/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S11/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S11/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S12/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S12/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S13/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S13/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S14/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S14/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S15/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S15/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S16/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S16/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S17/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S17/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S18/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S18/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S19/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S19/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S20/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S20/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S21/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S21/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S22/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S22/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S23/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S23/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S24/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S24/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
  9. GPT-5.6 Luna / Galaxy-API code / run 2 → result 5 (pair merges)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (24 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0
      • S02: 0
      • S03: 0
      • S04: 0
      • S05: 0
      • S06: 0
      • S07: 0
      • S08: 0
      • S09: 0
      • S10: 0
      • S11: 0
      • S12: 0
      • S13: 0
      • S14: 0
      • S15: 0
      • S16: 0
      • S17: 0
      • S18: 0
      • S19: 0
      • S20: 0
      • S21: 0
      • S22: 0
      • S23: 0
      • S24: 0
  10. GPT-5.6 Luna / Galaxy-API code / run 3 → result 2 (filtered reads)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (24 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0
      • S02: 0
      • S03: 0
      • S04: 0
      • S05: 0
      • S06: 0
      • S07: 0
      • S08: 0
      • S09: 0
      • S10: 0
      • S11: 0
      • S12: 0
      • S13: 0
      • S14: 0
      • S15: 0
      • S16: 0
      • S17: 0
      • S18: 0
      • S19: 0
      • S20: 0
      • S21: 0
      • S22: 0
      • S23: 0
      • S24: 0
  11. GPT-5.6 Luna / Galaxy-API code / run 3 → result 3 (error models)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (96 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0
      • S02: 0
      • S03: 0
      • S04: 0
      • S05: 0
      • S06: 0
      • S07: 0
      • S08: 0
      • S09: 0
      • S10: 0
      • S11: 0
      • S12: 0
      • S13: 0
      • S14: 0
      • S15: 0
      • S16: 0
      • S17: 0
      • S18: 0
      • S19: 0
      • S20: 0
      • S21: 0
      • S22: 0
      • S23: 0
      • S24: 0
    • Instruction: Required file is missing: 03_error_models/S01/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S01/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S02/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S02/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S03/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S03/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S04/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S04/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S05/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S05/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S06/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S06/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S07/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S07/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S08/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S08/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S09/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S09/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S10/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S10/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S11/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S11/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S12/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S12/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S13/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S13/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S14/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S14/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S15/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S15/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S16/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S16/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S17/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S17/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S18/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S18/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S19/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S19/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S20/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S20/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S21/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S21/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S22/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S22/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S23/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S23/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S24/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S24/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
  12. GPT-5.6 Luna / Galaxy-API code / run 3 → result 4 (denoising)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (240 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0
      • S02: 0
      • S03: 0
      • S04: 0
      • S05: 0
      • S06: 0
      • S07: 0
      • S08: 0
      • S09: 0
      • S10: 0
      • S11: 0
      • S12: 0
      • S13: 0
      • S14: 0
      • S15: 0
      • S16: 0
      • S17: 0
      • S18: 0
      • S19: 0
      • S20: 0
      • S21: 0
      • S22: 0
      • S23: 0
      • S24: 0
