Task 6: Replicate-supported CUT&RUN consensus

What the task asks for

Call peaks in two CUT&RUN libraries and in their depth-balanced pool, keep the pooled peaks whose summits both libraries support, and build signal tracks.

8 scored results8 required18 runs scored

Codex GPT-5.6 Luna

6 of 6 runs scored

Galaxy-API code 0.500 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.516

All results pass0 of 3 runsruns in which every scored result passes

run 10.6255/8run 20.1251/8run 30.7506/8

Open-ended code 0.208 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.339

All results pass0 of 3 runsruns in which every scored result passes

run 10.3753/8run 20.2502/8run 30.0000/8

Codex GPT-5.6 Sol

6 of 6 runs scored

Galaxy-API code 1.000 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.999

All results pass3 of 3 runsruns in which every scored result passes

run 11.0008/8run 21.0008/8run 31.0008/8

Open-ended code 0.958 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.987

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 0.708 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.778

All results pass1 of 3 runsruns in which every scored result passes

run 10.6255/8run 21.0008/8run 30.5004/8

Open-ended code 0.917 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.915

All results pass1 of 3 runsruns in which every scored result passes

run 10.8757/8run 21.0008/8run 30.8757/8

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 0.000, 0.999, 0.999, 1.000, 1.000, 0.000, 0.000 and 0.984 on its 8 results. 5 of them pass, so BixBench3 acc = 5/8 = 0.625; the average of all 8 scores is 0.623, 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 0.500 vs 0.208; GPT-5.6 Sol 1.000 vs 0.958; DeepSeek V4 Pro 0.708 vs 0.917.

What Galaxy added

Galaxy's duplicate-marking and subsampling tools carry out the specified read selection directly, and its pileup and signal tools form a standard chain to the final tracks. Galaxy runs passed the alignment stages, depth balance and signal tracks in 8 of 9 runs each. In Open-ended code, GPT-5.6 Luna wrote its own duplicate filter and depth balancing, and the Open-ended runs that failed the signal tracks built them with their own code, sorting chromosomes in the wrong order or measuring the wrong quantity.

Why Galaxy did not do better

Three Galaxy runs called peaks without summit splitting, which is off by default in the peak caller's form, so intervals with several summits came out as one row and the candidate relations failed; every DeepSeek V4 Pro Open-ended run kept summits. Galaxy's filter tool also read a count column as text because some rows hold a dot, which emptied one run's consensus. In another run the pileup ran past the end of the mitochondrial chromosome, the signal conversion failed, and the agent substituted a different coverage track.

Run-level details (6)

Three Galaxy runs, the first and third with DeepSeek V4 Pro and the third with GPT-5.6 Luna, called peaks without summit splitting. The task asks to retain distinct summits that share an interval; each interval instead came out as a single row with a single summit.
The second Galaxy run and third Open-ended code run with GPT-5.6 Luna set the quality cutoff to 30,0. That trims at Q30 from the 5′ end and leaves the 3′ end untrimmed, although the task asks for 3′ trimming only.
GPT-5.6 Luna substituted its own selection scripts in Open-ended code. Its first run balanced depth by SHA-256 hashes of template names instead of the specified subsample and subsample-seed selection. Its second duplicate filter keyed templates on the strands of both mates as well as their coordinates, changing which templates remained. The third run reimplemented both steps.
The first Open-ended run with DeepSeek V4 Pro and the second with GPT-5.6 Sol converted bedGraphs sorted in the supplied chromosome-list order rather than the required coordinate ordering, and their tracks failed the signal comparison. The third Open-ended run with DeepSeek V4 Pro used the fraction of covered bases in depth-balanced libraries instead of per-million pileup depth from complete libraries. The third Galaxy run with DeepSeek V4 Pro substituted a general coverage track with a read offset of -100 after its pileup conversion failed past the end of the mitochondrial chromosome.
In the first Galaxy run with GPT-5.6 Luna, a support-count column was treated as text because no-overlap rows contain a dot, so the filter accepted no rows and the consensus was empty. The run also delivered a later length-filtering JSON report as its trimming report.
The first Galaxy run with DeepSeek V4 Pro switched on clustering in the multi-intersect step, which the task does not ask for, and its all_segments.tsv no longer matched the reference.

