Task 4: Paired RNA-seq effects and donor robustness

Why results did not pass

1. GPT-5.6 Luna / Galaxy-API code / run 1 → result 1 (alignments)
   • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
     • Alignment records: 0.99851 to 0.998901 (8 checks)
     • Summary statistics within tolerance: 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
2. GPT-5.6 Luna / Galaxy-API code / run 1 → result 3 (fixed gene domain)
   • Instruction: The required eligible (0/1) column is missing from this table; membership in another table does not replace it.Task requirement: 3. final_answer/03_fixed_gene_domain/ TSV matrix.tsv and eligible.tsv have gene_id, S01–S08 and eligible (0/1); the former contains the full counted domain and the latter E. Preserve original/version-stripped identifiers in the crosswalk. Files: eligible.tsv, matrix.tsv.
3. GPT-5.6 Luna / Galaxy-API code / run 1 → result 4 (differential expression)
   • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
     • Required content missing or unreadable: 0 (5 checks)
   • Member: A required member scores below 0.80. Required minimum: 0.8.
     • member 1: 0
     • member 2: 0
     • member 3: 0
     • member 4: 0
     • member 5: 0
   • Format: Named columns/order differ from the required table.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
   • Instruction: A row does not contain the stated field domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
   • Format: Named columns/order differ from the required table.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
   • Instruction: A row does not contain the stated field domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
   • Format: Named columns/order differ from the required table.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
   • Instruction: A row does not contain the stated field domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
   • Format: Named columns/order differ from the required table.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
   • Instruction: A row does not contain the stated field domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
   • Format: Named columns/order differ from the required table.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
   • Instruction: A row does not contain the stated field domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
4. GPT-5.6 Luna / Galaxy-API code / run 1 → result 5 (normalization)
   • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
     • Numerical agreement (CCC): 0.999992 to 0.999993 (5 checks)
     • Required content missing or unreadable: 0 (5 checks)
   • Member: A required member scores below 0.80. Required minimum: 0.8.
     • member 1: 0
     • member 2: 0
     • member 3: 0
     • member 4: 0
     • member 5: 0
   • Format: Named columns/order differ from the required table.Task requirement: 5. final_answer/05_normalization/{fit}/ TSV counts.tsv: gene_id and every included sample; size_factors.tsv: sample, size_factor. Files: {fit}/counts.tsv, {fit}/size_factors.tsv.
   • Instruction: A row does not contain the stated field domain.Task requirement: 5. final_answer/05_normalization/{fit}/ TSV counts.tsv: gene_id and every included sample; size_factors.tsv: sample, size_factor. Files: {fit}/counts.tsv, {fit}/size_factors.tsv.
   • Format: Named columns/order differ from the required table.Task requirement: 5. final_answer/05_normalization/{fit}/ TSV counts.tsv: gene_id and every included sample; size_factors.tsv: sample, size_factor. Files: {fit}/counts.tsv, {fit}/size_factors.tsv.
   • Instruction: A row does not contain the stated field domain.Task requirement: 5. final_answer/05_normalization/{fit}/ TSV counts.tsv: gene_id and every included sample; size_factors.tsv: sample, size_factor. Files: {fit}/counts.tsv, {fit}/size_factors.tsv.
   • Format: Named columns/order differ from the required table.Task requirement: 5. final_answer/05_normalization/{fit}/ TSV counts.tsv: gene_id and every included sample; size_factors.tsv: sample, size_factor. Files: {fit}/counts.tsv, {fit}/size_factors.tsv.
   • Instruction: A row does not contain the stated field domain.Task requirement: 5. final_answer/05_normalization/{fit}/ TSV counts.tsv: gene_id and every included sample; size_factors.tsv: sample, size_factor. Files: {fit}/counts.tsv, {fit}/size_factors.tsv.
   • Format: Named columns/order differ from the required table.Task requirement: 5. final_answer/05_normalization/{fit}/ TSV counts.tsv: gene_id and every included sample; size_factors.tsv: sample, size_factor. Files: {fit}/counts.tsv, {fit}/size_factors.tsv.
   • Instruction: A row does not contain the stated field domain.Task requirement: 5. final_answer/05_normalization/{fit}/ TSV counts.tsv: gene_id and every included sample; size_factors.tsv: sample, size_factor. Files: {fit}/counts.tsv, {fit}/size_factors.tsv.
   • Format: Named columns/order differ from the required table.Task requirement: 5. final_answer/05_normalization/{fit}/ TSV counts.tsv: gene_id and every included sample; size_factors.tsv: sample, size_factor. Files: {fit}/counts.tsv, {fit}/size_factors.tsv.
   • Instruction: A row does not contain the stated field domain.Task requirement: 5. final_answer/05_normalization/{fit}/ TSV counts.tsv: gene_id and every included sample; size_factors.tsv: sample, size_factor. Files: {fit}/counts.tsv, {fit}/size_factors.tsv.
