Task 2: ATAC-seq peaks and normalized signal

What the task asks for

Trim, align, filter and deduplicate two mouse ATAC-seq libraries, call peaks and summits, and build two differently normalized signal tracks per library.

8 scored results8 required18 runs scored

Codex GPT-5.6 Luna

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 0.849

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

run 10.6255/8run 20.8757/8run 30.6255/8

Open-ended code 0.667 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.676

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

run 10.6255/8run 20.6255/8run 30.7506/8

Codex GPT-5.6 Sol

6 of 6 runs scored

Galaxy-API code 0.917 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.925

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

run 11.0008/8run 20.8757/8run 30.8757/8

Open-ended code 0.958 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.957

All results pass2 of 3 runsruns in which every scored result passes

run 10.8757/8run 21.0008/8run 31.0008/8

DeepSeek V4 Pro via Codex

6 of 6 runs scored

Galaxy-API code 0.542 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.641

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

run 10.6255/8run 20.5004/8run 30.5004/8

Open-ended code 0.833 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.881

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

run 10.7506/8run 20.8757/8run 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 0.977, 0.000, 0.988, 0.995, 1.000, 0.999, 0.752 and 0.752 on its 8 results. 5 of them pass, so BixBench3 acc = 5/8 = 0.625; the average of all 8 scores is 0.808, 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 0.708 vs 0.667; GPT-5.6 Sol 0.917 vs 0.958; DeepSeek V4 Pro 0.542 vs 0.833.

What Galaxy added

Peak calling and the raw pileups passed in every run of both conditions. Galaxy's trimming tool returned the complete current report in all nine runs, while two Open-ended runs installed older versions whose reports lack required fields.

Why Galaxy did not do better

The two 50-bp signal tracks need the per-base average of the pileup in each bin. Galaxy runs may not compute locally, so agents assembled this from interval and text tools, and five of nine chose operations that average the wrong way. Open-ended runs wrote the average in a few lines of code and passed 7 of 9. Result 2 failed in most runs of both conditions: agents switched on adapter auto-detection and returned other reports in place of the requested aligner and duplicate summaries.

Run-level details (4)

Five Galaxy runs averaged the 50-bp signal the wrong way. The first two with DeepSeek V4 Pro counted overlapping intervals per base, giving an all-zero track and a constant track. The third with DeepSeek V4 Pro and the first and third with GPT-5.6 Luna took plain means of overlapping intervals, ignoring uncovered bases.
All Galaxy runs with GPT-5.6 Luna and DeepSeek V4 Pro switched on adapter auto-detection in trimming, which changes the processed reads slightly. Several runs also delivered general alignment statistics in place of the aligner summary, or another tool's duplicate statistics in place of the requested duplicate metrics.
In the second Galaxy run with DeepSeek V4 Pro the peak windows were delivered merged (35,908 rows instead of 49,155); the third used the integer peak score in place of the summit score.
The first Open-ended run with DeepSeek V4 Pro and the third with GPT-5.6 Luna installed older versions of the trimming tool, whose reports lack fields of the current version.

Instruction, format and method errors (2)

The track is not the 50-bp mean per-base pileup times the delivered factor (uncovered bases = 0) on chr19: S01, S02.Task requirement: From the shifted/extended treatment pileup from Poisson-background narrow-enrichment calling, produce 50-bp bins of mean per-base signal, treating uncovered bases as zero; use only in-genome bases for a shortened terminal bin. Scale by 10^6 divided by either the total retained-record count or the union-overlapping count.
GPT-5.6 Luna / Galaxy-API code / run 3 → result 7; GPT-5.6 Luna / Galaxy-API code / run 3 → result 8; DeepSeek V4 Pro / Galaxy-API code / run 3 → result 7; DeepSeek V4 Pro / Galaxy-API code / run 3 → result 8
Windows or their union differ from summit ±500 bp clipped to the chromosome and merged when overlapping or book-ended: S01, S02.Task requirement: Expand each one-base summit by 500 bp on each side, clip to chromosome bounds and merge overlapping or book-ended windows within each library.
DeepSeek V4 Pro / Open-ended code / run 3 → result 4