Instruction, format and method errors (2)

Content container differs from the declared text format.Task requirement: 1. final_answer/01_read_processing/{sample}/ FASTQ + text Processed mate files and the complete native adapter/quality-trimming text report. Files: {sample}/forward.fastq.gz, {sample}/reverse.fastq.gz, {sample}/trimming.txt.
GPT-5.6 Luna / Galaxy-API code / run 1 → result 1; GPT-5.6 Luna / Galaxy-API code / run 1 → result 1
The consensus differs from the unique intervals of candidates whose summit lies in a segment supported by both libraries.Task requirement: Accept a pooled candidate only when its summit lies in a qualifying segment, using zero-based half-open coordinates; its relation to that segment is its accepted relation. / 7. final_answer/07_consensus.bed BED Headerless three columns: chromosome, start, end; the unique intervals of the accepted pooled candidates themselves.
DeepSeek V4 Pro / Galaxy-API code / run 3 → result 7

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
Model	Condition	Run	BixBench3 acc share passing	Continuous score	Tokens	Minutes	Records	1read processing	2alignment stages	3depth balance	4peaks	5replicate support	6candidate relations	7consensus	8signal tracks
GPT-5.6 Luna	Galaxy-API code	1trial run	5/8 = 0.625	0.623	28.8M	458	Trace History	0.00Format	0.99 Passed	0.99 Passed	1.00 Passed	1.00 Passed	0.00Check	0.00Content	0.98 Passed
		2	1/8 = 0.125	0.178	25.5M	558	Trace History	0.00Member	0.00Member	0.00Member	0.00Member	0.14Content	0.00Check	0.29Content	0.98 Passed
		3	6/8 = 0.750	0.747	28.8M	560	Trace History	0.99 Passed	0.99 Passed	0.99 Passed	0.00Member	1.00 Passed	0.00Check	0.98 Passed	0.98 Passed
	Open-ended code	1trial run	3/8 = 0.375	0.677	17.5M	175	Trace	1.00 Passed	0.85Member	0.93Check	0.14Member	1.00 Passed	0.05Check	0.47Content	0.94 Passed
		2	2/8 = 0.250	0.308	53.3M	185	Trace	1.00 Passed	0.00Member	0.00Member	0.00Member	0.19Content	0.00Check	0.32Content	0.93 Passed
		3	0/8 = 0.000	0.032	47.1M	164	Trace	0.00Member	0.00Member	0.00Member	0.00Member	0.07Content	0.00Check	0.17Content	0.00Member
GPT-5.6 Sol	Galaxy-API code	1	8/8 = 1.000	0.999	13.9M	478	Trace History	1.00 Passed	0.99 Passed	0.99 Passed	0.99 Passed	0.99 Passed	0.99 Passed	0.99 Passed	0.99 Passed
		2	8/8 = 1.000	0.999	20.1M	281	Trace History	1.00 Passed	0.99 Passed	0.99 Passed	0.99 Passed	0.99 Passed	0.99 Passed	0.99 Passed	0.99 Passed
		3	8/8 = 1.000	0.999	26.5M	513	Trace History	1.00 Passed	0.99 Passed	0.99 Passed	0.99 Passed	0.99 Passed	0.99 Passed	0.99 Passed	0.99 Passed
	Open-ended code	1	8/8 = 1.000	1.000	5.7M	157	Trace	1.00 Passed	0.99 Passed	0.99 Passed	0.99 Passed	1.00 Passed	1.00 Passed	1.00 Passed	0.99 Passed
		2	7/8 = 0.875	0.961	17.7M	162	Trace	1.00 Passed	0.99 Passed	0.99 Passed	1.00 Passed	1.00 Passed	1.00 Passed	1.00 Passed	0.69Member
		3	8/8 = 1.000	1.000	30.9M	164	Trace	1.00 Passed	0.99 Passed	0.99 Passed	0.99 Passed	1.00 Passed	1.00 Passed	1.00 Passed	0.99 Passed
DeepSeek V4 Pro	Galaxy-API code	1	5/8 = 0.625	0.710	38.9M	416	Trace History	0.99 Passed	0.99 Passed	0.99 Passed	0.00Member	0.76Content	0.00Check	0.99 Passed	0.91 Passed
		2	8/8 = 1.000	0.993	35.3M	327	Trace History	1.00 Passed	0.99 Passed	0.99 Passed	1.00 Passed	1.00 Passed	1.00 Passed	1.00 Passed	0.94 Passed
		3	4/8 = 0.500	0.630	26.0M	526	Trace History	0.99 Passed	0.99 Passed	0.99 Passed	0.00Member	1.00 Passed	0.00Check	0.99Method	0.04Member
	Open-ended code	1	7/8 = 0.875	0.905	11.9M	161	Trace	1.00 Passed	0.99 Passed	0.99 Passed	0.84 Passed	0.93 Passed	0.84 Passed	0.95 Passed	0.65Member
		2	8/8 = 1.000	0.972	10.5M	153	Trace	1.00 Passed	0.97 Passed	0.99 Passed	0.95 Passed	1.00 Passed	0.94 Passed	0.98 Passed	0.93 Passed
		3	7/8 = 0.875	0.869	8.3M	171	Trace	1.00 Passed	0.98 Passed	0.99 Passed	0.98 Passed	1.00 Passed	0.98 Passed	0.99 Passed	0.00Member