5. GPT-5.6 Luna / Galaxy-API code / run 1 → result 6 (GO full)
   • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
     • Category agreement (F1): 0.999071
     • Matching records (F1): 0.999765 (2 checks)
     • Numerical agreement (CCC): 0.999244 to 0.999986 (2 checks)
     • Within 5pct: 0 (2 checks)
6. GPT-5.6 Luna / Galaxy-API code / run 1 → result 7 (GO robustness)
   • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
     • Category agreement (F1): 0.998208 to 0.999071 (4 checks)
     • Matching records (F1): 0.999765 (10 checks)
     • Numerical agreement (CCC): 0.988574 to 0.999986 (10 checks)
     • Within 5pct: 0 (10 checks)
   • Member: A required member scores below 0.80. Required minimum: 0.8.
     • member 1: 0
     • member 2: 0
     • member 3: 0
     • member 4: 0
     • member 5: 0
7. GPT-5.6 Luna / Galaxy-API code / run 1 → result 8 (library assemblies)
   • Content: Content score below 0.80. Value: 0.00897197. Required minimum: 0.8.
     • Matching records (F1): 0.0855988 to 0.108782 (16 checks)
     • Numerical agreement (CCC): 0.961162 to 0.990503 (8 checks)
   • Member: A required member scores below 0.80. Required minimum: 0.8.
     • S01: 0.011517
     • S02: 0.0112474
     • S03: 0.00737641
     • S04: 0.00923008
     • S05: 0.00791334
     • S06: 0.00819315
     • S07: 0.00915211
     • S08: 0.00714627
8. GPT-5.6 Luna / Galaxy-API code / run 1 → result 9 (common assembly)
   • Content: Content score below 0.80. Value: 0.00764731. Required minimum: 0.8.
     • Matching records (F1): 0.0863827 to 0.0885282 (2 checks)
9. GPT-5.6 Luna / Galaxy-API code / run 1 → result 10 (splice junctions)
   • Method: Recorded STAR settings contradict the task (outFilterType Normal) in S01, S02, S03, S04, S05, S06, S07, S08.Task requirement: For spliced alignment use splice-junction-based filtering, at most 20 mapping loci, minimum splice overhang 8 (1 at annotated junctions), at most 4% mismatches relative to the read-pair length with no separate absolute mismatch cap, alignment score and matched bases each at least 66% of the read-pair length, intron length 20–1,000,000 and paired-read gap at most 1,000,000. Use the supplied annotation for junction indexing with overhang 100.
10. GPT-5.6 Luna / Galaxy-API code / run 2 → result 1 (alignments)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Alignment records: 0.999165 to 0.999432 (8 checks)
      • Summary statistics within tolerance: 0 (25 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
11. GPT-5.6 Luna / Galaxy-API code / run 2 → result 3 (fixed gene domain)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (2 checks)
    • Instruction: The required eligible (0/1) column is missing from this table; membership in another table does not replace it.Task requirement: 3. final_answer/03_fixed_gene_domain/ TSV matrix.tsv and eligible.tsv have gene_id, S01–S08 and eligible (0/1); the former contains the full counted domain and the latter E. Preserve original/version-stripped identifiers in the crosswalk. Files: eligible.tsv, matrix.tsv.
    • Instruction: A row does not contain the stated field domain.Task requirement: 3. final_answer/03_fixed_gene_domain/ TSV matrix.tsv and eligible.tsv have gene_id, S01–S08 and eligible (0/1); the former contains the full counted domain and the latter E. Preserve original/version-stripped identifiers in the crosswalk. Files: eligible.tsv, matrix.tsv.
    • Instruction: The required eligible (0/1) column is missing from this table; membership in another table does not replace it.Task requirement: 3. final_answer/03_fixed_gene_domain/ TSV matrix.tsv and eligible.tsv have gene_id, S01–S08 and eligible (0/1); the former contains the full counted domain and the latter E. Preserve original/version-stripped identifiers in the crosswalk. Files: eligible.tsv, matrix.tsv.
    • Instruction: A row does not contain the stated field domain.Task requirement: 3. final_answer/03_fixed_gene_domain/ TSV matrix.tsv and eligible.tsv have gene_id, S01–S08 and eligible (0/1); the former contains the full counted domain and the latter E. Preserve original/version-stripped identifiers in the crosswalk. Files: eligible.tsv, matrix.tsv.
12. GPT-5.6 Luna / Galaxy-API code / run 2 → result 4 (differential expression)
    • Content: Content score below 0.80. Value: 1.28678e-06. Required minimum: 0.8.
      • Matching records (F1): 0.00137363 (5 checks)
      • Numerical agreement (CCC): 0.580862 to 0.79636 (5 checks)
      • Present, finite data cells (F1): 0.00137363 to 0.00142548 (5 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 1.28115e-06
      • member 2: 1.16534e-06
      • member 3: 1.55933e-06
      • member 4: 1.096e-06
      • member 5: 1.33205e-06
13. GPT-5.6 Luna / Galaxy-API code / run 2 → result 5 (normalization)
    • Content: Content score below 0.80. Value: 1.75778e-07. Required minimum: 0.8.