    • Instruction: Required file is missing: 04_denoising/S01/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S01/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S02/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S02/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S03/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S03/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S04/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S04/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S05/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S05/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S06/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S06/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S07/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S07/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S08/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S08/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S09/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S09/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S10/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S10/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S11/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S11/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S12/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S12/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S13/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S13/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S14/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S14/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S15/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S15/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S16/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S16/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S17/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S17/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S18/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S18/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S19/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S19/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S20/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S20/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S21/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S21/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S22/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S22/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S23/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S23/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S24/forward.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 04_denoising/S24/reverse.rdsTask requirement: 4. final_answer/04_denoising/{sample}/ RDS Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
  13. GPT-5.6 Luna / Galaxy-API code / run 3 → result 5 (pair merges)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (24 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0
      • S02: 0
      • S03: 0
      • S04: 0
      • S05: 0
      • S06: 0
      • S07: 0
      • S08: 0
      • S09: 0
      • S10: 0
      • S11: 0
      • S12: 0
      • S13: 0
      • S14: 0
      • S15: 0
      • S16: 0
      • S17: 0
      • S18: 0
      • S19: 0
      • S20: 0
      • S21: 0
      • S22: 0
      • S23: 0
      • S24: 0
    • Instruction: Required file is missing: 05_pair_merges/S01/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S02/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S03/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S04/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S05/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S06/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S07/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S08/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S09/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S10/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S11/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S12/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S13/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S14/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S15/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S16/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S17/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S18/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S19/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S20/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S21/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S22/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S23/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
    • Instruction: Required file is missing: 05_pair_merges/S24/merged.rdsTask requirement: 5. final_answer/05_pair_merges/{sample}/ RDS merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
  14. GPT-5.6 Luna / Galaxy-API code / run 3 → result 6 (ASV counts unfiltered)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0
    • Format: Named columns/order differ from the required table.Task requirement: 6. final_answer/06_asv_counts_unfiltered/ TSV counts.tsv: one row per exact ASV sequence, first column sequence, then S01–S24 integer count columns; retain zero counts and all sample columns. Files: counts.tsv.
    • Format: Named fields are repeated.Task requirement: 6. final_answer/06_asv_counts_unfiltered/ TSV counts.tsv: one row per exact ASV sequence, first column sequence, then S01–S24 integer count columns; retain zero counts and all sample columns. Files: counts.tsv.
  15. GPT-5.6 Luna / Galaxy-API code / run 3 → result 7 (ASV counts nonchimeric)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0
    • Format: Named columns/order differ from the required table.Task requirement: 7. final_answer/07_asv_counts_nonchimeric/ TSV counts.tsv: one row per exact ASV sequence, first column sequence, then S01–S24 integer count columns; retain zero counts and all sample columns. Files: counts.tsv.
    • Format: Named fields are repeated.Task requirement: 7. final_answer/07_asv_counts_nonchimeric/ TSV counts.tsv: one row per exact ASV sequence, first column sequence, then S01–S24 integer count columns; retain zero counts and all sample columns. Files: counts.tsv.
  16. GPT-5.6 Luna / Galaxy-API code / run 3 → result 8 (taxonomy)
    • Content: Content score below 0.80. Value: 1.3162e-12. Required minimum: 0.8.
      • Matching records (F1): 0.000126393 (2 checks)
      • Numerical agreement (CCC): 0.651857
      • Present, finite data cells (F1): 0.000126393
  17. GPT-5.6 Luna / Galaxy-API code / run 3 → result 9 (read tracking)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0
    • Format: Named columns/order differ from the required table.Task requirement: 9. final_answer/09_read_tracking/ TSV counts.tsv columns: sample, input_pairs, filtered_pairs, denoised_forward, denoised_reverse, merged_pairs, pre_chimera, nonchimeric. Explain major losses briefly in method.md. Files: counts.tsv.
  18. GPT-5.6 Luna / Open-ended code / run 3 → result 5 (pair merges)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (24 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0
      • S02: 0
      • S03: 0
      • S04: 0
      • S05: 0
      • S06: 0
      • S07: 0
      • S08: 0
      • S09: 0
      • S10: 0
      • S11: 0
      • S12: 0
      • S13: 0
      • S14: 0
      • S15: 0
      • S16: 0
      • S17: 0
      • S18: 0
      • S19: 0
      • S20: 0
      • S21: 0
      • S22: 0
      • S23: 0
      • S24: 0
  19. GPT-5.6 Sol / Galaxy-API code / run 2 → result 4 (denoising)
    • Content: Content score below 0.80. Value: 0.794034. Required minimum: 0.8.