Why results did not pass

GPT-5.6 Luna / Galaxy-API code / run 1 → result 1 (read processing)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Matching records (F1): 1 to 1 (2 checks)
  - Required content missing or unreadable: 0 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0
  - S02: 0
- Format: Content container differs from the declared text format.Task requirement: 1. final_answer/01_read_processing/{sample}/ FASTQ + text Processed mate files and the complete native adapter/quality-trimming text report. Files: {sample}/forward.fastq.gz, {sample}/reverse.fastq.gz, {sample}/trimming.txt.
- Format: Content container differs from the declared text format.Task requirement: 1. final_answer/01_read_processing/{sample}/ FASTQ + text Processed mate files and the complete native adapter/quality-trimming text report. Files: {sample}/forward.fastq.gz, {sample}/reverse.fastq.gz, {sample}/trimming.txt.
GPT-5.6 Luna / Galaxy-API code / run 1 → result 6 (candidate relations)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Matching records (F1): 0
- Check: A required check is below its minimum. Required minimum: 0.9.
  - Matching records (F1): 0
GPT-5.6 Luna / Galaxy-API code / run 1 → result 7 (consensus)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Matching records (F1): 0
GPT-5.6 Luna / Galaxy-API code / run 2 → result 1 (read processing)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Matching records (F1): 0.706196 to 0.759268 (2 checks)
  - Summary statistics within tolerance: 0 (7 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0
  - S02: 0
GPT-5.6 Luna / Galaxy-API code / run 2 → result 2 (alignment stages)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Alignment records: 0.739499 to 0.797226 (6 checks)
  - Summary statistics within tolerance: 0 (25 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0
  - S02: 0
GPT-5.6 Luna / Galaxy-API code / run 2 → result 3 (depth balance)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Alignment records: 0.771283 to 0.77747 (2 checks)
  - Matching records (F1): 0.849887 to 0.851392 (2 checks)
  - Summary statistics within tolerance: 0 (3 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0
  - S02: 0
- Check: A required check is below its minimum. Required minimum: 0.95.
  - Alignment records: 0.771283 to 0.77747 (2 checks)
GPT-5.6 Luna / Galaxy-API code / run 2 → result 4 (peaks)
- Content: Content score below 0.80. Value: 0.000943468. Required minimum: 0.8.
  - Matching records (F1): 0.128737 to 0.285079 (3 checks)
  - Numerical agreement (CCC): 0.99222 to 0.997448 (3 checks)
  - Present, finite data cells (F1): 0.128737 to 0.285079 (3 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.000318227
  - S02: 0.00156871
GPT-5.6 Luna / Galaxy-API code / run 2 → result 5 (replicate support)
- Content: Content score below 0.80. Value: 0.145802. Required minimum: 0.8.
  - Matching records (F1): 0.35345 to 0.41251 (2 checks)
GPT-5.6 Luna / Galaxy-API code / run 2 → result 6 (candidate relations)
- Content: Content score below 0.80. Value: 0.00242154. Required minimum: 0.8.
  - Matching records (F1): 0.034728 to 0.0697288 (2 checks)
- Check: A required check is below its minimum. Required minimum: 0.9.
  - Matching records (F1): 0.034728