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	3peaks	4peak windows	5signal scaling	6raw pileup	7signal total	8signal in union
GPT-5.6 Luna	Galaxy-API code	1trial run	5/8 = 0.625	0.808	23.8M	189	Trace History	0.97 Passed	0.00Member	0.98 Passed	0.99 Passed	1.00 Passed	0.99 Passed	0.75Member	0.75Member
		2	7/8 = 0.875	0.870	13.6M	189	Trace History	0.97 Passed	0.00Member	0.98 Passed	0.99 Passed	1.00 Passed	0.99 Passed	0.99 Passed	0.99 Passed
		3	5/8 = 0.625	0.870	12.6M	155	Trace History	0.97 Passed	0.00Member	0.98 Passed	0.99 Passed	1.00 Passed	0.99 Passed	0.99Method	0.99Method
	Open-ended code	1trial run	5/8 = 0.625	0.640	25.9M	125	Trace	0.97 Passed	0.00Member	0.98 Passed	0.99 Passed	1.00 Passed	0.99 Passed	0.08Member	0.08Member
		2	5/8 = 0.625	0.640	11.5M	128	Trace	0.97 Passed	0.00Member	0.98 Passed	0.99 Passed	1.00 Passed	0.99 Passed	0.08Member	0.08Member
		3	6/8 = 0.750	0.748	5.6M	147	Trace	0.00Member	0.00Member	0.99 Passed	0.99 Passed	1.00 Passed	0.99 Passed	0.99 Passed	0.99 Passed
GPT-5.6 Sol	Galaxy-API code	1	8/8 = 1.000	1.000	10.3M	237	Trace History	1.00 Passed	1.00 Passed	1.00 Passed	1.00 Passed	1.00 Passed	1.00 Passed	0.99 Passed	0.99 Passed
		2	7/8 = 0.875	0.901	17.0M	201	Trace History	1.00 Passed	0.20Member	1.00 Passed	1.00 Passed	1.00 Passed	1.00 Passed	0.99 Passed	0.99 Passed
		3	7/8 = 0.875	0.875	10.2M	181	Trace History	1.00 Passed	0.00Member	1.00 Passed	1.00 Passed	1.00 Passed	1.00 Passed	0.99 Passed	0.99 Passed
	Open-ended code	1	7/8 = 0.875	0.870	8.8M	126	Trace	0.97 Passed	0.00Member	0.98 Passed	0.99 Passed	1.00 Passed	0.99 Passed	0.99 Passed	0.99 Passed
		2	8/8 = 1.000	1.000	5.8M	156	Trace	1.00 Passed	0.99 Passed	0.99 Passed	1.00 Passed	1.00 Passed	1.00 Passed	0.99 Passed	0.99 Passed
		3	8/8 = 1.000	1.000	3.5M	127	Trace	1.00 Passed	0.99 Passed	0.99 Passed	0.99 Passed	1.00 Passed	1.00 Passed	0.99 Passed	0.99 Passed
DeepSeek V4 Pro	Galaxy-API code	1	5/8 = 0.625	0.620	18.7M	210	Trace History	0.97 Passed	0.00Member	0.98 Passed	0.99 Passed	1.00 Passed	0.99 Passed	0.00Member	0.00Member
		2	4/8 = 0.500	0.540	17.5M	209	Trace History	0.97 Passed	0.00Member	0.98 Passed	0.35Member	1.00 Passed	0.99 Passed	0.00Member	0.00Member
		3	4/8 = 0.500	0.764	16.8M	201	Trace History	0.97 Passed	0.00Member	0.98 Passed	0.14Member	1.00 Passed	0.99 Passed	0.99Method	0.99Method
	Open-ended code	1	6/8 = 0.750	0.750	17.0M	133	Trace	0.00Member	0.00Member	0.99 Passed	0.99 Passed	1.00 Passed	1.00 Passed	0.99 Passed	0.99 Passed
		2	7/8 = 0.875	0.892	13.8M	136	Trace	1.00 Passed	0.13Member	0.99 Passed	0.99 Passed	1.00 Passed	1.00 Passed	0.99 Passed	0.99 Passed
		3	7/8 = 0.875	1.000	9.9M	140	Trace	0.99 Passed	0.99 Passed	0.99 Passed	0.99Method	1.00 Passed	1.00 Passed	0.99 Passed	0.99 Passed

