Question
You are given a single end RNA-seq fastq file (contaminated.rna.q2.fq.gz). This file contains mostly human reads and a small fraction of contaminant reads. Identify the contaminant species present. Report the answer as the exact scientific name of the species in all lowercase letters with a single space separating genus and species, for example "mus musculus".
- Inferred answer
sus scrofaUniquely inferred from submitted scores.
- Domain
- Transcriptomics
- 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 + standard tools
Answersus scrofa
WorkflowKraken2→Kraken taxon counts→Hisat2→Kraken taxon counts filtered
- Total tokens
- 1.6M
- Output
- 13.1K
Codex GPT-5.5
Replicate 2
IncorrectStandard tools only
Answerlymphocryptovirus humangamma4
WorkflowKraken2→Krakentools Extract Kraken Reads→Ncbi Blastn Wrapper
- Total tokens
- 1.1M
- Output
- 11.3K
Codex GPT-5.5
Replicate 3
RerunCorrectUDT + standard tools
Answersus scrofa
WorkflowKraken2→FASTQ header diagnostic→Remote BLAST sampled FASTQ→NCBI URL BLAST sampled FASTQ→NCBI URL BLAST sampled FASTQ small→10 more tools
- Total tokens
- 4.3M
- Output
- 38.3K
Codex GPT-5.6 Sol
3 replicates
Codex GPT-5.6 Sol
Replicate 1
CorrectStandard tools only
Answersus scrofa
WorkflowKraken2→Filter Tabular→Grep→Tp Sort Header Tool→Sort rows→1 more tools
- Total tokens
- 36.6M
- Output
- 51.1K
Codex GPT-5.6 Sol
Replicate 2
IncorrectStandard tools only
Answerlymphocryptovirus humangamma4
WorkflowKraken2→Filter rows→Sort rows→Tp Head Tool→Hisat2→1 more tools
- Total tokens
- 1.6M
- Output
- 7.4K
Codex GPT-5.6 Sol
Replicate 3
CorrectStandard tools only
Answersus scrofa
WorkflowKraken2→Filter Tabular→Filter rows→Sort rows→Show Beginning1→4 more tools
- Total tokens
- 52.8M
- Output
- 32.6K
Codex + DeepSeek-v4-pro-0813
3 replicates
Codex + DeepSeek-v4-pro-0813
Replicate 1
RerunCorrectStandard tools only
Answersus scrofa
Workflowkraken2 → hisat2 → cshl fastq to fasta → ncbi blastn wrapper → samtools flagstat
- Total tokens
- 7.8M
- Output
- 36.7K
Codex + DeepSeek-v4-pro-0813
Replicate 2
CorrectStandard tools only
Answersus scrofa
WorkflowKraken2→Datamash Ops→Group and aggregate→Count1→Sylph Profile
- Total tokens
- 43.2M
- Output
- 87.5K
Codex + DeepSeek-v4-pro-0813
Replicate 3
CorrectStandard tools only
Answersus scrofa
- Total tokens
- 48.5M
- Output
- 82.9K
Codex GPT-5.6 Luna
3 replicates
Codex GPT-5.6 Luna
Replicate 1
CorrectStandard tools only
Answersus scrofa
WorkflowSeqtk Sample→Kraken2→Bamtools Split Mapped→Bedtools Bamtofastq→Fastq To Fasta Python→2 more tools
- Total tokens
- 39.8M
- Output
- 113.4K
Codex GPT-5.6 Luna
Replicate 2
IncorrectStandard tools only
Answerlymphocryptovirus humangamma4
WorkflowFastq Stats→Seqtk Sample→Kraken2→Tp Grep Tool→Krakentools Extract Kraken Reads
- Total tokens
- 5.3M
- Output
- 27.1K
Codex GPT-5.6 Luna
Replicate 3
IncorrectStandard tools only
Answerhuman gammaherpesvirus 4
WorkflowFastq Stats→Fastqc→Kraken2
- Total tokens
- 6.2M
- Output
- 26.0K