GPT-5.6 Luna / Galaxy-API code / run 2 → result 7 (consensus)
- Content: Content score below 0.80. Value: 0.290211. Required minimum: 0.8.
  - Matching records (F1): 0.290211
GPT-5.6 Luna / Galaxy-API code / run 3 → result 4 (peaks)
- Content: Content score below 0.80. Value: 1.67436e-06. Required minimum: 0.8.
  - Matching records (F1): 0.0321923 to 0.0457846 (3 checks)
  - Numerical agreement (CCC): 1
  - Present, finite data cells (F1): 0.0321923 to 0.0457846 (3 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 1.1763e-06
  - S02: 2.17243e-06
GPT-5.6 Luna / Galaxy-API code / run 3 → result 6 (candidate relations)
- Content: Content score below 0.80. Value: 0.000339217. Required minimum: 0.8.
  - Matching records (F1): 0.014343 to 0.0236504 (2 checks)
- Check: A required check is below its minimum. Required minimum: 0.9.
  - Matching records (F1): 0.014343
GPT-5.6 Luna / Open-ended code / run 1 → result 2 (alignment stages)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.799067
GPT-5.6 Luna / Open-ended code / run 1 → result 3 (depth balance)
- Check: A required check is below its minimum. Required minimum: 0.95.
  - Alignment records: 0.931247
GPT-5.6 Luna / Open-ended code / run 1 → result 4 (peaks)
- Content: Content score below 0.80. Value: 0.141723. Required minimum: 0.8.
  - Matching records (F1): 0.37652
  - Numerical agreement (CCC): 0.999693
  - Present, finite data cells (F1): 0.37652
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.141723
  - S02: 0.141723
GPT-5.6 Luna / Open-ended code / run 1 → result 6 (candidate relations)
- Content: Content score below 0.80. Value: 0.0578309. Required minimum: 0.8.
  - Matching records (F1): 0.20654 to 0.279999 (2 checks)
- Check: A required check is below its minimum. Required minimum: 0.9.
  - Matching records (F1): 0.20654
GPT-5.6 Luna / Open-ended code / run 1 → result 7 (consensus)
- Content: Content score below 0.80. Value: 0.475702. Required minimum: 0.8.
  - Matching records (F1): 0.475702
GPT-5.6 Luna / Open-ended code / run 2 → result 2 (alignment stages)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Alignment records: 0.938806 to 0.978032 (2 checks)
  - Required content missing or unreadable: 0 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0
  - S02: 0
GPT-5.6 Luna / Open-ended code / run 2 → result 3 (depth balance)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Alignment records: 0.909731 to 0.978032 (2 checks)
  - Matching records (F1): 0.925949 to 0.982844 (2 checks)
  - Summary statistics within tolerance: 0 (3 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0
  - S02: 0
- Check: A required check is below its minimum. Required minimum: 0.95.
  - Alignment records: 0.909731
GPT-5.6 Luna / Open-ended code / run 2 → result 4 (peaks)
- Content: Content score below 0.80. Value: 0.00447297. Required minimum: 0.8.
  - Matching records (F1): 0.122968 to 0.482806 (3 checks)
  - Numerical agreement (CCC): 0.985162 to 0.994694 (3 checks)
  - Present, finite data cells (F1): 0.122968 to 0.482806 (3 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.000540058
  - S02: 0.00840588
GPT-5.6 Luna / Open-ended code / run 2 → result 5 (replicate support)
- Content: Content score below 0.80. Value: 0.193042. Required minimum: 0.8.