      • Matching records (F1): 0.00137363 (5 checks)
      • Numerical agreement (CCC): 0.0691515 to 0.993118 (10 checks)
      • Present, finite data cells (F1): 0.00137363 (5 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 1.4131e-07
      • member 2: 2.22159e-07
      • member 3: 2.87262e-07
      • member 4: 1.23976e-07
      • member 5: 1.04184e-07
14. GPT-5.6 Luna / Galaxy-API code / run 2 → result 6 (GO full)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (6 checks)
      • Within 5pct: 0 (2 checks)
    • Format: A field explicitly specified as 0/1 uses another encoding.Task requirement: 6. final_answer/06_go_full/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: down/categories.tsv, down/membership.tsv, down/universe.tsv, up/categories.tsv, up/membership.tsv, up/universe.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 6. final_answer/06_go_full/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: down/categories.tsv, down/membership.tsv, down/universe.tsv, up/categories.tsv, up/membership.tsv, up/universe.tsv.
    • Format: A field explicitly specified as 0/1 uses another encoding.Task requirement: 6. final_answer/06_go_full/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: down/categories.tsv, down/membership.tsv, down/universe.tsv, up/categories.tsv, up/membership.tsv, up/universe.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 6. final_answer/06_go_full/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: down/categories.tsv, down/membership.tsv, down/universe.tsv, up/categories.tsv, up/membership.tsv, up/universe.tsv.
15. GPT-5.6 Luna / Galaxy-API code / run 2 → result 7 (GO robustness)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (30 checks)
      • Within 5pct: 0 (10 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
      • member 5: 0
    • Instruction: Required file is missing: 07_go_robustness/F0/up/universe.tsvTask requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Instruction: Required file is missing: 07_go_robustness/F0/up/membership.tsvTask requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Instruction: Required file is missing: 07_go_robustness/F0/up/categories.tsvTask requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Instruction: Required file is missing: 07_go_robustness/F0/down/universe.tsvTask requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Instruction: Required file is missing: 07_go_robustness/F0/down/membership.tsvTask requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Instruction: Required file is missing: 07_go_robustness/F0/down/categories.tsvTask requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: A field explicitly specified as 0/1 uses another encoding.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: A field explicitly specified as 0/1 uses another encoding.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: A field explicitly specified as 0/1 uses another encoding.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: A field explicitly specified as 0/1 uses another encoding.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: A field explicitly specified as 0/1 uses another encoding.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: A field explicitly specified as 0/1 uses another encoding.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: A field explicitly specified as 0/1 uses another encoding.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: A field explicitly specified as 0/1 uses another encoding.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
16. GPT-5.6 Luna / Galaxy-API code / run 2 → result 8 (library assemblies)
    • Content: Content score below 0.80. Value: 0.424092. Required minimum: 0.8.
      • Matching records (F1): 0.637132 to 0.667416 (16 checks)
      • Numerical agreement (CCC): 0.984215 to 0.987576 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0.404981
      • S02: 0.425432
      • S03: 0.434712
      • S04: 0.427991
      • S05: 0.427239
      • S06: 0.433877
      • S07: 0.412942
      • S08: 0.425563
17. GPT-5.6 Luna / Galaxy-API code / run 2 → result 9 (common assembly)
    • Content: Content score below 0.80. Value: 0.121426. Required minimum: 0.8.
      • Matching records (F1): 0.340187 to 0.35694 (2 checks)
18. GPT-5.6 Luna / Galaxy-API code / run 2 → result 10 (splice junctions)
    • Method: Recorded STAR settings contradict the task (outFilterType Normal) in S01, S02, S03, S04, S05, S06, S07, S08.Task requirement: For spliced alignment use splice-junction-based filtering, at most 20 mapping loci, minimum splice overhang 8 (1 at annotated junctions), at most 4% mismatches relative to the read-pair length with no separate absolute mismatch cap, alignment score and matched bases each at least 66% of the read-pair length, intron length 20–1,000,000 and paired-read gap at most 1,000,000. Use the supplied annotation for junction indexing with overhang 100.
19. GPT-5.6 Luna / Galaxy-API code / run 3 → result 6 (GO full)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Category agreement (F1): 0.999961 (2 checks)
      • Matching records (F1): 0.999903 to 0.999951 (4 checks)
      • Numerical agreement (CCC): 0.99729 to 0.999996 (2 checks)
      • Present, finite data cells (F1): 0.999951 (2 checks)
      • Within 5pct: 0 (2 checks)
20. GPT-5.6 Luna / Galaxy-API code / run 3 → result 7 (GO robustness)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Category agreement (F1): 0.999961 (6 checks)
      • Matching records (F1): 0.999888 to 0.999951 (12 checks)
      • Numerical agreement (CCC): 0.996042 to 0.999998 (6 checks)
      • Present, finite data cells (F1): 0.999902 to 0.999951 (6 checks)
      • Required content missing or unreadable: 0 (12 checks)
      • Within 5pct: 0 (10 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
      • member 5: 0
21. GPT-5.6 Luna / Galaxy-API code / run 3 → result 9 (common assembly)
    • Content: Content score below 0.80. Value: 0.183897. Required minimum: 0.8.
