IWC multi-step task

Task 10: LC-MS features and ion relationships

What the task asks for

Detect and align chromatographic peaks across all LC-MS runs, fill in missing peaks from the raw signal, and annotate isotopes and co-eluting ions.

8 scored results8 required18 runs scored

Codex GPT-5.6 Luna

6 of 6 runs scored
Galaxy-API code 0.458 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.539
All results pass0 of 3 runsruns in which every scored result passes
run 10.6255/8run 20.3753/8run 30.3753/8
Open-ended code 0.125 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.127
All results pass0 of 3 runsruns in which every scored result passes
run 10.1251/8run 20.1251/8run 30.1251/8

Codex GPT-5.6 Sol

6 of 6 runs scored
Galaxy-API code 0.667 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.917
All results pass0 of 3 runsruns in which every scored result passes
run 10.7506/8run 20.7506/8run 30.5004/8
Open-ended code 0.958 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.978
All results pass2 of 3 runsruns in which every scored result passes
run 11.0008/8run 20.8757/8run 31.0008/8

DeepSeek V4 Pro via Codex

6 of 6 runs scored
Galaxy-API code 0.250 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.292
All results pass0 of 3 runsruns in which every scored result passes
run 10.3753/8run 20.2502/8run 30.1251/8
Open-ended code 0.125 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.140
All results pass0 of 3 runsruns in which every scored result passes
run 10.1251/8run 20.1251/8run 30.1251/8

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 1.000, 1.000, 0.000, 1.000, 0.000, 0.000, 0.946 and 1.000 on its 8 results. 5 of them pass, so BixBench3 acc = 5/8 = 0.625; the average of all 8 scores is 0.618, 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 0.458 vs 0.125; GPT-5.6 Sol 0.667 vs 0.958; DeepSeek V4 Pro 0.250 vs 0.125.

What Galaxy added

Galaxy has the specified peak detection, grouping, retention-time correction, gap filling and ion annotation as ready tools, and every Galaxy run used them; retention-time correction passed in 8 of 9 Galaxy runs. In Open-ended code, GPT-5.6 Luna and DeepSeek V4 Pro never installed these methods and wrote their own peak detection and alignment, which matched the reference poorly. GPT-5.6 Sol installed them locally and passed nearly everything.

Why Galaxy did not do better

No Galaxy run passed the two peak-group membership results. The grouping tool lists member peaks by row number as R prints them, so 100000 appears as 1e+05, and splitting that list with text tools gave identifiers that do not match the peak table. Other runs mixed identifier schemes between tables or kept the form's default of writing missing intensities as zero. Assembling tables from native outputs also cost the raw-signal result in three runs, and two DeepSeek V4 Pro runs grouped with a minimum sample fraction of 0 instead of 0.9.

Run-level details (4)
  • All Open-ended code runs with GPT-5.6 Luna and DeepSeek V4 Pro wrote their own peak detection, grouping and alignment in Python instead of installing the specified methods; peak agreement was 0.24 or lower.
  • The grouping tool lists member peaks by row number in R's notation, so 100000 becomes 1e+05. The first and second Galaxy runs with GPT-5.6 Sol and the third with DeepSeek V4 Pro split that list with text tools and delivered identifiers that do not match the peak table. Other Galaxy runs paired row numbers with peak names from another table, among them the first with GPT-5.6 Luna, and the third GPT-5.6 Sol run kept the form's default of writing missing intensities as zero.
  • The first and third Galaxy runs with DeepSeek V4 Pro grouped with a minimum sample fraction of 0 instead of 0.9, giving 16,201 features instead of 4,218.
  • Three Galaxy runs lost the raw-signal result while assembling tables: the second with DeepSeek V4 Pro concatenated 76 tables with their header rows, the third dropped the last character of every value, and the second with GPT-5.6 Luna kept the file extension in sample names.
Instruction, format and method errors (18)
  • Membership identifiers do not literally match the submitted peak identifiers; 271478 distinct mismatches.Task requirement: 3. final_answer/03_initial_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.

    GPT-5.6 Luna / Galaxy-API code / run 1 → result 3

  • Membership identifiers do not literally match the submitted peak identifiers; 271782 distinct mismatches.Task requirement: 5. final_answer/05_aligned_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.

    GPT-5.6 Luna / Galaxy-API code / run 1 → result 5

  • Required collection members are missing, repeated or outside the fixed input domain.Task requirement: 1. final_answer/01_raw_signals/ TSV scans.tsv columns: acquisition, scan, rt, tic, bpi; every original scan. Files: scans.tsv.

    GPT-5.6 Luna / Galaxy-API code / run 2 → result 1

  • Required collection members are missing, repeated or outside the fixed input domain.Task requirement: 2. final_answer/02_detected_peaks/ TSV peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled. Include every detected peak. Files: peaks.tsv.

    GPT-5.6 Luna / Galaxy-API code / run 2 → result 2

  • Required collection members are missing, repeated or outside the fixed input domain.Task requirement: 3. final_answer/03_initial_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.

    GPT-5.6 Luna / Galaxy-API code / run 2 → result 3

  • Required collection members are missing, repeated or outside the fixed input domain.Task requirement: 5. final_answer/05_aligned_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.

    GPT-5.6 Luna / Galaxy-API code / run 2 → result 5

  • Named columns/order differ from the required table. Named fields are repeated. A row does not contain the stated field domain.Task requirement: 2. final_answer/02_detected_peaks/ TSV peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled. Include every detected peak. Files: peaks.tsv.

    GPT-5.6 Luna / Galaxy-API code / run 3 → result 2

  • An explicit peak_id does not uniquely identify its stored row.Task requirement: 6. final_answer/06_final_intensities/ TSV peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt and each acquisition. Preserve filled status and integration bounds. Files: intensities.tsv, peaks.tsv.

    GPT-5.6 Luna / Open-ended code / run 2 → result 6

  • Membership identifiers do not literally match the submitted peak identifiers; 3 distinct mismatches.Task requirement: 3. final_answer/03_initial_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.