  - Matching records (F1): 0.384334 to 0.502275 (2 checks)
GPT-5.6 Luna / Open-ended code / run 2 → result 6 (candidate relations)
- Content: Content score below 0.80. Value: 0.00398969. Required minimum: 0.8.
  - Matching records (F1): 0.0425839 to 0.0936901 (2 checks)
- Check: A required check is below its minimum. Required minimum: 0.9.
  - Matching records (F1): 0.0425839
GPT-5.6 Luna / Open-ended code / run 2 → result 7 (consensus)
- Content: Content score below 0.80. Value: 0.327351. Required minimum: 0.8.
  - Matching records (F1): 0.327351
GPT-5.6 Luna / Open-ended code / run 3 → result 1 (read processing)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Matching records (F1): 0.706196 to 0.759268 (2 checks)
  - Summary statistics within tolerance: 0 (7 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0
  - S02: 0
GPT-5.6 Luna / Open-ended code / run 3 → result 2 (alignment stages)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Alignment records: 0.742111 to 0.797999 (6 checks)
  - Required content missing or unreadable: 0 (2 checks)
  - Summary statistics within tolerance: 0 (21 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0
  - S02: 0
GPT-5.6 Luna / Open-ended code / run 3 → result 3 (depth balance)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Alignment records: 0.697099 to 0.765185 (2 checks)
  - Matching records (F1): 0.77381 to 0.842053 (2 checks)
  - Summary statistics within tolerance: 0 (3 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0
  - S02: 0
- Check: A required check is below its minimum. Required minimum: 0.95.
  - Alignment records: 0.697099 to 0.765185 (2 checks)
GPT-5.6 Luna / Open-ended code / run 3 → result 4 (peaks)
- Content: Content score below 0.80. Value: 8.4589e-05. Required minimum: 0.8.
  - Matching records (F1): 0.0548549 to 0.227337 (3 checks)
  - Numerical agreement (CCC): 0.97096 to 0.990404 (3 checks)
  - Present, finite data cells (F1): 0.0548549 to 0.227337 (3 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 9.13513e-06
  - S02: 0.000160043
GPT-5.6 Luna / Open-ended code / run 3 → result 5 (replicate support)
- Content: Content score below 0.80. Value: 0.0782419. Required minimum: 0.8.
  - Matching records (F1): 0.245697 to 0.318448 (2 checks)
GPT-5.6 Luna / Open-ended code / run 3 → result 6 (candidate relations)
- Content: Content score below 0.80. Value: 0.000196085. Required minimum: 0.8.
  - Matching records (F1): 0.00839987 to 0.0233439 (2 checks)
- Check: A required check is below its minimum. Required minimum: 0.9.
  - Matching records (F1): 0.00839987
GPT-5.6 Luna / Open-ended code / run 3 → result 7 (consensus)
- Content: Content score below 0.80. Value: 0.178904. Required minimum: 0.8.
  - Matching records (F1): 0.178904
GPT-5.6 Luna / Open-ended code / run 3 → result 8 (signal tracks)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Numerical agreement (CCC): 0.995467
  - Occupied base f1: 0.996007
  - Required content missing or unreadable: 0 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0
  - S02: 0
GPT-5.6 Sol / Open-ended code / run 2 → result 8 (signal tracks)
- Content: Content score below 0.80. Value: 0.691038. Required minimum: 0.8.
  - Numerical agreement (CCC): 0.906912 to 0.916555 (3 checks)