      • Category agreement (F1): 0.997915 to 0.999937 (37 checks)
      • Matching records (F1): 0.973693 to 0.999841 (96 checks)
      • Numerical agreement (CCC): 0.818342 to 0.999955 (192 checks)
      • Present, finite data cells (F1): 0.998723 to 0.999841 (48 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S02: 0.717139
      • S03: 0.734028
      • S08: 0.799127
      • S09: 0.71205
      • S10: 0.616753
      • S11: 0.616887
      • S12: 0.730149
      • S17: 0.689973
      • S18: 0.770241
      • S19: 0.701263
      • S20: 0.719442
  20. GPT-5.6 Sol / Galaxy-API code / run 3 → result 2 (filtered reads)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (24 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0
      • S02: 0
      • S03: 0
      • S04: 0
      • S05: 0
      • S06: 0
      • S07: 0
      • S08: 0
      • S09: 0
      • S10: 0
      • S11: 0
      • S12: 0
      • S13: 0
      • S14: 0
      • S15: 0
      • S16: 0
      • S17: 0
      • S18: 0
      • S19: 0
      • S20: 0
      • S21: 0
      • S22: 0
      • S23: 0
      • S24: 0
  21. GPT-5.6 Sol / Galaxy-API code / run 3 → result 4 (denoising)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Category agreement (F1): 0 (48 checks)
      • Matching records (F1): 0 (144 checks)
      • Numerical agreement (CCC): 0 to 0.99987 (192 checks)
      • Present, finite data cells (F1): 0 (96 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0
      • S02: 0
      • S03: 0
      • S04: 0
      • S05: 0
      • S06: 0
      • S07: 0
      • S08: 0
      • S09: 0
      • S10: 0
      • S11: 0
      • S12: 0
      • S13: 0
      • S14: 0
      • S15: 0
      • S16: 0
      • S17: 0
      • S18: 0
      • S19: 0
      • S20: 0
      • S21: 0
      • S22: 0
      • S23: 0
      • S24: 0
  22. GPT-5.6 Sol / Galaxy-API code / run 3 → result 5 (pair merges)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Category agreement (F1): 0 (24 checks)
      • Matching records (F1): 0 (24 checks)
      • Numerical agreement (CCC): 0 (24 checks)
      • Present, finite data cells (F1): 0 (24 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0
      • S02: 0
      • S03: 0
      • S04: 0
      • S05: 0
      • S06: 0
      • S07: 0
      • S08: 0
      • S09: 0
      • S10: 0
      • S11: 0
      • S12: 0
      • S13: 0
      • S14: 0
      • S15: 0
      • S16: 0
      • S17: 0
      • S18: 0
      • S19: 0
      • S20: 0
      • S21: 0
      • S22: 0
      • S23: 0
      • S24: 0
  23. GPT-5.6 Sol / Galaxy-API code / run 3 → result 6 (ASV counts unfiltered)
    • Content: Content score below 0.80. Value: 0.782884. Required minimum: 0.8.
      • Matching records (F1): 0.896722
      • Numerical agreement (CCC): 0.973602
      • Present, finite data cells (F1): 0.896722
  24. GPT-5.6 Sol / Galaxy-API code / run 3 → result 7 (ASV counts nonchimeric)
    • Content: Content score below 0.80. Value: 0.798686. Required minimum: 0.8.
      • Matching records (F1): 0.905349
      • Numerical agreement (CCC): 0.974415
      • Present, finite data cells (F1): 0.905349
  25. GPT-5.6 Sol / Galaxy-API code / run 3 → result 8 (taxonomy)
    • Content: Content score below 0.80. Value: 0.716489. Required minimum: 0.8.
      • Category agreement (F1): 0.977075
      • Matching records (F1): 0.905349 (2 checks)
      • Numerical agreement (CCC): 0.988174
      • Present, finite data cells (F1): 0.905349
  26. DeepSeek V4 Pro / Galaxy-API code / run 1 → result 4 (denoising)
    • Content: Content score below 0.80. Value: 0.794034. Required minimum: 0.8.
      • Category agreement (F1): 0.997915 to 0.999937 (37 checks)
      • Matching records (F1): 0.973693 to 0.999841 (96 checks)
      • Numerical agreement (CCC): 0.818342 to 0.999955 (192 checks)
      • Present, finite data cells (F1): 0.998723 to 0.999841 (48 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S02: 0.717139
      • S03: 0.734028
      • S08: 0.799127
      • S09: 0.71205
      • S10: 0.616753
      • S11: 0.616887
      • S12: 0.730149
      • S17: 0.689973
      • S18: 0.770241
      • S19: 0.701263
      • S20: 0.719442
  27. DeepSeek V4 Pro / Galaxy-API code / run 2 → result 4 (denoising)
    • Content: Content score below 0.80. Value: 0.794034. Required minimum: 0.8.
      • Category agreement (F1): 0.997915 to 0.999937 (37 checks)
      • Matching records (F1): 0.973693 to 0.999841 (96 checks)
      • Numerical agreement (CCC): 0.818342 to 0.999955 (192 checks)
      • Present, finite data cells (F1): 0.998723 to 0.999841 (48 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S02: 0.717139
      • S03: 0.734028
      • S08: 0.799127
      • S09: 0.71205
      • S10: 0.616753
      • S11: 0.616887
      • S12: 0.730149
      • S17: 0.689973
      • S18: 0.770241
      • S19: 0.701263
      • S20: 0.719442
  28. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 3 (error models)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (96 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0
      • S02: 0
      • S03: 0
      • S04: 0
      • S05: 0
      • S06: 0
      • S07: 0
      • S08: 0
      • S09: 0
      • S10: 0
      • S11: 0
      • S12: 0
      • S13: 0
      • S14: 0
      • S15: 0
      • S16: 0
      • S17: 0
      • S18: 0
      • S19: 0
      • S20: 0
      • S21: 0
      • S22: 0
      • S23: 0
      • S24: 0
    • Instruction: Required file is missing: 03_error_models/S01/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S01/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S02/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S02/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S03/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S03/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S04/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S04/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S05/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S05/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S06/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S06/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S07/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S07/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S08/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S08/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S09/forward.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
    • Instruction: Required file is missing: 03_error_models/S09/reverse.rdsTask requirement: 3. final_answer/03_error_models/{sample}/ RDS Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
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  29. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 4 (denoising)
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  30. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 5 (pair merges)
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  32. DeepSeek V4 Pro / Open-ended code / run 1 → result 4 (denoising)
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  36. DeepSeek V4 Pro / Open-ended code / run 3 → result 3 (error models)
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Task text