    GPT-5.6 Sol / Galaxy-API code / run 1 → result 3; GPT-5.6 Sol / Galaxy-API code / run 2 → result 3; DeepSeek V4 Pro / Galaxy-API code / run 3 → result 3

  • Membership identifiers do not match the submitted peak table.Task requirement: 5. final_answer/05_aligned_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.

    GPT-5.6 Sol / Galaxy-API code / run 1 → result 5; GPT-5.6 Sol / Galaxy-API code / run 2 → result 5; DeepSeek V4 Pro / Galaxy-API code / run 2 → result 5

  • Undetected or unfillable intensity cells were written as 0 instead of NA.Task requirement: Use integrated areas (into). An undetected or still-unfillable feature/acquisition cell is NA, not zero. The supplied class labels define the eight grouping classes; do not substitute batch. Missing-peak integration uses the medians of the group members’ m/z and RT bounds, with no extra expansion. Coelution annotation uses only the FWHM grouping and isotope steps, without correlation-based regrouping or adduct inference.

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

  • Required file is missing: 06_final_intensities/peaks.tsvTask requirement: 6. final_answer/06_final_intensities/ TSV peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt and each acquisition. Preserve filled status and integration bounds. Files: intensities.tsv, peaks.tsv.

    DeepSeek V4 Pro / Galaxy-API code / run 1 → result 6

  • Required file is missing: 02_detected_peaks/peaks.tsvTask requirement: 2. final_answer/02_detected_peaks/ TSV peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled. Include every detected peak. Files: peaks.tsv.

    DeepSeek V4 Pro / Galaxy-API code / run 2 → result 2

  • Required file is missing: 03_initial_groups/peaks.tsvTask requirement: 3. final_answer/03_initial_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.

    DeepSeek V4 Pro / Galaxy-API code / run 2 → result 3

  • Unresolved isotope fields must use NA.Task requirement: 8. final_answer/08_ion_annotations/ TSV annotations.tsv: feature_id, mz, rt, coelution_group, isotope_group, isotope_number, charge; unresolved isotope fields are NA. Files: annotations.tsv.

    DeepSeek V4 Pro / Galaxy-API code / run 2 → result 8

  • Membership identifiers do not literally match the submitted peak identifiers; 3 distinct mismatches.Task requirement: 5. final_answer/05_aligned_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.

    DeepSeek V4 Pro / Galaxy-API code / run 3 → result 5

  • Missingness fields differ from the supplied class domain.Task requirement: 7. final_answer/07_missing_detection/ TSV missingness.tsv: feature_id, mz, rt, NA_<class>, Pct_NA_<class> for each supplied class; counts and percentages before filling. Files: missingness.tsv.

    DeepSeek V4 Pro / Galaxy-API code / run 3 → result 7

  • Missing intensity cells must use NA.Task requirement: Use integrated areas (into). An undetected or still-unfillable feature/acquisition cell is NA, not zero. The supplied class labels define the eight grouping classes; do not substitute batch. Missing-peak integration uses the medians of the group members’ m/z and RT bounds, with no extra expansion. Coelution annotation uses only the FWHM grouping and isotope steps, without correlation-based regrouping or adduct inference.

    DeepSeek V4 Pro / Open-ended code / run 2 → result 3; DeepSeek V4 Pro / Open-ended code / run 2 → result 5; DeepSeek V4 Pro / Open-ended code / run 2 → result 6; DeepSeek V4 Pro / Open-ended code / run 3 → result 3; DeepSeek V4 Pro / Open-ended code / run 3 → result 5; DeepSeek V4 Pro / Open-ended code / run 3 → result 6

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 TokensMinutesRecords1raw signals2detected peaks3initial groups4retention time correction5aligned groups6final intensities7missing detection8ion annotations
GPT-5.6 LunaGalaxy-API code1trial run5/8 = 0.6250.61828.6M385Trace
History		1.00 Passed1.00 Passed0.00Instruction1.00 Passed0.00Instruction0.00Content0.94 Passed1.00 Passed
23/8 = 0.3750.62512.6M138Trace
History		1.00Instruction1.00Instruction0.00Instruction1.00 Passed0.00Instruction1.00 Passed0.00Content1.00 Passed
33/8 = 0.3750.37524.2M301Trace
History		1.00 Passed0.00Format0.00Content1.00 Passed0.00Content0.00Content0.00Content1.00 Passed
Open-ended code1trial run1/8 = 0.1250.1282.2M34Trace1.00 Passed0.00Content0.00Content0.01Check0.00Content0.00Content0.00Content0.00Content
21/8 = 0.1250.1252.5M19Trace1.00 Passed0.00Content0.00Content0.00Check0.00Content0.00Instruction0.00Content0.00Content
31/8 = 0.1250.1278.5M51Trace1.00 Passed0.00Content0.00Content0.00Check0.00Content0.00Content0.01Content0.00Content
GPT-5.6 SolGalaxy-API code16/8 = 0.7501.00011.4M281Trace
History		1.00 Passed1.00 Passed1.00Instruction1.00 Passed1.00Instruction1.00 Passed1.00 Passed1.00 Passed
26/8 = 0.7501.0005.8M346Trace
History		1.00 Passed1.00 Passed1.00Instruction1.00 Passed1.00Instruction1.00 Passed1.00 Passed1.00 Passed
34/8 = 0.5000.75017.6M460Trace
History		1.00 Passed0.00Content1.00Instruction1.00 Passed1.00Instruction1.00 Passed0.00Content1.00 Passed
Open-ended code18/8 = 1.0000.9871.7M20Trace1.00 Passed0.99 Passed0.99 Passed0.98 Passed0.98 Passed0.98 Passed0.99 Passed0.96 Passed
27/8 = 0.8750.9602.9M36Trace1.00 Passed0.99 Passed0.99 Passed0.98 Passed0.98 Passed0.78Content0.99 Passed0.93 Passed
38/8 = 1.0000.9874.6M22Trace1.00 Passed0.99 Passed0.99 Passed0.98 Passed0.98 Passed0.98 Passed0.99 Passed0.96 Passed
DeepSeek V4 ProGalaxy-API code13/8 = 0.3750.37528.4M268Trace
History		1.00 Passed1.00 Passed0.00Content0.99 Passed0.00Content0.00Instruction0.00Content0.00Content
22/8 = 0.2500.37532.6M559Trace
History		0.00Content0.00Instruction0.00Instruction0.99 Passed0.99Instruction0.00Content0.99 Passed0.00Format
31/8 = 0.1250.12669.8M364Trace
History		0.00Content1.00 Passed0.00Instruction0.00Check0.00Instruction0.00Content0.00Format0.00Content
Open-ended code11/8 = 0.1250.12711.3M71Trace1.00 Passed0.00Content0.00Content0.01Check0.00Content0.00Content0.00Content0.00Content
21/8 = 0.1250.1607.5M117Trace1.00 Passed0.01Content0.00Format0.21Check0.00Format0.00Format0.05Content0.00Content
31/8 = 0.1250.13319.5M105Trace1.00 Passed0.00Content0.00Format0.06Check0.00Format0.00Format0.00Content0.00Content