  - Occupied base f1: 0.908723 to 0.910372 (3 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.687297
  - S02: 0.694778
DeepSeek V4 Pro / Galaxy-API code / run 1 → result 4 (peaks)
- Content: Content score below 0.80. Value: 1.71035e-06. Required minimum: 0.8.
  - Matching records (F1): 0.0325364 to 0.0457846 (3 checks)
  - Numerical agreement (CCC): 1
  - Present, finite data cells (F1): 0.0325364 to 0.0457846 (3 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 1.20158e-06
  - S02: 2.21911e-06
DeepSeek V4 Pro / Galaxy-API code / run 1 → result 5 (replicate support)
- Content: Content score below 0.80. Value: 0.765068. Required minimum: 0.8.
  - Matching records (F1): 0.765068
DeepSeek V4 Pro / Galaxy-API code / run 1 → result 6 (candidate relations)
- Content: Content score below 0.80. Value: 0.000318796. Required minimum: 0.8.
  - Matching records (F1): 0.0144526 to 0.0220581 (2 checks)
- Check: A required check is below its minimum. Required minimum: 0.9.
  - Matching records (F1): 0.0144526
DeepSeek V4 Pro / Galaxy-API code / run 3 → result 4 (peaks)
- Content: Content score below 0.80. Value: 4.45188e-06. Required minimum: 0.8.
  - Matching records (F1): 0.0414151 to 0.0570429 (3 checks)
  - Present, finite data cells (F1): 0.0414151 to 0.0570429 (3 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 3.32265e-06
  - S02: 5.5811e-06
DeepSeek V4 Pro / Galaxy-API code / run 3 → result 6 (candidate relations)
- Content: Content score below 0.80. Value: 0.000344264. Required minimum: 0.8.
  - Matching records (F1): 0.0124098 to 0.0277412 (2 checks)
- Check: A required check is below its minimum. Required minimum: 0.9.
  - Matching records (F1): 0.0124098
DeepSeek V4 Pro / Galaxy-API code / run 3 → result 7 (consensus)
- Method: The consensus differs from the unique intervals of candidates whose summit lies in a segment supported by both libraries.Task requirement: Accept a pooled candidate only when its summit lies in a qualifying segment, using zero-based half-open coordinates; its relation to that segment is its accepted relation. / 7. final_answer/07_consensus.bed BED Headerless three columns: chromosome, start, end; the unique intervals of the accepted pooled candidates themselves.
DeepSeek V4 Pro / Galaxy-API code / run 3 → result 8 (signal tracks)
- Content: Content score below 0.80. Value: 0.0454939. Required minimum: 0.8.
  - Numerical agreement (CCC): 0.360345 to 0.404755 (3 checks)
  - Occupied base f1: 0.477873 to 0.597676 (3 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.0416571
  - S02: 0.0493307
DeepSeek V4 Pro / Open-ended code / run 1 → result 8 (signal tracks)
- Content: Content score below 0.80. Value: 0.656459. Required minimum: 0.8.
  - Numerical agreement (CCC): 0.899174 to 0.916555 (3 checks)
  - Occupied base f1: 0.870525 to 0.909891 (3 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.653666
  - S02: 0.659251
DeepSeek V4 Pro / Open-ended code / run 3 → result 8 (signal tracks)
- Content: Content score below 0.80. Value: 0.000400912. Required minimum: 0.8.
  - Numerical agreement (CCC): 0.00898441 to 0.0306335 (3 checks)
  - Occupied base f1: 0.945016 to 0.994648 (3 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.000541203
  - S02: 0.00026062