Why results did not pass

GPT-5.6 Luna / Galaxy-API code / run 1 → result 2 (alignment stages)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Alignment records: 0.994337 to 0.995659 (6 checks)
  - Numerical agreement (CCC): 0.99997 to 0.999999 (4 checks)
  - Required content missing or unreadable: 0 (2 checks)
  - Summary statistics within tolerance: 0 (2 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: 0.998.
  - Alignment records: 0.995294 to 0.995659 (4 checks)
GPT-5.6 Luna / Galaxy-API code / run 1 → result 7 (signal total)
- Content: Content score below 0.80. Value: 0.752276. Required minimum: 0.8.
  - Numerical agreement (CCC): 0.732288 to 0.772316 (2 checks)
  - Occupied base f1: 0.999964 to 0.999967 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.732263
  - S02: 0.772288
GPT-5.6 Luna / Galaxy-API code / run 1 → result 8 (signal in union)
- Content: Content score below 0.80. Value: 0.752291. Required minimum: 0.8.
  - Numerical agreement (CCC): 0.732315 to 0.77232 (2 checks)
  - Occupied base f1: 0.999964 to 0.999967 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.732291
  - S02: 0.772292
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: 0.994337 to 0.995659 (6 checks)
  - Numerical agreement (CCC): 0.99997 to 0.999999 (4 checks)
  - Required content missing or unreadable: 0 (2 checks)
  - Summary statistics within tolerance: 0 (2 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: 0.998.
  - Alignment records: 0.995294 to 0.995659 (4 checks)
GPT-5.6 Luna / Galaxy-API code / run 3 → result 2 (alignment stages)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Alignment records: 0.994337 to 0.995662 (6 checks)
  - Numerical agreement (CCC): 0.999998 to 1 (4 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
- Check: A required check is below its minimum. Required minimum: 0.998.
  - Alignment records: 0.995657 to 0.995662 (4 checks)
GPT-5.6 Luna / Galaxy-API code / run 3 → result 7 (signal total)
- Method: The track is not the 50-bp mean per-base pileup times the delivered factor (uncovered bases = 0) on chr19: S01, S02.Task requirement: From the shifted/extended treatment pileup from Poisson-background narrow-enrichment calling, produce 50-bp bins of mean per-base signal, treating uncovered bases as zero; use only in-genome bases for a shortened terminal bin. Scale by 10^6 divided by either the total retained-record count or the union-overlapping count.
GPT-5.6 Luna / Galaxy-API code / run 3 → result 8 (signal in union)
- Method: The track is not the 50-bp mean per-base pileup times the delivered factor (uncovered bases = 0) on chr19: S01, S02.Task requirement: From the shifted/extended treatment pileup from Poisson-background narrow-enrichment calling, produce 50-bp bins of mean per-base signal, treating uncovered bases as zero; use only in-genome bases for a shortened terminal bin. Scale by 10^6 divided by either the total retained-record count or the union-overlapping count.
GPT-5.6 Luna / Open-ended code / run 1 → result 2 (alignment stages)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Alignment records: 0.98489 to 0.995662 (6 checks)
  - Matching records (F1): 0.999001 (2 checks)
  - Numerical agreement (CCC): 0.931207 to 1 (4 checks)
  - Present, finite data cells (F1): 0.999001 (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
- Check: A required check is below its minimum. Required minimum: 0.998.
  - Alignment records: 0.995657 to 0.995662 (4 checks)
GPT-5.6 Luna / Open-ended code / run 1 → result 7 (signal total)
- Content: Content score below 0.80. Value: 0.0803426. Required minimum: 0.8.
  - Numerical agreement (CCC): 0.23919 to 0.252788 (2 checks)
  - Occupied base f1: 0.325302 to 0.327849 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.0778089
  - S02: 0.0828763
GPT-5.6 Luna / Open-ended code / run 1 → result 8 (signal in union)
- Content: Content score below 0.80. Value: 0.0803404. Required minimum: 0.8.
  - Numerical agreement (CCC): 0.239178 to 0.252786 (2 checks)
  - Occupied base f1: 0.325302 to 0.327849 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.077805
  - S02: 0.0828757