Why results did not pass

  1. GPT-5.6 Luna / Galaxy-API code / run 1 → result 3 (initial groups)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (2 checks)
    • Instruction: Membership identifiers do not literally match the submitted peak identifiers; 271478 distinct mismatches.Task requirement: 3. final_answer/03_initial_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.
  2. GPT-5.6 Luna / Galaxy-API code / run 1 → result 5 (aligned groups)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (2 checks)
    • Instruction: Membership identifiers do not literally match the submitted peak identifiers; 271782 distinct mismatches.Task requirement: 5. final_answer/05_aligned_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.
  3. GPT-5.6 Luna / Galaxy-API code / run 1 → result 6 (final intensities)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0
  4. GPT-5.6 Luna / Galaxy-API code / run 2 → result 1 (raw signals)
    • Instruction: Required collection members are missing, repeated or outside the fixed input domain.Task requirement: 1. final_answer/01_raw_signals/ TSV scans.tsv columns: acquisition, scan, rt, tic, bpi; every original scan. Files: scans.tsv.
  5. GPT-5.6 Luna / Galaxy-API code / run 2 → result 2 (detected peaks)
    • Instruction: Required collection members are missing, repeated or outside the fixed input domain.Task requirement: 2. final_answer/02_detected_peaks/ TSV peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled. Include every detected peak. Files: peaks.tsv.
  6. GPT-5.6 Luna / Galaxy-API code / run 2 → result 3 (initial groups)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (2 checks)
    • Instruction: Required collection members are missing, repeated or outside the fixed input domain.Task requirement: 3. final_answer/03_initial_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.
  7. GPT-5.6 Luna / Galaxy-API code / run 2 → result 5 (aligned groups)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (2 checks)
    • Instruction: Required collection members are missing, repeated or outside the fixed input domain.Task requirement: 5. final_answer/05_aligned_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.
  8. GPT-5.6 Luna / Galaxy-API code / run 2 → result 7 (missing detection)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0
  9. GPT-5.6 Luna / Galaxy-API code / run 3 → result 2 (detected peaks)
    • 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: 2. final_answer/02_detected_peaks/ TSV peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled. Include every detected peak. Files: peaks.tsv.
    • Format: Named fields are repeated.Task requirement: 2. final_answer/02_detected_peaks/ TSV peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled. Include every detected peak. Files: peaks.tsv.
    • Instruction: A row does not contain the stated field domain.Task requirement: 2. final_answer/02_detected_peaks/ TSV peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled. Include every detected peak. Files: peaks.tsv.
  10. GPT-5.6 Luna / Galaxy-API code / run 3 → result 3 (initial groups)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Present, finite data cells (F1): 0.77698
      • Required content missing or unreadable: 0 (2 checks)
  11. GPT-5.6 Luna / Galaxy-API code / run 3 → result 5 (aligned groups)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Present, finite data cells (F1): 0.777885
      • Required content missing or unreadable: 0 (2 checks)
  12. GPT-5.6 Luna / Galaxy-API code / run 3 → result 6 (final intensities)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Present, finite data cells (F1): 0.938745
      • Required content missing or unreadable: 0
  13. GPT-5.6 Luna / Galaxy-API code / run 3 → result 7 (missing detection)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0
  14. GPT-5.6 Luna / Open-ended code / run 1 → result 2 (detected peaks)
    • Content: Content score below 0.80. Value: 0.000575631. Required minimum: 0.8.
      • Matching records (F1): 0.0841567
      • Numerical agreement (CCC): 0.965824 to 0.999953 (2 checks)
      • Present, finite data cells (F1): 0.0841567 (2 checks)
  15. GPT-5.6 Luna / Open-ended code / run 1 → result 3 (initial groups)
    • Content: Content score below 0.80. Value: 6.14295e-05. Required minimum: 0.8.
      • Matching records (F1): 0.0976486 to 0.192733 (3 checks)
      • Numerical agreement (CCC): 0.817645 to 0.838322 (2 checks)
      • Present, finite data cells (F1): 0.128194 to 0.192733 (2 checks)
  16. GPT-5.6 Luna / Open-ended code / run 1 → result 4 (retention time correction)
    • Content: Content score below 0.80. Value: 0.0180859. Required minimum: 0.8.
      • Numerical agreement (CCC): 0.0180859
    • Check: A required check is below its minimum. Required minimum: 0.97.
      • Numerical agreement (CCC): 0.0180859
  17. GPT-5.6 Luna / Open-ended code / run 1 → result 5 (aligned groups)
    • Content: Content score below 0.80. Value: 6.63058e-05. Required minimum: 0.8.
      • Matching records (F1): 0.0989908 to 0.193795 (3 checks)
      • Numerical agreement (CCC): 0.819761 to 0.858619 (2 checks)
      • Present, finite data cells (F1): 0.130749 to 0.193795 (2 checks)
  18. GPT-5.6 Luna / Open-ended code / run 1 → result 6 (final intensities)
    • Content: Content score below 0.80. Value: 8.90957e-07. Required minimum: 0.8.
      • Matching records (F1): 0.0384646 to 0.193795 (2 checks)
      • Numerical agreement (CCC): 0.798444 to 0.999917 (3 checks)
      • Present, finite data cells (F1): 0.0384646 to 0.124851 (3 checks)
  19. GPT-5.6 Luna / Open-ended code / run 1 → result 7 (missing detection)
    • Content: Content score below 0.80. Value: 0.00674807. Required minimum: 0.8.
      • Required content missing or unreadable: 0.179678 to 0.193795 (3 checks)
  20. GPT-5.6 Luna / Open-ended code / run 1 → result 8 (ion annotations)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0 to 0.193795 (4 checks)