      • Matching records (F1): 0.386844 to 0.475378 (2 checks)
22. GPT-5.6 Luna / Open-ended code / run 1 → result 1 (alignments)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Alignment records: 0.988778 to 0.995683 (8 checks)
      • Summary statistics within tolerance: 0 (41 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
23. GPT-5.6 Luna / Open-ended code / run 1 → result 2 (gene counts)
    • Method: More fragments are assigned than the library has read pairs (2,000,000), which is impossible when each fragment is counted at most once: S01, S02, S03, S04, S05, S06, S07, S08.Task requirement: Eight libraries with 2,000,000 read pairs each / Count unstranded fragments over annotated gene-exon unions with at least one overlapping base.
24. GPT-5.6 Luna / Open-ended code / run 1 → result 3 (fixed gene domain)
    • Content: Content score below 0.80. Value: 0.66179. Required minimum: 0.8.
      • Matching records (F1): 0.939953
      • Numerical agreement (CCC): 0.869908 to 0.984622 (3 checks)
      • Present, finite data cells (F1): 0.939953 (2 checks)
    • Check: A required check is below its minimum. Required minimum: 0.99.
      • Matching records (F1): 0.939953
      • Numerical agreement (CCC): 0.930377
25. GPT-5.6 Luna / Open-ended code / run 1 → result 4 (differential expression)
    • Content: Content score below 0.80. Value: 0.438439. Required minimum: 0.8.
      • Matching records (F1): 0.939953 (5 checks)
      • Numerical agreement (CCC): 0.481062 to 0.508235 (5 checks)
      • Present, finite data cells (F1): 0.939953 to 0.940023 (5 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.435591
      • member 2: 0.449032
      • member 3: 0.425024
      • member 4: 0.433747
      • member 5: 0.448801
26. GPT-5.6 Luna / Open-ended code / run 1 → result 5 (normalization)
    • Content: Content score below 0.80. Value: 0.74253. Required minimum: 0.8.
      • Matching records (F1): 0.939953 (5 checks)
      • Numerical agreement (CCC): 0.866547 to 0.973081 (10 checks)
      • Present, finite data cells (F1): 0.939953 (5 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.743602
      • member 2: 0.744067
      • member 3: 0.745883
      • member 4: 0.741263
      • member 5: 0.737836
27. GPT-5.6 Luna / Open-ended code / run 1 → result 6 (GO full)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Category agreement (F1): 0.49528 to 0.992429 (4 checks)
      • Matching records (F1): 0.940164 to 0.991858 (6 checks)
      • Numerical agreement (CCC): 0.166034 to 0.19864 (2 checks)
      • Present, finite data cells (F1): 0.940164 to 0.991858 (4 checks)
      • Within 5pct: 0 (2 checks)
28. GPT-5.6 Luna / Open-ended code / run 1 → result 7 (GO robustness)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Category agreement (F1): 0.494756 to 0.992429 (20 checks)
      • Matching records (F1): 0.940164 to 0.991858 (30 checks)
      • Numerical agreement (CCC): 0.166034 to 0.19864 (10 checks)
      • Present, finite data cells (F1): 0.940164 to 0.991858 (20 checks)
      • Within 5pct: 0 (10 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
      • member 5: 0
29. GPT-5.6 Luna / Open-ended code / run 1 → result 10 (splice junctions)
    • Method: Recorded STAR settings contradict the task (outFilterMismatchNoverReadLmax 1.0) in S01, S02, S03, S04, S05, S06, S07, S08.Task requirement: For spliced alignment use splice-junction-based filtering, at most 20 mapping loci, minimum splice overhang 8 (1 at annotated junctions), at most 4% mismatches relative to the read-pair length with no separate absolute mismatch cap, alignment score and matched bases each at least 66% of the read-pair length, intron length 20–1,000,000 and paired-read gap at most 1,000,000. Use the supplied annotation for junction indexing with overhang 100.
30. GPT-5.6 Luna / Open-ended code / run 2 → result 1 (alignments)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Alignment records: 0.948656 to 0.958859 (8 checks)
      • Summary statistics within tolerance: 0 (156 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
31. GPT-5.6 Luna / Open-ended code / run 2 → result 2 (gene counts)
    • Method: More fragments are assigned than the library has read pairs (2,000,000), which is impossible when each fragment is counted at most once: S01, S02, S03, S04, S05, S06, S07, S08.Task requirement: Eight libraries with 2,000,000 read pairs each / Count unstranded fragments over annotated gene-exon unions with at least one overlapping base.
32. GPT-5.6 Luna / Open-ended code / run 2 → result 3 (fixed gene domain)
    • Content: Content score below 0.80. Value: 0.674781. Required minimum: 0.8.
      • Matching records (F1): 0.941931
      • Numerical agreement (CCC): 0.878474 to 0.985459 (3 checks)
      • Present, finite data cells (F1): 0.941931 (2 checks)
    • Check: A required check is below its minimum. Required minimum: 0.99.