The scientific part of the task, identical in both conditions. The general submission rules and the instructions for each condition are on the overview page.

Full task text

Task

Reconstruct sequence variants and taxonomic assignments for all 24 environmental 16S V4 libraries, preserving sample identities and uncertainty. Infer exact amplicon sequence variants with a quality-dependent sequencing-error model rather than fixed-similarity OTU clustering. Reconstruct paired sequences from their overlap and assess chimeras across samples. Assign taxonomy using a reference-trained sequence classifier with bootstrap support.

Inputs

  • Twenty-four paired 2×250 MiSeq 515F/806R libraries and their sample/mate manifest; library-name prefixes are not verified run labels.
  • Supplied 515F/806R primer definitions: primers.tsv.
  • SILVA 132 taxonomy resources.

Key parameters and conditions

  • Remove fixed leading prefixes equal to the lengths of the supplied forward 515F and reverse 806R primers. The truncation positions in the original reads are 199 forward and 200 reverse, before removing those prefixes. This is fixed positional trimming, not primer-match filtering. Discard a read pair if either trimmed mate is shorter than its required post-trimming length. Allow at most two expected errors per mate, no ambiguous bases, quality truncation at 2 and PhiX removal.
  • Infer sequence variants by testing abundance against a quality-dependent substitution-error model learned with LOESS and self-consistent sequence inference. Learn directional errors separately for each library and do not pool libraries for inference. Require at least 12 bp of exact paired overlap rather than concatenation. Error learning uses input order, a 10^8-base learning target (or all available bases when fewer), at most ten self-consistency iterations and OMEGA_C=0; this learning target does not subsample the reads submitted for denoising.
  • Combine all samples before consensus chimera removal. Do not rarefy, drop samples or apply another ASV abundance/length filter. Use taxonomy bootstrap threshold 50 and seed 0; retain unclassified ranks and confidence evidence. Use reference-trained k-mer naive-Bayes taxonomy assignment on the supplied orientation, without reverse-complement searching or an additional exact species-match stage.

Required results

  1. final_answer/01_quality/{sample}/
    native quality reports + plots
    Input quality profiles and filtering/retention reports for both mates.
  2. final_answer/02_filtered_reads/{sample}/
    FASTQ
    Both complete filtered mate files. Files: {sample}/forward.fastq.gz, {sample}/reverse.fastq.gz.
  3. final_answer/03_error_models/{sample}/
    RDS
    Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
  4. final_answer/04_denoising/{sample}/
    RDS
    Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
  5. final_answer/05_pair_merges/{sample}/
    RDS
    merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
  6. final_answer/06_asv_counts_unfiltered/
    TSV
    counts.tsv: one row per exact ASV sequence, first column sequence, then S01–S24 integer count columns; retain zero counts and all sample columns. Files: counts.tsv.
  7. final_answer/07_asv_counts_nonchimeric/
    TSV
    counts.tsv: one row per exact ASV sequence, first column sequence, then S01–S24 integer count columns; retain zero counts and all sample columns. Files: counts.tsv.
  8. final_answer/08_taxonomy/
    TSV
    taxonomy.tsv and bootstrap.tsv: sequence followed by Kingdom, Phylum, Class, Order, Family, Genus. Use NA for unclassified/missing values; bootstrap values are percentages. Files: bootstrap.tsv, taxonomy.tsv.
  9. final_answer/09_read_tracking/
    TSV
    counts.tsv columns: sample, input_pairs, filtered_pairs, denoised_forward, denoised_reverse, merged_pairs, pre_chimera, nonchimeric. Explain major losses briefly in method.md. Files: counts.tsv.