      • Present, finite data cells (F1): 0.0762977
      • Required fields: 0.0976384
  21. GPT-5.6 Luna / Open-ended code / run 2 → result 2 (detected peaks)
    • Content: Content score below 0.80. Value: 4.68741e-07. Required minimum: 0.8.
      • Matching records (F1): 0.00821994
      • Numerical agreement (CCC): 0.844092 to 0.999856 (2 checks)
      • Present, finite data cells (F1): 0.00821994 (2 checks)
  22. GPT-5.6 Luna / Open-ended code / run 2 → result 3 (initial groups)
    • Content: Content score below 0.80. Value: 1.53058e-08. Required minimum: 0.8.
      • Matching records (F1): 0.00975638 to 0.0657238 (3 checks)
      • Numerical agreement (CCC): 0.528843 to 0.801432 (2 checks)
      • Present, finite data cells (F1): 0.0130379 to 0.0657238 (2 checks)
  23. GPT-5.6 Luna / Open-ended code / run 2 → result 4 (retention time correction)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Numerical agreement (CCC): 0
    • Check: A required check is below its minimum. Required minimum: 0.97.
      • Numerical agreement (CCC): 0
  24. GPT-5.6 Luna / Open-ended code / run 2 → result 5 (aligned groups)
    • Content: Content score below 0.80. Value: 9.18072e-12. Required minimum: 0.8.
      • Matching records (F1): 0.00419686 to 0.00982456 (3 checks)
      • Numerical agreement (CCC): 0.495735 to 0.833711 (2 checks)
      • Present, finite data cells (F1): 0.00558145 to 0.00982456 (2 checks)
  25. GPT-5.6 Luna / Open-ended code / run 2 → result 6 (final intensities)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0.00982456
      • Numerical agreement (CCC): 0.676566
      • Present, finite data cells (F1): 0.00704508
      • Required content missing or unreadable: 0
    • Instruction: An explicit peak_id does not uniquely identify its stored row.Task requirement: 6. final_answer/06_final_intensities/ TSV peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt and each acquisition. Preserve filled status and integration bounds. Files: intensities.tsv, peaks.tsv.
  26. GPT-5.6 Luna / Open-ended code / run 2 → result 7 (missing detection)
    • Content: Content score below 0.80. Value: 3.51143e-05. Required minimum: 0.8.
      • Required content missing or unreadable: 0.00982456 to 0.363796 (3 checks)
  27. GPT-5.6 Luna / Open-ended code / run 2 → result 8 (ion annotations)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0 to 0.00982456 (4 checks)
      • Present, finite data cells (F1): 0
      • Required fields: 0
  28. GPT-5.6 Luna / Open-ended code / run 3 → result 2 (detected peaks)
    • Content: Content score below 0.80. Value: 0.00100989. Required minimum: 0.8.
      • Matching records (F1): 0.103412
      • Numerical agreement (CCC): 0.913206 to 0.999982 (2 checks)
      • Present, finite data cells (F1): 0.103412 (2 checks)
  29. GPT-5.6 Luna / Open-ended code / run 3 → result 3 (initial groups)
    • Content: Content score below 0.80. Value: 0.000170099. Required minimum: 0.8.
      • Matching records (F1): 0.149317 to 0.19728 (3 checks)
      • Numerical agreement (CCC): 0.844932 to 0.918343 (2 checks)
      • Present, finite data cells (F1): 0.191212 to 0.19728 (2 checks)
  30. GPT-5.6 Luna / Open-ended code / run 3 → result 4 (retention time correction)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Numerical agreement (CCC): 0
    • Check: A required check is below its minimum. Required minimum: 0.97.
      • Numerical agreement (CCC): 0
  31. GPT-5.6 Luna / Open-ended code / run 3 → result 5 (aligned groups)
    • Content: Content score below 0.80. Value: 0.0001678. Required minimum: 0.8.
      • Matching records (F1): 0.149297 to 0.195538 (3 checks)
      • Numerical agreement (CCC): 0.846913 to 0.929927 (2 checks)
      • Present, finite data cells (F1): 0.190879 to 0.195538 (2 checks)
  32. GPT-5.6 Luna / Open-ended code / run 3 → result 6 (final intensities)
    • Content: Content score below 0.80. Value: 4.6113e-06. Required minimum: 0.8.
      • Matching records (F1): 0.0521846 to 0.195538 (2 checks)
      • Numerical agreement (CCC): 0.874408 to 0.99998 (3 checks)
      • Present, finite data cells (F1): 0.0521846 to 0.199873 (3 checks)
  33. GPT-5.6 Luna / Open-ended code / run 3 → result 7 (missing detection)
    • Content: Content score below 0.80. Value: 0.0122722. Required minimum: 0.8.
      • Required content missing or unreadable: 0.195538 to 0.320968 (3 checks)
  34. GPT-5.6 Luna / Open-ended code / run 3 → result 8 (ion annotations)
    • Content: Content score below 0.80. Value: 2.05063e-07. Required minimum: 0.8.
      • Matching records (F1): 0.0075 to 0.170869 (4 checks)
      • Present, finite data cells (F1): 0.0855432
      • Required fields: 0.599494
  35. GPT-5.6 Sol / Galaxy-API code / run 1 → result 3 (initial groups)
    • Instruction: Membership identifiers do not literally match the submitted peak identifiers; 3 distinct mismatches.Task requirement: 3. final_answer/03_initial_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.
  36. GPT-5.6 Sol / Galaxy-API code / run 1 → result 5 (aligned groups)
    • Instruction: Membership identifiers do not match the submitted peak table.Task requirement: 5. final_answer/05_aligned_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.
  37. GPT-5.6 Sol / Galaxy-API code / run 2 → result 3 (initial groups)
    • Instruction: Membership identifiers do not literally match the submitted peak identifiers; 3 distinct mismatches.Task requirement: 3. final_answer/03_initial_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.
  38. GPT-5.6 Sol / Galaxy-API code / run 2 → result 5 (aligned groups)
    • Instruction: Membership identifiers do not match the submitted peak table.Task requirement: 5. final_answer/05_aligned_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.
  39. GPT-5.6 Sol / Galaxy-API code / run 3 → result 2 (detected peaks)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0