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: 0.98489 to 0.995659 (6 checks)
  - Numerical agreement (CCC): 0.931207 to 0.999972 (4 checks)
  - Required content missing or unreadable: 0 (4 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: 0.998.
  - Alignment records: 0.995294 to 0.995659 (4 checks)
GPT-5.6 Luna / Open-ended code / run 2 → result 7 (signal total)
- Content: Content score below 0.80. Value: 0.080324. Required minimum: 0.8.
  - Numerical agreement (CCC): 0.23919 to 0.25276 (2 checks)
  - Occupied base f1: 0.325302 to 0.327738 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.0778089
  - S02: 0.0828391
GPT-5.6 Luna / Open-ended code / run 2 → result 8 (signal in union)
- Content: Content score below 0.80. Value: 0.0803242. Required minimum: 0.8.
  - Numerical agreement (CCC): 0.239193 to 0.252758 (2 checks)
  - Occupied base f1: 0.325302 to 0.327738 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.0778099
  - S02: 0.0828386
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): 0.994655 to 0.994656 (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 3 → result 2 (alignment stages)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Alignment records: 0.995521 to 0.996846 (6 checks)
  - Numerical agreement (CCC): 0.999998 to 1 (4 checks)
  - Required content missing or unreadable: 0 (2 checks)
  - Summary statistics within tolerance: 0 (2 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: 0.998.
  - Alignment records: 0.996686 to 0.996846 (4 checks)
GPT-5.6 Sol / Galaxy-API code / run 2 → result 2 (alignment stages)
- Content: Content score below 0.80. Value: 0.204793. Required minimum: 0.8.
  - Numerical agreement (CCC): 0.139682 to 0.269903 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.139682
  - S02: 0.269903
GPT-5.6 Sol / Galaxy-API code / run 3 → result 2 (alignment stages)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - 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 1 → result 2 (alignment stages)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Alignment records: 0.994107 to 0.995661 (6 checks)
  - Matching records (F1): 0.999001 (2 checks)
  - Numerical agreement (CCC): 0.999998 to 1 (4 checks)
  - Present, finite data cells (F1): 0.999001 (2 checks)
  - Summary statistics within tolerance: 0 (2 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: 0.998.
  - Alignment records: 0.995656 to 0.995661 (4 checks)
DeepSeek V4 Pro / Galaxy-API code / run 1 → result 2 (alignment stages)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Alignment records: 0.994337 to 0.995662 (6 checks)
  - Matching records (F1): 0.968074 (2 checks)
  - Numerical agreement (CCC): 0.999993 to 0.999999 (4 checks)
  - Present, finite data cells (F1): 0.968074 (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
- Check: A required check is below its minimum. Required minimum: 0.998.
  - Alignment records: 0.995657 to 0.995662 (4 checks)
DeepSeek V4 Pro / Galaxy-API code / run 1 → result 7 (signal total)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Numerical agreement (CCC): 0 (2 checks)
  - Occupied base f1: 0 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0
  - S02: 0
DeepSeek V4 Pro / Galaxy-API code / run 1 → result 8 (signal in union)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Numerical agreement (CCC): 0 (2 checks)
  - Occupied base f1: 0 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0
  - S02: 0
DeepSeek V4 Pro / Galaxy-API code / run 2 → result 2 (alignment stages)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Alignment records: 0.994337 to 0.995662 (6 checks)
  - Matching records (F1): 0.968074 (2 checks)
  - Numerical agreement (CCC): 0.999993 to 0.999999 (4 checks)
  - Present, finite data cells (F1): 0.968074 (2 checks)
  - Summary statistics within tolerance: 0 (2 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: 0.998.
  - Alignment records: 0.995657 to 0.995662 (4 checks)
DeepSeek V4 Pro / Galaxy-API code / run 2 → result 4 (peak windows)
- Content: Content score below 0.80. Value: 0.354533. Required minimum: 0.8.
