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CompBioBench item

afgr-1000g-intersect-atac-q1

Question

From the 1000G Phase 3 (3202 individuals), find all individuals that also have ATAC-seq filtered BAMs in the African Functional Genomics Resource (AFGR). Using only publicly available data, collect the md5sums of the filtered BAMs for these individuals (GRCh38 aligned), write the md5sums (one per line) to a text file sorted alphabetically. Return the count of samples and the file’s md5sum as a single comma-separated line, e.g., 42,md5hash.

Inferred answer
83,1127bd47e06e7c19e8f0d5b5458a244aUniquely inferred from submitted scores.
Domain
Population Genetics
Question style
Retrieval

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
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
AFGR 1000G filtered BAM md5sVerify AFGR md5 list result
Total tokens
1.8M
Output
13.5K
Codex GPT-5.5

Replicate 2

CorrectUDT-only
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
AFGR diagnosticAFGR diagnostic v2AFGR 1000G md5sumsAFGR 1000G md5sums official
Total tokens
2.1M
Output
10.4K
Codex GPT-5.5

Replicate 3

CorrectUDT + standard tools
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
AFGR 1000G filtered BAM md5 intersectionAFGR 1000G filtered BAM md5 intersection v2UDT smoke echoUDT smoke catTp Cut Tool7 more tools
Total tokens
6.0M
Output
23.8K

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

CorrectUDT-only
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
Inspect ENCODE public JSON fieldsAFGR filtered BAM MD5 intersection with 1000G 3202Independent MD5 checksum
Codex GPT-5.6 Sol

Replicate 2

CorrectUDT-only
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
AFGR public metadata discoveryAFGR filtered BAM MD5 finalization
Total tokens
1.1M
Output
8.7K
Codex GPT-5.6 Sol

Replicate 3

CorrectUDT-only
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
AFGR ATAC filtered BAM metadata diagnosticAFGR 1000G overlap filtered BAM md5 final
Total tokens
15.9M
Output
23.2K

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

RerunCorrectStandard tools only
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
Sample identifier mappingJoin datasetsSort rowsCount linesSecure Hash Message Digest
Total tokens
20.4M
Output
45.6K
Codex + DeepSeek-v4-pro-0813

Replicate 2

RerunCorrectStandard tools only
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
Sample identifier mappingJoin datasetsSort rowsCount linesSecure Hash Message Digest
Total tokens
15.9M
Output
41.8K
Codex + DeepSeek-v4-pro-0813

Replicate 3

CorrectStandard tools only
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
Comp1Select columnsSort rowsSecure Hash Message DigestWc Gnu
Total tokens
6.0M
Output
30.4K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

CorrectUDT-only
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
AFGR Phase 3 identity diagnosticAFGR Phase 3 identity diagnostic v2AFGR Phase 3 identity diagnostic v3AFGR Phase 3 identity diagnostic v4AFGR 3202-sample identity diagnostic4 more tools
Total tokens
12.1M
Output
50.2K
Codex GPT-5.6 Luna

Replicate 2

IncorrectUDT + standard tools
Answer50,054938323525a222bcc6154a05996ace
Workflow
Upload1AFGR 1000G Phase 3 matching diagnosticAFGR 1000G Phase 3 matching diagnostic v2AFGR 1000G Phase 3 directory-listing overlap diagnosticWrite AFGR 1000G Phase 3 filtered BAM MD5 sums3 more tools
Total tokens
20.0M
Output
71.8K
Codex GPT-5.6 Luna

Replicate 3

IncorrectUDT + standard tools
Answer50,054938323525a222bcc6154a05996ace
Workflow
AFGR 1000G filtered BAM md5 intersectionSecure Hash Message Digest
Total tokens
7.3M
Output
25.3K

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Correct
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
Local code
Codex GPT-5.5

Replicate 2

Correct
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
Local codePython
Codex GPT-5.5

Replicate 3

Correct
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
Local codePython

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Correct
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
Local codePython
Codex GPT-5.6 Sol

Replicate 2

Correct
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
Local codePython
Codex GPT-5.6 Sol

Replicate 3

Correct
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
Local codePython

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Incorrect
Answer50,054938323525a222bcc6154a05996ace
Workflow
Local codePython
Total tokens
882.9K
Output
13.7K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Incorrect
Answer50,054938323525a222bcc6154a05996ace
Workflow
Local codePython
Total tokens
1.0M
Output
9.0K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Correct
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
Local codePython
Total tokens
4.6M
Output
27.7K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Correct
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
Local codePython
Codex GPT-5.6 Luna

Replicate 2

Correct
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
Local codePython
Codex GPT-5.6 Luna

Replicate 3

Incorrect
Answer50,054938323525a222bcc6154a05996ace
Workflow
Local codePython

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Correct
Answer83,1127bd47e06e7c19e8f0d5b5458a244a
Workflow
Local codePython
Total tokens
898.7K
Output
5.8K