  40. GPT-5.6 Sol / Galaxy-API code / run 3 → result 3 (initial groups)
    • Instruction: Undetected or unfillable intensity cells were written as 0 instead of NA.Task requirement: Use integrated areas (into). An undetected or still-unfillable feature/acquisition cell is NA, not zero. The supplied class labels define the eight grouping classes; do not substitute batch. Missing-peak integration uses the medians of the group members’ m/z and RT bounds, with no extra expansion. Coelution annotation uses only the FWHM grouping and isotope steps, without correlation-based regrouping or adduct inference.
  41. GPT-5.6 Sol / Galaxy-API code / run 3 → result 5 (aligned groups)
    • Instruction: Undetected or unfillable intensity cells were written as 0 instead of NA.Task requirement: Use integrated areas (into). An undetected or still-unfillable feature/acquisition cell is NA, not zero. The supplied class labels define the eight grouping classes; do not substitute batch. Missing-peak integration uses the medians of the group members’ m/z and RT bounds, with no extra expansion. Coelution annotation uses only the FWHM grouping and isotope steps, without correlation-based regrouping or adduct inference.
  42. GPT-5.6 Sol / Galaxy-API code / run 3 → result 7 (missing detection)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0
  43. GPT-5.6 Sol / Open-ended code / run 2 → result 6 (final intensities)
    • Content: Content score below 0.80. Value: 0.786761. Required minimum: 0.8.
      • Matching records (F1): 0.928336 to 0.997629 (2 checks)
      • Numerical agreement (CCC): 0.994338 to 0.999997 (3 checks)
      • Present, finite data cells (F1): 0.928336 to 0.994918 (3 checks)
  44. DeepSeek V4 Pro / Galaxy-API code / run 1 → result 3 (initial groups)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0.413066
      • Numerical agreement (CCC): 0.999994
      • Present, finite data cells (F1): 0.771927
      • Required content missing or unreadable: 0 (2 checks)
  45. DeepSeek V4 Pro / Galaxy-API code / run 1 → result 5 (aligned groups)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0.412949
      • Numerical agreement (CCC): 0.999616
      • Present, finite data cells (F1): 0.772097
      • Required content missing or unreadable: 0 (2 checks)
  46. DeepSeek V4 Pro / Galaxy-API code / run 1 → result 6 (final intensities)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0.412949
      • Numerical agreement (CCC): 0.999699
      • Present, finite data cells (F1): 0.429403
      • Required content missing or unreadable: 0
    • Instruction: Required file is missing: 06_final_intensities/peaks.tsvTask requirement: 6. final_answer/06_final_intensities/ TSV peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt and each acquisition. Preserve filled status and integration bounds. Files: intensities.tsv, peaks.tsv.
  47. DeepSeek V4 Pro / Galaxy-API code / run 1 → result 7 (missing detection)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0
  48. DeepSeek V4 Pro / Galaxy-API code / run 1 → result 8 (ion annotations)
    • Content: Content score below 0.80. Value: 0.00472784. Required minimum: 0.8.
      • Matching records (F1): 0.1758 to 0.454693 (4 checks)
      • Present, finite data cells (F1): 0.454693
      • Required fields: 0.834627
  49. DeepSeek V4 Pro / Galaxy-API code / run 2 → result 1 (raw signals)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0
  50. DeepSeek V4 Pro / Galaxy-API code / run 2 → result 2 (detected peaks)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0
    • Instruction: Required file is missing: 02_detected_peaks/peaks.tsvTask requirement: 2. final_answer/02_detected_peaks/ TSV peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled. Include every detected peak. Files: peaks.tsv.
  51. DeepSeek V4 Pro / Galaxy-API code / run 2 → result 3 (initial groups)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0.999525
      • Numerical agreement (CCC): 0.999999
      • Present, finite data cells (F1): 0.999614
      • Required content missing or unreadable: 0 (2 checks)
    • Instruction: Required file is missing: 03_initial_groups/peaks.tsvTask requirement: 3. final_answer/03_initial_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.
  52. DeepSeek V4 Pro / Galaxy-API code / run 2 → result 5 (aligned groups)
    • Instruction: Membership identifiers do not match the submitted peak table.Task requirement: 5. final_answer/05_aligned_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.
  53. DeepSeek V4 Pro / Galaxy-API code / run 2 → result 6 (final intensities)
    • Content: Content score below 0.80. Value: 0.00802599. Required minimum: 0.8.
      • Matching records (F1): 0.20038 to 0.999051 (2 checks)
      • Numerical agreement (CCC): 0.999712 to 1 (3 checks)
      • Present, finite data cells (F1): 0.20038 to 0.998922 (3 checks)
  54. DeepSeek V4 Pro / Galaxy-API code / run 2 → result 8 (ion annotations)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0 to 0.701466 (4 checks)
      • Present, finite data cells (F1): 0.701466
      • Required fields: 0.383757
    • Format: Unresolved isotope fields must use NA.Task requirement: 8. final_answer/08_ion_annotations/ TSV annotations.tsv: feature_id, mz, rt, coelution_group, isotope_group, isotope_number, charge; unresolved isotope fields are NA. Files: annotations.tsv.
  55. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 1 (raw signals)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Numerical agreement (CCC): 0 to 1 (2 checks)
  56. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 3 (initial groups)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0.999525
      • Numerical agreement (CCC): 0.999999
      • Present, finite data cells (F1): 0.999614
      • Required content missing or unreadable: 0 (2 checks)