      • Matching records (F1): 0.941931
      • Numerical agreement (CCC): 0.932693
33. GPT-5.6 Luna / Open-ended code / run 2 → result 4 (differential expression)
    • List: Up/down gene lists do not meet the required overlap. Required minimum: 0.95.
      • member 1 / up: 0.903654
      • member 2 / down: 0.835267
      • member 3 / up: 0.90595
      • member 4 / down: 0.829268
      • member 5 / up: 0.899358
      • member 6 / down: 0.789474
      • member 7 / up: 0.922261
      • member 8 / down: 0.827763
      • member 9 / up: 0.89781
      • member 10 / down: 0.840336
34. GPT-5.6 Luna / Open-ended code / run 2 → result 5 (normalization)
    • Content: Content score below 0.80. Value: 0.768392. Required minimum: 0.8.
      • Matching records (F1): 0.941931 (5 checks)
      • Numerical agreement (CCC): 0.878216 to 0.987828 (10 checks)
      • Present, finite data cells (F1): 0.941931 (5 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.768278
      • member 2: 0.765933
      • member 3: 0.769848
      • member 4: 0.769307
      • member 5: 0.768594
35. GPT-5.6 Luna / Open-ended code / run 2 → result 6 (GO full)
    • Content: Content score below 0.80. Value: 0.0286976. Required minimum: 0.8.
      • Category agreement (F1): 0.742728 to 0.970572 (4 checks)
      • Matching records (F1): 0.941931 to 0.992284 (6 checks)
      • Numerical agreement (CCC): 0.914091 to 0.962059 (2 checks)
      • Present, finite data cells (F1): 0.941931 to 0.992284 (4 checks)
      • Within 5pct: 0.17628 to 0.518656 (2 checks)
36. GPT-5.6 Luna / Open-ended code / run 2 → result 7 (GO robustness)
    • Content: Content score below 0.80. Value: 0.00899907. Required minimum: 0.8.
      • Category agreement (F1): 0.742728 to 0.974731 (20 checks)
      • Matching records (F1): 0.941931 to 0.992284 (30 checks)
      • Numerical agreement (CCC): 0.809839 to 0.962059 (10 checks)
      • Present, finite data cells (F1): 0.941931 to 0.992284 (20 checks)
      • Within 5pct: 0 to 0.96729 (10 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.0286976
      • member 2: 0
      • member 3: 0
      • member 4: 0.0162977
      • member 5: 0
37. GPT-5.6 Luna / Open-ended code / run 2 → result 8 (library assemblies)
    • Content: Content score below 0.80. Value: 0.615968. Required minimum: 0.8.
      • Matching records (F1): 0.73504 to 0.834406 (16 checks)
      • Numerical agreement (CCC): 0.996876 to 0.999451 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0.592113
      • S02: 0.541016
      • S03: 0.694755
      • S04: 0.618319
      • S05: 0.619377
      • S06: 0.613146
      • S07: 0.625657
      • S08: 0.623362
38. GPT-5.6 Luna / Open-ended code / run 2 → result 9 (common assembly)
    • Content: Content score below 0.80. Value: 0.466765. Required minimum: 0.8.
      • Matching records (F1): 0.682084 to 0.684321 (2 checks)
39. GPT-5.6 Luna / Open-ended code / run 2 → result 10 (splice junctions)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (8 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
40. GPT-5.6 Luna / Open-ended code / run 3 → result 1 (alignments)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Alignment records: 0.984439 to 0.9913 (8 checks)
      • Summary statistics within tolerance: 0 (59 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
41. GPT-5.6 Luna / Open-ended code / run 3 → result 10 (splice junctions)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (8 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
42. GPT-5.6 Sol / Galaxy-API code / run 2 → result 2 (gene counts)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (16 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
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 2. final_answer/02_gene_counts/{sample}/ native count tables Complete counts, assignment summaries and exon-union gene lengths. Use gene_id/count, status/count and gene_id/length tables with headers. Files: {sample}/assignment.tsv, {sample}/counts.tsv, {sample}/lengths.tsv.
43. GPT-5.6 Sol / Galaxy-API code / run 2 → result 5 (normalization)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (10 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
      • member 5: 0
    • Format: Named columns/order differ from the required table.Task requirement: 5. final_answer/05_normalization/{fit}/ TSV counts.tsv: gene_id and every included sample; size_factors.tsv: sample, size_factor. Files: {fit}/counts.tsv, {fit}/size_factors.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 5. final_answer/05_normalization/{fit}/ TSV counts.tsv: gene_id and every included sample; size_factors.tsv: sample, size_factor. Files: {fit}/counts.tsv, {fit}/size_factors.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 5. final_answer/05_normalization/{fit}/ TSV counts.tsv: gene_id and every included sample; size_factors.tsv: sample, size_factor. Files: {fit}/counts.tsv, {fit}/size_factors.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 5. final_answer/05_normalization/{fit}/ TSV counts.tsv: gene_id and every included sample; size_factors.tsv: sample, size_factor. Files: {fit}/counts.tsv, {fit}/size_factors.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 5. final_answer/05_normalization/{fit}/ TSV counts.tsv: gene_id and every included sample; size_factors.tsv: sample, size_factor. Files: {fit}/counts.tsv, {fit}/size_factors.tsv.