How this task is scored

Each scored result is compared with the reference result, which the task authors made by running the IWC workflow behind this task on usegalaxy.org with the settings in the task text. A result's score is the product of the checks listed for it, each from 0 to 1. When a result is scored per sample or other unit, each copy gets its own score and the result's score is their average; if any copy is missing or cannot be read, the result scores 0. A passing result must score at least 0.80 and meet the required member checks, method and output instructions. A failing result retains its numerical score in the continuous average. The overview page describes the checks in more detail.

No.Required resultWhat the task asks for How it is scored
101_quality/{sample}/
native quality reports + plots		Input quality profiles and filtering/retention reports for both mates.Required, not scored.
202_filtered_reads/{sample}/
FASTQ		Both complete filtered mate files. Files: {sample}/forward.fastq.gz, {sample}/reverse.fastq.gz.
  • the same rows or records as the reference (F1 of their identifiers)
Scored for each of the 24 samples and averaged.
303_error_models/{sample}/
RDS		Forward/reverse learned error models and numeric error estimates. Files: {sample}/forward.rds, {sample}/reverse.rds.
  • the same rows or records as the reference (F1 of their identifiers)
  • the required columns or fields are present (F1)
  • values are present in the same cells (F1)
  • values agree (Lin's concordance correlation)
Scored for each of the 24 samples and averaged.
404_denoising/{sample}/
RDS		Directional sequence inference and abundance evidence. Files: {sample}/forward.rds, {sample}/reverse.rds.
  • the same rows or records as the reference (F1 of their identifiers)
  • the required columns or fields are present (F1)
  • values are present in the same cells (F1)
  • values agree (Lin's concordance correlation)
  • category labels agree (macro F1)
Scored for each of the 24 samples and averaged.
505_pair_merges/{sample}/
RDS		merged.rds: the accepted paired-merge data frame, including sequence, abundance, forward/reverse inference-row references, nmatch, nmismatch, nindel, prefer and accept. Failed overlaps are represented by losses in read tracking, not fabricated merge rows. Files: {sample}/merged.rds.
  • the same rows or records as the reference (F1 of their identifiers)
  • the required columns or fields are present (F1)
  • values are present in the same cells (F1)
  • values agree (Lin's concordance correlation)
  • category labels agree (macro F1)
Scored for each of the 24 samples and averaged.
606_asv_counts_unfiltered/
TSV		counts.tsv: one row per exact ASV sequence, first column sequence, then S01–S24 integer count columns; retain zero counts and all sample columns. Files: counts.tsv.
  • the same rows or records as the reference (F1 of their identifiers)
  • the required columns or fields are present (F1)
  • values are present in the same cells (F1)
  • counts or intensities agree on a log(1 + x) scale (concordance correlation)
707_asv_counts_nonchimeric/
TSV		counts.tsv: one row per exact ASV sequence, first column sequence, then S01–S24 integer count columns; retain zero counts and all sample columns. Files: counts.tsv.
  • the same rows or records as the reference (F1 of their identifiers)
  • the required columns or fields are present (F1)
  • values are present in the same cells (F1)
  • counts or intensities agree on a log(1 + x) scale (concordance correlation)
808_taxonomy/
TSV		taxonomy.tsv and bootstrap.tsv: sequence followed by Kingdom, Phylum, Class, Order, Family, Genus. Use NA for unclassified/missing values; bootstrap values are percentages. Files: bootstrap.tsv, taxonomy.tsv.
  • the same rows or records as the reference (F1 of their identifiers)
  • the required columns or fields are present (F1)
  • values are present in the same cells (F1)
  • values agree (Lin's concordance correlation)
  • category labels agree (macro F1)
909_read_tracking/
TSV		counts.tsv columns: sample, input_pairs, filtered_pairs, denoised_forward, denoised_reverse, merged_pairs, pre_chimera, nonchimeric. Explain major losses briefly in method.md. Files: counts.tsv.
  • the same rows or records as the reference (F1 of their identifiers)
  • the required columns or fields are present (F1)
  • values are present in the same cells (F1)
  • counts or intensities agree on a log(1 + x) scale (concordance correlation)

Data updated 27 October 2026, 08:48 EDT.