    • Instruction: Membership identifiers do not literally match the submitted peak identifiers; 3 distinct mismatches.Task requirement: 3. final_answer/03_initial_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.
  57. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 4 (retention time correction)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Numerical agreement (CCC): 0
    • Check: A required check is below its minimum. Required minimum: 0.97.
      • Numerical agreement (CCC): 0
  58. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 5 (aligned groups)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0.999051
      • Numerical agreement (CCC): 0.99962
      • Present, finite data cells (F1): 0.998843
      • Required content missing or unreadable: 0 (2 checks)
    • Instruction: Membership identifiers do not literally match the submitted peak identifiers; 3 distinct mismatches.Task requirement: 5. final_answer/05_aligned_groups/ TSV features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.
  59. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 6 (final intensities)
    • Content: Content score below 0.80. Value: 0.00453571. Required minimum: 0.8.
      • Matching records (F1): 0.175344 to 0.999051 (2 checks)
      • Numerical agreement (CCC): 0.843373 to 0.999905 (3 checks)
      • Present, finite data cells (F1): 0.175344 to 0.998922 (3 checks)
  60. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 7 (missing detection)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0
    • Format: Missingness fields differ from the supplied class domain.Task requirement: 7. final_answer/07_missing_detection/ TSV missingness.tsv: feature_id, mz, rt, NA_<class>, Pct_NA_<class> for each supplied class; counts and percentages before filling. Files: missingness.tsv.
  61. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 8 (ion annotations)
    • Content: Content score below 0.80. Value: 0.00472784. Required minimum: 0.8.
      • Matching records (F1): 0.1758 to 0.454693 (4 checks)
      • Present, finite data cells (F1): 0.454693
      • Required fields: 0.834627
  62. DeepSeek V4 Pro / Open-ended code / run 1 → result 2 (detected peaks)
    • Content: Content score below 0.80. Value: 3.82679e-05. Required minimum: 0.8.
      • Matching records (F1): 0.0356875
      • Numerical agreement (CCC): 0.841993 to 0.99995 (2 checks)
      • Present, finite data cells (F1): 0.0356875 (2 checks)
  63. DeepSeek V4 Pro / Open-ended code / run 1 → result 3 (initial groups)
    • Content: Content score below 0.80. Value: 2.36408e-09. Required minimum: 0.8.
      • Matching records (F1): 0.0114602 to 0.0266556 (3 checks)
      • Numerical agreement (CCC): 0.731623 to 0.855005 (2 checks)
      • Present, finite data cells (F1): 0.017412 to 0.0266556 (2 checks)
  64. DeepSeek V4 Pro / Open-ended code / run 1 → result 4 (retention time correction)
    • Content: Content score below 0.80. Value: 0.0156408. Required minimum: 0.8.
      • Numerical agreement (CCC): 0.0156408
    • Check: A required check is below its minimum. Required minimum: 0.97.
      • Numerical agreement (CCC): 0.0156408
  65. DeepSeek V4 Pro / Open-ended code / run 1 → result 5 (aligned groups)
    • Content: Content score below 0.80. Value: 2.46175e-09. Required minimum: 0.8.
      • Matching records (F1): 0.0107382 to 0.0274143 (3 checks)
      • Numerical agreement (CCC): 0.686451 to 0.926087 (2 checks)
      • Present, finite data cells (F1): 0.0175033 to 0.0274143 (2 checks)
  66. DeepSeek V4 Pro / Open-ended code / run 1 → result 6 (final intensities)
    • Content: Content score below 0.80. Value: 1.07289e-10. Required minimum: 0.8.
      • Matching records (F1): 0.00680823 to 0.0274143 (2 checks)
      • Numerical agreement (CCC): 0.646037 to 0.999927 (3 checks)
      • Present, finite data cells (F1): 0.00680823 to 0.0260691 (3 checks)
  67. DeepSeek V4 Pro / Open-ended code / run 1 → result 7 (missing detection)
    • Content: Content score below 0.80. Value: 5.07588e-05. Required minimum: 0.8.
      • Required content missing or unreadable: 0.0274143 to 0.0675393 (3 checks)
  68. DeepSeek V4 Pro / Open-ended code / run 1 → result 8 (ion annotations)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0 to 0.0274143 (4 checks)
      • Present, finite data cells (F1): 0.00160256
  69. DeepSeek V4 Pro / Open-ended code / run 2 → result 2 (detected peaks)
    • Content: Content score below 0.80. Value: 0.0110583. Required minimum: 0.8.
      • Matching records (F1): 0.238231
      • Numerical agreement (CCC): 0.824126 to 0.992433 (2 checks)
      • Present, finite data cells (F1): 0.238231 (2 checks)
  70. DeepSeek V4 Pro / Open-ended code / run 2 → result 3 (initial groups)
    • Content: Content score below 0.80. Value: 2.06169e-06. Required minimum: 0.8.
      • Matching records (F1): 0.0607888 to 0.118701 (3 checks)
      • Numerical agreement (CCC): 0.71825 to 0.751398 (2 checks)
      • Present, finite data cells (F1): 0.0607888 to 0.143268 (2 checks)
    • Format: Missing intensity cells must use NA.Task requirement: Use integrated areas (into). An undetected or still-unfillable feature/acquisition cell is NA, not zero. The supplied class labels define the eight grouping classes; do not substitute batch. Missing-peak integration uses the medians of the group members’ m/z and RT bounds, with no extra expansion. Coelution annotation uses only the FWHM grouping and isotope steps, without correlation-based regrouping or adduct inference.
  71. DeepSeek V4 Pro / Open-ended code / run 2 → result 4 (retention time correction)
    • Content: Content score below 0.80. Value: 0.216251. Required minimum: 0.8.
      • Numerical agreement (CCC): 0.216251
    • Check: A required check is below its minimum. Required minimum: 0.97.
      • Numerical agreement (CCC): 0.216251
  72. DeepSeek V4 Pro / Open-ended code / run 2 → result 5 (aligned groups)