  - Matching records (F1): 0.59135 to 0.998518 (4 checks)
  - Numerical agreement (CCC): 1 to 1 (2 checks)
  - Present, finite data cells (F1): 0.59135 to 0.600355 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.359889
  - S02: 0.349176
DeepSeek V4 Pro / Galaxy-API code / run 2 → result 7 (signal total)
- Content: Content score below 0.80. Value: 2.01965e-08. Required minimum: 0.8.
  - Numerical agreement (CCC): 0 to 5.73021e-08 (2 checks)
  - Occupied base f1: 0.704914 to 0.708219 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 4.0393e-08
  - S02: 0
DeepSeek V4 Pro / Galaxy-API code / run 2 → result 8 (signal in union)
- Content: Content score below 0.80. Value: 2.01951e-08. Required minimum: 0.8.
  - Numerical agreement (CCC): 0 to 5.72982e-08 (2 checks)
  - Occupied base f1: 0.704914 to 0.708219 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 4.03903e-08
  - S02: 0
DeepSeek V4 Pro / Galaxy-API code / run 3 → result 2 (alignment stages)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Alignment records: 0.994337 to 0.995662 (6 checks)
  - Numerical agreement (CCC): 0.999998 to 1 (4 checks)
  - Summary statistics within tolerance: 0 (2 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: 0.998.
  - Alignment records: 0.995657 to 0.995662 (4 checks)
DeepSeek V4 Pro / Galaxy-API code / run 3 → result 4 (peak windows)
- Content: Content score below 0.80. Value: 0.148169. Required minimum: 0.8.
  - Matching records (F1): 0.99851 to 0.998576 (4 checks)
  - Numerical agreement (CCC): 0.148025 to 0.149609 (2 checks)
  - Present, finite data cells (F1): 0.99855 to 0.998576 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.148961
  - S02: 0.147378
DeepSeek V4 Pro / Galaxy-API code / run 3 → result 7 (signal total)
- Method: The track is not the 50-bp mean per-base pileup times the delivered factor (uncovered bases = 0) on chr19: S01, S02.Task requirement: From the shifted/extended treatment pileup from Poisson-background narrow-enrichment calling, produce 50-bp bins of mean per-base signal, treating uncovered bases as zero; use only in-genome bases for a shortened terminal bin. Scale by 10^6 divided by either the total retained-record count or the union-overlapping count.
DeepSeek V4 Pro / Galaxy-API code / run 3 → result 8 (signal in union)
- Method: The track is not the 50-bp mean per-base pileup times the delivered factor (uncovered bases = 0) on chr19: S01, S02.Task requirement: From the shifted/extended treatment pileup from Poisson-background narrow-enrichment calling, produce 50-bp bins of mean per-base signal, treating uncovered bases as zero; use only in-genome bases for a shortened terminal bin. Scale by 10^6 divided by either the total retained-record count or the union-overlapping count.
DeepSeek V4 Pro / Open-ended code / run 1 → result 1 (read processing)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Required content missing or unreadable: 0 (2 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0
  - S02: 0
DeepSeek V4 Pro / Open-ended code / run 1 → result 2 (alignment stages)
- Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
  - Alignment records: 0.994047 to 0.99966 (4 checks)
  - Matching records (F1): 0.994985 to 0.995992 (2 checks)
  - Numerical agreement (CCC): 0.666667 to 0.999972 (4 checks)
  - Present, finite data cells (F1): 0.994985 to 0.995992 (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
DeepSeek V4 Pro / Open-ended code / run 2 → result 2 (alignment stages)
- Content: Content score below 0.80. Value: 0.135793. Required minimum: 0.8.
  - Alignment records: 0.994047 to 1 (3 checks)
  - Numerical agreement (CCC): 0.139682 to 0.666667 (4 checks)
- Member: A required member scores below 0.80. Required minimum: 0.8.
  - S01: 0.0925671
  - S02: 0.179018
DeepSeek V4 Pro / Open-ended code / run 3 → result 4 (peak windows)
- Method: Windows or their union differ from summit ±500 bp clipped to the chromosome and merged when overlapping or book-ended: S01, S02.Task requirement: Expand each one-base summit by 500 bp on each side, clip to chromosome bounds and merge overlapping or book-ended windows within each library.

