Question
read.proportions.q1.fa contains a synthetic genome with four chromosomes. read.proportions.q1.fq.gz contains 40,000 single-end 36 bp reads drawn from this genome. A read is generated by first picking a chromosome with probability pi =(pi_1, ..., pi_4), then sampling a position uniformly along that chromosome, with some small error rate. Estimate pi and report four integers (percentages) in FASTA contig order (chr1–chr4), each rounded to the nearest 5; if needed, adjust the last value so the total is 100. Expected output format: 15,25,25,35.
- Inferred answer
50,20,20,10Uniquely inferred from submitted scores.
- Domain
- Genomics
- Question style
- Synthetic/Augmented Data
An answer can be uniquely inferred for 54 of 100 questions from submitted scores. Green: correct · Red: incorrect. For questions without a uniquely determined answer: Blue: matches prediction · Orange: differs from prediction. These are inferred answer checks, not official per-question grades.
Galaxy
12/12 terminal item results
UDT = user-defined tool: custom code executed by Galaxy. Route badges summarize analysis tools, excluding uploads and automatic conversions. How usage is counted.
Codex GPT-5.5
3 replicates
Codex GPT-5.5
Replicate 1
CorrectUDT-only
Answer50,20,20,10
WorkflowEstimate read proportions→Estimate read proportions v2→Estimate read proportions EM→Validate read proportions variants
Codex GPT-5.5
Replicate 2
CorrectUDT + standard tools
Answer50,20,20,10
WorkflowEstimate read chromosome proportions by EM→Estimate read chromosome proportions by EM forward check
- Total tokens
- 2.8M
- Output
- 20.4K
Codex GPT-5.5
Replicate 3
RerunCorrectUDT + standard tools
Answer50,20,20,10
WorkflowBowtie2→Read proportions best-hit estimator→Read proportions EM best-hit estimator→FASTQ header origin diagnostic→Read proportions EM best-hit rescue estimator
- Total tokens
- 1.4M
- Output
- 12.2K
Codex GPT-5.6 Sol
3 replicates
Codex GPT-5.6 Sol
Replicate 1
CorrectStandard tools only
Answer50,20,20,10
WorkflowBowtie2→Samtools Idxstats→Samtools View→Converter Fasta To Fai→Bedtools Makewindowsbed→3 more tools
- Total tokens
- 4.1M
- Output
- 11.9K
Codex GPT-5.6 Sol
Replicate 2
CorrectUDT + standard tools
Answer50,20,20,10
WorkflowBowtie2→Bam To Sam→Chromosome mixture EM from all Bowtie2 alignments
- Total tokens
- 1.5M
- Output
- 9.0K
Codex GPT-5.6 Sol
Replicate 3
CorrectUDT + standard tools
Answer50,20,20,10
WorkflowBowtie2→Samtools Idxstats→Exhaustive seeded contig classifier→Contig proportion likelihood EM→Kallisto Quant
- Total tokens
- 1.7M
- Output
- 14.5K
Codex + DeepSeek-v4-pro-0813
3 replicates
Codex + DeepSeek-v4-pro-0813
Replicate 1
IncorrectStandard tools only
Answer35,25,25,15
WorkflowBowtie2→Samtools Idxstats
- Total tokens
- 824.7K
- Output
- 11.6K
Codex + DeepSeek-v4-pro-0813
Replicate 2
CorrectUDT + standard tools
Answer50,20,20,10
WorkflowBwa Mem→Samtools Idxstats→Bwa→Samtools View→SciPy→8 more tools
- Total tokens
- 19.4M
- Output
- 71.4K
Codex + DeepSeek-v4-pro-0813
Replicate 3
CorrectUDT + standard tools
Answer50,20,20,10
WorkflowBowtie2→Samtools Coverage→Samtools Flagstat→Fasta Stats→Samtools View→4 more tools
- Total tokens
- 6.4M
- Output
- 67.1K
Codex GPT-5.6 Luna
3 replicates
Codex GPT-5.6 Luna
Replicate 1
CorrectUDT + standard tools
Answer50,20,20,10
WorkflowFasta Stats→Bowtie2→Samtools Idxstats→Bam To Sam→Minimap2→8 more tools
- Total tokens
- 18.4M
- Output
- 62.3K
Codex GPT-5.6 Luna
Replicate 2
CorrectUDT + standard tools
Answer50,20,20,10
WorkflowBowtie2→Samtools Idxstats→Datamash Ops→Add A Column1→Bwa Mem→8 more tools
- Total tokens
- 11.5M
- Output
- 67.2K
Codex GPT-5.6 Luna
Replicate 3
CorrectStandard tools only
Answer50,20,20,10
WorkflowFasta Compute Length→Bwa Mem→Samtools Idxstats→Samtools Flagstat→Bowtie2→4 more tools
- Total tokens
- 4.3M
- Output
- 19.8K