    • Content: Content score below 0.80. Value: 2.08806e-06. Required minimum: 0.8.
      • Matching records (F1): 0.0608579 to 0.118989 (3 checks)
      • Numerical agreement (CCC): 0.719195 to 0.754314 (2 checks)
      • Present, finite data cells (F1): 0.0608579 to 0.143511 (2 checks)
    • Format: Missing intensity cells must use NA.Task requirement: Use integrated areas (into). An undetected or still-unfillable feature/acquisition cell is NA, not zero. The supplied class labels define the eight grouping classes; do not substitute batch. Missing-peak integration uses the medians of the group members’ m/z and RT bounds, with no extra expansion. Coelution annotation uses only the FWHM grouping and isotope steps, without correlation-based regrouping or adduct inference.
  73. DeepSeek V4 Pro / Open-ended code / run 2 → result 6 (final intensities)
    • Content: Content score below 0.80. Value: 0.000103909. Required minimum: 0.8.
      • Matching records (F1): 0.116508 to 0.314761 (2 checks)
      • Numerical agreement (CCC): 0.811265 to 0.993478 (3 checks)
      • Present, finite data cells (F1): 0.116508 to 0.316037 (3 checks)
    • Format: Missing intensity cells must use NA.Task requirement: Use integrated areas (into). An undetected or still-unfillable feature/acquisition cell is NA, not zero. The supplied class labels define the eight grouping classes; do not substitute batch. Missing-peak integration uses the medians of the group members’ m/z and RT bounds, with no extra expansion. Coelution annotation uses only the FWHM grouping and isotope steps, without correlation-based regrouping or adduct inference.
  74. DeepSeek V4 Pro / Open-ended code / run 2 → result 7 (missing detection)
    • Content: Content score below 0.80. Value: 0.0542159. Required minimum: 0.8.
      • Required content missing or unreadable: 0.314761 to 0.547225 (3 checks)
  75. DeepSeek V4 Pro / Open-ended code / run 2 → result 8 (ion annotations)
    • Content: Content score below 0.80. Value: 4.40971e-05. Required minimum: 0.8.
      • Matching records (F1): 0.0341324 to 0.314761 (4 checks)
      • Present, finite data cells (F1): 0.211376
      • Required fields: 0.62691
  76. DeepSeek V4 Pro / Open-ended code / run 3 → result 2 (detected peaks)
    • Content: Content score below 0.80. Value: 1.08461e-05. Required minimum: 0.8.
      • Matching records (F1): 0.0234879
      • Numerical agreement (CCC): 0.837079 to 0.999951 (2 checks)
      • Present, finite data cells (F1): 0.0234879 (2 checks)
  77. DeepSeek V4 Pro / Open-ended code / run 3 → result 3 (initial groups)
    • Content: Content score below 0.80. Value: 5.46123e-13. Required minimum: 0.8.
      • Matching records (F1): 0.00197134 to 0.00561191 (3 checks)
      • Numerical agreement (CCC): 0.637257 to 0.799795 (2 checks)
      • Present, finite data cells (F1): 0.00307541 to 0.00561191 (2 checks)
    • Format: Missing intensity cells must use NA.Task requirement: Use integrated areas (into). An undetected or still-unfillable feature/acquisition cell is NA, not zero. The supplied class labels define the eight grouping classes; do not substitute batch. Missing-peak integration uses the medians of the group members’ m/z and RT bounds, with no extra expansion. Coelution annotation uses only the FWHM grouping and isotope steps, without correlation-based regrouping or adduct inference.
  78. DeepSeek V4 Pro / Open-ended code / run 3 → result 4 (retention time correction)
    • Content: Content score below 0.80. Value: 0.0608811. Required minimum: 0.8.
      • Numerical agreement (CCC): 0.0608811
    • Check: A required check is below its minimum. Required minimum: 0.97.
      • Numerical agreement (CCC): 0.0608811
  79. DeepSeek V4 Pro / Open-ended code / run 3 → result 5 (aligned groups)
    • Content: Content score below 0.80. Value: 3.9548e-14. Required minimum: 0.8.
      • Matching records (F1): 0.00105219 to 0.00389442 (3 checks)
      • Numerical agreement (CCC): 0.333255 to 0.808316 (2 checks)
      • Present, finite data cells (F1): 0.00236236 to 0.00389442 (2 checks)
    • Format: Missing intensity cells must use NA.Task requirement: Use integrated areas (into). An undetected or still-unfillable feature/acquisition cell is NA, not zero. The supplied class labels define the eight grouping classes; do not substitute batch. Missing-peak integration uses the medians of the group members’ m/z and RT bounds, with no extra expansion. Coelution annotation uses only the FWHM grouping and isotope steps, without correlation-based regrouping or adduct inference.
  80. DeepSeek V4 Pro / Open-ended code / run 3 → result 6 (final intensities)
    • Content: Content score below 0.80. Value: 1.62512e-16. Required minimum: 0.8.
      • Matching records (F1): 0.000465813 to 0.00389442 (2 checks)
      • Numerical agreement (CCC): 0.35761 to 0.999931 (3 checks)
      • Present, finite data cells (F1): 0.000465813 to 0.00290057 (3 checks)
    • Format: Missing intensity cells must use NA.Task requirement: Use integrated areas (into). An undetected or still-unfillable feature/acquisition cell is NA, not zero. The supplied class labels define the eight grouping classes; do not substitute batch. Missing-peak integration uses the medians of the group members’ m/z and RT bounds, with no extra expansion. Coelution annotation uses only the FWHM grouping and isotope steps, without correlation-based regrouping or adduct inference.
  81. DeepSeek V4 Pro / Open-ended code / run 3 → result 7 (missing detection)
    • Content: Content score below 0.80. Value: 2.35469e-06. Required minimum: 0.8.
      • Required content missing or unreadable: 0.00389442 to 0.155256 (3 checks)
  82. DeepSeek V4 Pro / Open-ended code / run 3 → result 8 (ion annotations)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0 to 0.00389442 (4 checks)
      • Present, finite data cells (F1): 0
      • Required fields: 0