44. GPT-5.6 Sol / Open-ended code / run 1 → result 1 (alignments)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Alignment records: 0.988778 to 0.995683 (8 checks)
      • Summary statistics within tolerance: 0 (41 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
45. GPT-5.6 Sol / Open-ended code / run 1 → result 10 (splice junctions)
    • Method: Recorded STAR settings contradict the task (outFilterMismatchNoverReadLmax 1.0) in S01, S02, S03, S04, S05, S06, S07, S08.Task requirement: For spliced alignment use splice-junction-based filtering, at most 20 mapping loci, minimum splice overhang 8 (1 at annotated junctions), at most 4% mismatches relative to the read-pair length with no separate absolute mismatch cap, alignment score and matched bases each at least 66% of the read-pair length, intron length 20–1,000,000 and paired-read gap at most 1,000,000. Use the supplied annotation for junction indexing with overhang 100.
46. GPT-5.6 Sol / Open-ended code / run 2 → result 1 (alignments)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Alignment records: 0.988778 to 0.995683 (8 checks)
      • Summary statistics within tolerance: 0 (41 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
47. GPT-5.6 Sol / Open-ended code / run 2 → result 10 (splice junctions)
    • Method: Recorded STAR settings contradict the task (outFilterMismatchNoverReadLmax 1.0) in S01, S02, S03, S04, S05, S06, S07, S08.Task requirement: For spliced alignment use splice-junction-based filtering, at most 20 mapping loci, minimum splice overhang 8 (1 at annotated junctions), at most 4% mismatches relative to the read-pair length with no separate absolute mismatch cap, alignment score and matched bases each at least 66% of the read-pair length, intron length 20–1,000,000 and paired-read gap at most 1,000,000. Use the supplied annotation for junction indexing with overhang 100.
48. GPT-5.6 Sol / Open-ended code / run 3 → result 1 (alignments)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Alignment records: 0.988778 to 0.995683 (8 checks)
      • Summary statistics within tolerance: 0 (41 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
49. GPT-5.6 Sol / Open-ended code / run 3 → result 10 (splice junctions)
    • Method: Recorded STAR settings contradict the task (outFilterMismatchNoverReadLmax 1.0) in S01, S02, S03, S04, S05, S06, S07, S08.Task requirement: For spliced alignment use splice-junction-based filtering, at most 20 mapping loci, minimum splice overhang 8 (1 at annotated junctions), at most 4% mismatches relative to the read-pair length with no separate absolute mismatch cap, alignment score and matched bases each at least 66% of the read-pair length, intron length 20–1,000,000 and paired-read gap at most 1,000,000. Use the supplied annotation for junction indexing with overhang 100.
50. DeepSeek V4 Pro / Galaxy-API code / run 1 → result 3 (fixed gene domain)
    • Instruction: The required eligible (0/1) column is missing from this table; membership in another table does not replace it.Task requirement: 3. final_answer/03_fixed_gene_domain/ TSV matrix.tsv and eligible.tsv have gene_id, S01–S08 and eligible (0/1); the former contains the full counted domain and the latter E. Preserve original/version-stripped identifiers in the crosswalk. Files: eligible.tsv, matrix.tsv.
51. DeepSeek V4 Pro / Galaxy-API code / run 1 → result 4 (differential expression)
    • Instruction: DE rows differ from the submitted fixed E labels/domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
    • Instruction: DE rows differ from the submitted fixed E labels/domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
    • Instruction: DE rows differ from the submitted fixed E labels/domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
    • Instruction: DE rows differ from the submitted fixed E labels/domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
    • Instruction: DE rows differ from the submitted fixed E labels/domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
52. DeepSeek V4 Pro / Galaxy-API code / run 1 → result 6 (GO full)
    • Method: GO background or up/down selection differs from the stated rule applied to the delivered fits: full-full-up, full-full-down.Task requirement: Select up/down lists separately using gene-level BH-adjusted p<0.05 and |log2 effect|≥1, with direction determined by sign. / The full-fit background requires positive length and finite effect/p/adjusted-p in F0; the shared background requires these in all five fits.
53. DeepSeek V4 Pro / Galaxy-API code / run 1 → result 7 (GO robustness)
    • Method: GO background or up/down selection differs from the stated rule applied to the delivered fits: common-full-up, common-full-down, common-leave_D01-up, common-leave_D01-down, common-leave_D02-up, common-leave_D02-down, common-leave_D03-up, common-leave_D03-down, common-leave_D04-up, common-leave_D04-down.Task requirement: Select up/down lists separately using gene-level BH-adjusted p<0.05 and |log2 effect|≥1, with direction determined by sign. / The full-fit background requires positive length and finite effect/p/adjusted-p in F0; the shared background requires these in all five fits.