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

Construct a replicate-supported CUT&RUN consensus from two paired-end human libraries, preserving the evidence for both accepted and unsupported candidates. Use depth-balanced pooled reads to nominate narrow enrichment candidates, and require summit support from both individual libraries. Preserve the distinction between candidate discovery, replicate support and signal averaging; a simple union of the individual peak lists is not the requested consensus.

Inputs

Paired-end S01 and S02 libraries, hg19 reference/chromosome lengths and supplied adapters; no control library.

Key parameters and conditions

Use error-tolerant 3′ adapter alignment to the supplied sequences with minimum overlap 3 nt, error rate 0.10 and indels allowed; trim 3′ low-quality ends at Q30, not 5′ ends. Discard a pair if either mate is shorter than 15 nt. Use an FM-index multiseed, gapped end-to-end paired alignment method with a very-sensitive search, inward-facing orientation, insert range 0–1,000 bp and dovetail allowed. Select each record by proper-pair flag and MAPQ≥30; do not add a requirement that both mates pass MAPQ together. Remove coordinate duplicates by aligned template coordinates with the highest base-quality-sum representative. Do not add mitochondrial, blacklist or other regional exclusions.
Call narrow peaks for each library from its complete deduplicated alignments (before depth balancing) and for the balanced pool, using per-alignment BED, genome size 2.7e9, q≤0.05, shift −100, extension 200 and no additional peak-caller duplicate removal. Retain distinct summits sharing an interval.
Balance library depth by template-name-hashed proportional selection of SAM/BAM alignment records (subsample / subsample-seed, seed 1), retaining or discarding all records of a template together. Set the retention fraction from the smaller retained-alignment count divided by the current library count; report the target and realized counts. This is reproducible proportional sampling, not exact-count reservoir sampling, truncation or signal normalization.
Partition the union of unpooled peak intervals into support segments, retaining segments covered by either one or both libraries; the qualifying segments are those supported by both. Relate every pooled candidate to every support segment it overlaps, one- or two-library alike, and keep one no-overlap row for a candidate that overlaps none. Accept a pooled candidate only when its summit lies in a qualifying segment, using zero-based half-open coordinates; its relation to that segment is its accepted relation.
Deliver each library's shifted/extended treatment pileup per million retained alignment records and their equal-library mean in 50 bp bins, treating absent values as zero; do not substitute unshifted aligned-block coverage or the pooled signal.
Use the complete supplied 93-sequence chromosome dictionary. The balance target and realized counts count retained alignment records, not templates.

Required results

final_answer/01_read_processing/{sample}/
FASTQ + text
Processed mate files and the complete native adapter/quality-trimming text report. Files: {sample}/forward.fastq.gz, {sample}/reverse.fastq.gz, {sample}/trimming.txt.
final_answer/02_alignment_stages/{sample}/
BAM + index + native reports
Coordinate-sorted alignment, selection and deduplication stages and their metrics; mapping.txt is the aligner's own paired-alignment summary (concordant, discordant and mate-level alignment counts). Files: {sample}/aligned.bam, {sample}/deduplicated.bam, {sample}/duplicates.txt, {sample}/filtered.bam, {sample}/mapping.txt.
final_answer/03_depth_balance/
BAM + BED6 + text
Each library’s balanced BAM, the corresponding BED6 used for joint calling, and realized record count; target.txt contains one integer. Preserve S01/S02 identities. Files: S01.bam, S01.bed, S01.count.txt, S02.bam, S02.bed, S02.count.txt, target.txt.
final_answer/04_peaks/{S01,S02,pool}/
narrowPeak
Complete ten-column unpooled and pooled peak candidates including summit offsets. Files: S01/peaks.narrowPeak, S02/peaks.narrowPeak, pool/peaks.narrowPeak.
final_answer/05_replicate_support/
TSV
Headerless all_segments.tsv and supported_segments.tsv: chromosome, start, end, number of supporting libraries, comma-separated library indices, S01 indicator, S02 indicator. Library indices are 1 for S01 and 2 for S02. Files: all_segments.tsv, supported_segments.tsv.
final_answer/06_candidate_relations/
TSV
relationships.tsv: the ten pooled narrowPeak columns, seven support-segment columns and overlap length (18 columns); accepted_parents.tsv contains the corresponding first 17 columns for accepted relations. Keep native no-overlap sentinels. Files: accepted_parents.tsv, relationships.tsv.
final_answer/07_consensus.bed
BED
Headerless three columns: chromosome, start, end; the unique intervals of the accepted pooled candidates themselves.
final_answer/08_signal_tracks/
bigWig; native signal reports may accompany the tracks
S01.bw, S02.bw and mean.bw with the specified scaling and 50 bp mean. Files: S01.bw, S02.bw, mean.bw.