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

Analyze every supplied liquid chromatography–mass spectrometry acquisition to produce a peak-area matrix and ion-feature annotations, accounting for retention-time drift and missing detections. Compound identification and biological differential-abundance testing are outside scope. Detect chromatographic peaks by continuous-wavelet analysis of accurate-mass regions of interest built from successive centroid scans. Use shared peak landmarks for nonlinear retention-time correction and establish correspondence on corrected times. Recover missing peak areas by integrating the underlying signal, and assess coelution/isotope relationships without claiming confirmed metabolite identities.

Inputs

  • All supplied liquid chromatography–mass spectrometry acquisitions and sample identities.
  • Class metadata including blanks, batches and distinct pooled-QC preparations; do not combine these classes.

Key parameters and conditions

  • For wavelet peak detection, use mass tolerance 3 ppm, peak widths 5–20 s and S/N≥10. Require at least three mass-trace centroids with intensity≥5,000 and apply an intensity-noise threshold of 1,000. Use intensity-weighted mean m/z, wavelet-derived integration limits and minimum overlapping-peak m/z difference −0.001 Da. Recover missing peak areas by integrating raw signal within the established feature bounds, not by rerunning another peak detector or imputing values.
  • Use density-based correspondence with RT bandwidth 5 s and m/z bin width 0.01 Da. Before missing-peak integration, require detection in at least 90% of acquisitions in at least one supplied class (minimum sample count 1). Apply the same rule before and after RT correction; do not pool or drop classes.
  • For RT landmarks, require peak groups present in at least 70% of all acquisitions and no more than one peak beyond the total number of acquisitions. Fit LOESS correction with span 0.2 and Gaussian-family fitting. Quantify integrated areas in every acquisition; fill missing peaks from the raw signal with no extra m/z or RT window expansion, not with zero or a sample mean.
  • For coelution/isotope annotation, group around abundant peaks using a retention-time window whose total width is 0.6 times the estimated FWHM (±0.3×FWHM). Estimate FWHM as 2.35 times the peak’s full time span divided by 6. Use mass tolerances 5 ppm and 0.015 Da, maximum charge 2 and at most 4 expected isotopes. Require the isotope-abundance rule in at least 50% of samples. These annotations are not confirmed compound identities.
  • Preserve sample/feature identities, original and corrected times, units and coordinate conventions, and distinguish directly detected peaks from newly integrated peaks. Arbitrary feature/group names do not change scientific credit; plots are optional.
  • Use integrated areas (into). An undetected or still-unfillable feature/acquisition cell is NA, not zero. The supplied class labels define the eight grouping classes; do not substitute batch. Missing-peak integration uses the medians of the group members’ m/z and RT bounds, with no extra expansion. Coelution annotation uses only the FWHM grouping and isotope steps, without correlation-based regrouping or adduct inference.

Required results

  1. final_answer/01_raw_signals/
    TSV
    scans.tsv columns: acquisition, scan, rt, tic, bpi; every original scan. Files: scans.tsv.
  2. final_answer/02_detected_peaks/
    TSV
    peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled. Include every detected peak. Files: peaks.tsv.
  3. final_answer/03_initial_groups/
    TSV
    features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.
  4. final_answer/04_retention_time_correction/
    TSV
    times.tsv columns: acquisition, scan, raw_time, adjusted_time; every scan, including unchanged times. Files: times.tsv.
  5. final_answer/05_aligned_groups/
    TSV
    features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.tsv.
  6. final_answer/06_final_intensities/
    TSV
    peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt and each acquisition. Preserve filled status and integration bounds. Files: intensities.tsv, peaks.tsv.
  7. final_answer/07_missing_detection/
    TSV
    missingness.tsv: feature_id, mz, rt, NA_<class>, Pct_NA_<class> for each supplied class; counts and percentages before filling. Files: missingness.tsv.
  8. final_answer/08_ion_annotations/
    TSV
    annotations.tsv: feature_id, mz, rt, coelution_group, isotope_group, isotope_number, charge; unresolved isotope fields are NA. Files: annotations.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. 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_raw_signals/
TSV		scans.tsv columns: acquisition, scan, rt, tic, bpi; every original scan. Files: scans.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)
  • counts or intensities agree on a log(1 + x) scale (concordance correlation)
202_detected_peaks/
TSV		peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled. Include every detected peak. Files: peaks.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)
  • counts or intensities agree on a log(1 + x) scale (concordance correlation)
303_initial_groups/
TSV		features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.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)
  • counts or intensities agree on a log(1 + x) scale (concordance correlation)
404_retention_time_correction/
TSV		times.tsv columns: acquisition, scan, raw_time, adjusted_time; every scan, including unchanged times. Files: times.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)
505_aligned_groups/
TSV		features.tsv: feature_id, mz, rt, mzmin, mzmax, rtmin, rtmax, npeaks; membership.tsv: feature_id, peak_id; peaks.tsv: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt, then one column per acquisition. Feature/peak identifiers must link the files; mz is in Da, rt in seconds. Files: features.tsv, intensities.tsv, membership.tsv, peaks.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)
  • counts or intensities agree on a log(1 + x) scale (concordance correlation)
606_final_intensities/
TSV		peaks.tsv columns: peak_id, acquisition, mz, rt, mzmin, mzmax, rtmin, rtmax, into, is_filled; intensities.tsv: feature_id, mz, rt and each acquisition. Preserve filled status and integration bounds. Files: intensities.tsv, peaks.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)
  • counts or intensities agree on a log(1 + x) scale (concordance correlation)
707_missing_detection/
TSV		missingness.tsv: feature_id, mz, rt, NA_<class>, Pct_NA_<class> for each supplied class; counts and percentages before filling. Files: missingness.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)
808_ion_annotations/
TSV		annotations.tsv: feature_id, mz, rt, coelution_group, isotope_group, isotope_number, charge; unresolved isotope fields are NA. Files: annotations.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)

Data updated 27 October 2026, 08:48 EDT.