54. DeepSeek V4 Pro / Galaxy-API code / run 2 → result 3 (fixed gene domain)
    • Instruction: The required eligible (0/1) column is missing from this table; membership in another table does not replace it.Task requirement: 3. final_answer/03_fixed_gene_domain/ TSV matrix.tsv and eligible.tsv have gene_id, S01–S08 and eligible (0/1); the former contains the full counted domain and the latter E. Preserve original/version-stripped identifiers in the crosswalk. Files: eligible.tsv, matrix.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 3. final_answer/03_fixed_gene_domain/ TSV matrix.tsv and eligible.tsv have gene_id, S01–S08 and eligible (0/1); the former contains the full counted domain and the latter E. Preserve original/version-stripped identifiers in the crosswalk. Files: eligible.tsv, matrix.tsv.
55. DeepSeek V4 Pro / Galaxy-API code / run 2 → result 6 (GO full)
    • Content: Content score below 0.80. Value: 0.254198. Required minimum: 0.8.
      • Matching records (F1): 0.999903 to 0.999951 (4 checks)
      • Numerical agreement (CCC): 1
      • Present, finite data cells (F1): 0.999951 (2 checks)
      • Within 5pct: 0.459047 to 0.553968 (2 checks)
56. DeepSeek V4 Pro / Galaxy-API code / run 2 → result 7 (GO robustness)
    • Content: Content score below 0.80. Value: 0.104134. Required minimum: 0.8.
      • Matching records (F1): 0.999903 to 0.999985 (20 checks)
      • Numerical agreement (CCC): 0.999999 to 1 (7 checks)
      • Present, finite data cells (F1): 0.999951 (10 checks)
      • Within 5pct: 0.0625306 to 0.553968 (10 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.254198
      • member 2: 0.0287254
      • member 3: 0.0549498
      • member 4: 0.159194
      • member 5: 0.023602
57. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 1 (alignments)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Alignment records: 0.995105 to 0.996255 (8 checks)
      • Summary statistics within tolerance: 0 (25 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
58. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 3 (fixed gene domain)
    • Instruction: The required eligible (0/1) column is missing from this table; membership in another table does not replace it.Task requirement: 3. final_answer/03_fixed_gene_domain/ TSV matrix.tsv and eligible.tsv have gene_id, S01–S08 and eligible (0/1); the former contains the full counted domain and the latter E. Preserve original/version-stripped identifiers in the crosswalk. Files: eligible.tsv, matrix.tsv.
59. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 4 (differential expression)
    • Instruction: DE rows differ from the submitted fixed E labels/domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
    • Instruction: DE rows differ from the submitted fixed E labels/domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
    • Instruction: DE rows differ from the submitted fixed E labels/domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
    • Instruction: DE rows differ from the submitted fixed E labels/domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
    • Instruction: DE rows differ from the submitted fixed E labels/domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
60. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 7 (GO robustness)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Category agreement (F1): 0.4923 to 0.782057 (8 checks)
      • Numerical agreement (CCC): 0.483698 to 0.606606 (8 checks)
      • Required content missing or unreadable: 0 (6 checks)
      • Within 5pct: 0 to 0.0577299 (10 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 1.63912e-07
      • member 4: 0
      • member 5: 0
    • Instruction: Required file is missing: 07_go_robustness/F0/up/universe.tsvTask requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Instruction: Required file is missing: 07_go_robustness/F0/up/membership.tsvTask requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Instruction: Required file is missing: 07_go_robustness/F0/up/categories.tsvTask requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Instruction: Required file is missing: 07_go_robustness/F0/down/universe.tsvTask requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Instruction: Required file is missing: 07_go_robustness/F0/down/membership.tsvTask requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
    • Instruction: Required file is missing: 07_go_robustness/F0/down/categories.tsvTask requirement: 7. final_answer/07_go_robustness/{fit}/{direction}/ TSV universe.tsv: gene_id, length, pwf, selected (0/1); membership.tsv: gene_id, category, one row per link; categories.tsv: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat, term, ontology, p_adjust_over_represented, p_adjust_under_represented. Retain the complete tested family, including Other, and both adjustment directions. Files: {fit}/down/categories.tsv, {fit}/down/membership.tsv, {fit}/down/universe.tsv, {fit}/up/categories.tsv, {fit}/up/membership.tsv, {fit}/up/universe.tsv.
61. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 10 (splice junctions)
    • Method: Recorded STAR settings contradict the task (outFilterType Normal) in S01, S02, S03, S04, S05, S06, S07, S08.Task requirement: For spliced alignment use splice-junction-based filtering, at most 20 mapping loci, minimum splice overhang 8 (1 at annotated junctions), at most 4% mismatches relative to the read-pair length with no separate absolute mismatch cap, alignment score and matched bases each at least 66% of the read-pair length, intron length 20–1,000,000 and paired-read gap at most 1,000,000. Use the supplied annotation for junction indexing with overhang 100.