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. When a result is scored per sample or other unit, each copy gets its own score and the result's score is their average; if any copy is missing or cannot be read, the result scores 0. 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 result	What the task asks for	How it is scored
1	`01_read_processing/{sample}/` FASTQ + text	Processed mate files and the complete native adapter/quality-trimming text report. Files: {sample}/forward.fastq.gz, {sample}/reverse.fastq.gz, {sample}/trimming.txt.	the same rows or records as the reference (F1 of their identifiers) the required columns or fields are present (F1) every reported statistic is within 1% of the reference value Scored for each of the 2 samples and averaged.
2	`02_alignment_stages/{sample}/` BAM + index + native reports	Coordinate-sorted alignment, selection and deduplication stages and their metrics; mapping.txt is the aligner's own paired-alignment summary (concordant, discordant and mate-level alignment counts). Files: {sample}/aligned.bam, {sample}/deduplicated.bam, {sample}/duplicates.txt, {sample}/filtered.bam, {sample}/mapping.txt.	the required columns or fields are present (F1) every reported statistic is within 1% of the reference value alignment records agree (F1) Scored for each of the 2 samples and averaged.
3	`03_depth_balance/` BAM + BED6 + text	Each library’s balanced BAM, the corresponding BED6 used for joint calling, and realized record count; target.txt contains one integer. Preserve S01/S02 identities. Files: S01.bam, S01.bed, S01.count.txt, S02.bam, S02.bed, S02.count.txt, target.txt.	the same rows or records as the reference (F1 of their identifiers) the required columns or fields are present (F1) every reported statistic is within 1% of the reference value alignment records agree (F1) Scored for each of the 2 samples and averaged; the target read count is scored once and multiplied in.
4	`04_peaks/{S01,S02,pool}/` narrowPeak	Complete ten-column unpooled and pooled peak candidates including summit offsets. Files: S01/peaks.narrowPeak, S02/peaks.narrowPeak, pool/peaks.narrowPeak.	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) Scored for each of the 2 samples and averaged; the peak file of the pooled library is scored once and multiplied in.
5	`05_replicate_support/` TSV	Headerless all_segments.tsv and supported_segments.tsv: chromosome, start, end, number of supporting libraries, comma-separated library indices, S01 indicator, S02 indicator. Library indices are 1 for S01 and 2 for S02. Files: all_segments.tsv, supported_segments.tsv.	the same rows or records as the reference (F1 of their identifiers)
6	`06_candidate_relations/` TSV	relationships.tsv: the ten pooled narrowPeak columns, seven support-segment columns and overlap length (18 columns); accepted_parents.tsv contains the corresponding first 17 columns for accepted relations. Keep native no-overlap sentinels. Files: accepted_parents.tsv, relationships.tsv.	the same rows or records as the reference (F1 of their identifiers)
7	`07_consensus.bed` BED	Headerless three columns: chromosome, start, end; the unique intervals of the accepted pooled candidates themselves.	the same rows or records as the reference (F1 of their identifiers)
8	`08_signal_tracks/` bigWig; native signal reports may accompany the tracks	S01.bw, S02.bw and mean.bw with the specified scaling and 50 bp mean. Files: S01.bw, S02.bw, mean.bw.	the signal covers the same bases with agreeing values (F1 and concordance correlation) the same chromosome names and lengths Scored for each of the 2 samples and averaged; the mean track is scored once and multiplied in.

Data updated 27 October 2026, 08:48 EDT.