62. DeepSeek V4 Pro / Open-ended code / run 1 → result 1 (alignments)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (8 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
63. DeepSeek V4 Pro / Open-ended code / run 1 → result 3 (fixed gene domain)
    • Instruction: The required eligible (0/1) column is missing from this table; membership in another table does not replace it.Task requirement: 3. final_answer/03_fixed_gene_domain/ TSV matrix.tsv and eligible.tsv have gene_id, S01–S08 and eligible (0/1); the former contains the full counted domain and the latter E. Preserve original/version-stripped identifiers in the crosswalk. Files: eligible.tsv, matrix.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 3. final_answer/03_fixed_gene_domain/ TSV matrix.tsv and eligible.tsv have gene_id, S01–S08 and eligible (0/1); the former contains the full counted domain and the latter E. Preserve original/version-stripped identifiers in the crosswalk. Files: eligible.tsv, matrix.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 3. final_answer/03_fixed_gene_domain/ TSV matrix.tsv and eligible.tsv have gene_id, S01–S08 and eligible (0/1); the former contains the full counted domain and the latter E. Preserve original/version-stripped identifiers in the crosswalk. Files: eligible.tsv, matrix.tsv.
64. DeepSeek V4 Pro / Open-ended code / run 1 → result 8 (library assemblies)
    • Content: Content score below 0.80. Value: 0.735704. Required minimum: 0.8.
      • Matching records (F1): 0.838966 to 0.8681 (16 checks)
      • Numerical agreement (CCC): 0.999772 to 0.999958 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0.720755
      • S02: 0.704729
      • S03: 0.744257
      • S04: 0.748671
      • S05: 0.742666
      • S06: 0.740757
      • S07: 0.730737
      • S08: 0.753062
65. DeepSeek V4 Pro / Open-ended code / run 1 → result 9 (common assembly)
    • Content: Content score below 0.80. Value: 0.565548. Required minimum: 0.8.
      • Matching records (F1): 0.75161 to 0.752449 (2 checks)
66. DeepSeek V4 Pro / Open-ended code / run 2 → result 1 (alignments)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Alignment records: 0.999165 to 0.999432 (8 checks)
      • Summary statistics within tolerance: 0 (25 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
67. DeepSeek V4 Pro / Open-ended code / run 2 → result 3 (fixed gene domain)
    • Instruction: The required eligible (0/1) column is missing from this table; membership in another table does not replace it.Task requirement: 3. final_answer/03_fixed_gene_domain/ TSV matrix.tsv and eligible.tsv have gene_id, S01–S08 and eligible (0/1); the former contains the full counted domain and the latter E. Preserve original/version-stripped identifiers in the crosswalk. Files: eligible.tsv, matrix.tsv.
    • Format: Named columns/order differ from the required table.Task requirement: 3. final_answer/03_fixed_gene_domain/ TSV matrix.tsv and eligible.tsv have gene_id, S01–S08 and eligible (0/1); the former contains the full counted domain and the latter E. Preserve original/version-stripped identifiers in the crosswalk. Files: eligible.tsv, matrix.tsv.
68. DeepSeek V4 Pro / Open-ended code / run 2 → result 4 (differential expression)
    • Instruction: DE rows differ from the submitted fixed E labels/domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
    • Instruction: DE rows differ from the submitted fixed E labels/domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
    • Instruction: DE rows differ from the submitted fixed E labels/domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
    • Instruction: DE rows differ from the submitted fixed E labels/domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
    • Instruction: DE rows differ from the submitted fixed E labels/domain.Task requirement: 4. final_answer/04_differential_expression/{fit}/ TSV results.tsv columns: gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj. Keep all E rows and NA. Fit directory names are F0 and LO_D01–LO_D04. Files: {fit}/results.tsv.
69. DeepSeek V4 Pro / Open-ended code / run 2 → result 7 (GO robustness)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.548545
70. DeepSeek V4 Pro / Open-ended code / run 2 → result 10 (splice junctions)
    • Method: Recorded STAR settings contradict the task (outFilterType Normal) in S01, S02, S03, S04, S05, S06, S07, S08.Task requirement: For spliced alignment use splice-junction-based filtering, at most 20 mapping loci, minimum splice overhang 8 (1 at annotated junctions), at most 4% mismatches relative to the read-pair length with no separate absolute mismatch cap, alignment score and matched bases each at least 66% of the read-pair length, intron length 20–1,000,000 and paired-read gap at most 1,000,000. Use the supplied annotation for junction indexing with overhang 100.
71. DeepSeek V4 Pro / Open-ended code / run 3 → result 1 (alignments)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (8 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
72. DeepSeek V4 Pro / Open-ended code / run 3 → result 8 (library assemblies)
    • Content: Content score below 0.80. Value: 0.736099. Required minimum: 0.8.
      • Matching records (F1): 0.838966 to 0.868249 (16 checks)
      • Numerical agreement (CCC): 0.99977 to 0.999957 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • S01: 0.720755
      • S02: 0.704729
      • S03: 0.744256
      • S04: 0.749031
      • S05: 0.743788
      • S06: 0.741568
      • S07: 0.731345
      • S08: 0.753322
73. DeepSeek V4 Pro / Open-ended code / run 3 → result 9 (common assembly)
    • Content: Content score below 0.80. Value: 0.566235. Required minimum: 0.8.
      • Matching records (F1): 0.752126 to 0.752846 (2 checks)