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

Analyze the two mouse paired-end ATAC-seq libraries separately on mm10. Produce accessible-region evidence and two explicitly defined normalized signal profiles per library. Treat accessibility as local narrow enrichment in reference-aligned reads without an external control. Use summit-centered windows to define the accessible-region union, and compare total-library versus accessible-region normalization of the same shifted/extended signal. Keep the alignment-record and paired-fragment units distinct.

Inputs

Two complete paired-read libraries with sample/mate identities.
mm10 reference and chromosome lengths.

Key parameters and conditions

Use Q30 as the qualified-base threshold and allow at most 70% unqualified bases. Preserve library and mate identities. Keep paired reads with at most five ambiguous bases per mate and length at least 15 nt after overlap-based adapter removal; do not merge mates or add fixed/sliding-window trimming.
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 pairs allowed. Apply MAPQ≥30 to each alignment record independently and require its proper-pair flag; do not add a requirement that both mates pass MAPQ together. Exclude mitochondrial alignments, then remove duplicates. Report chromosome statistics, duplicate metrics and insert-size distribution through 500 bp. Identify coordinate duplicates by aligned template coordinates, retaining the representative with the greatest sum of base qualities.
For no-control narrow peaks and signal, use a per-alignment BED representation, effective genome size 2,308,840,607, shift −100, extension 200 and q<0.05; retain all records reaching peak calling. Expand each one-base summit by 500 bp on each side, clip to chromosome bounds and merge overlapping or book-ended windows within each library.
Count all post-deduplication alignment records and records whose reference spans overlap the merged window union. Count each record at most once; do not substitute fragment counts or aligned-block overlap.
From the shifted/extended treatment pileup from Poisson-background narrow-enrichment calling, produce 50-bp bins of mean per-base signal, treating uncovered bases as zero; use only in-genome bases for a shortened terminal bin. Scale by 10^6 divided by either the total retained-record count or the union-overlapping count. A zero denominator makes that profile undefined: retain the zero count and report it, rather than fabricate a zero profile. These are not bin sums or unextended-read coverage tracks.
Call sub-peak summits, retaining distinct summits sharing an interval. Report chromosome counts on the unfiltered alignment and insert lengths on deduplicated read pairs (one observation per pair). Use the complete supplied chromosome dictionary and coordinate-sorted BAMs. Signal bins begin at the first genomic base.

Required results

final_answer/01_read_processing/{sample}/
FASTQ + JSON
Processed mate files and the complete native JSON quality/processing report. Files: {sample}/forward.fastq.gz, {sample}/qc.json, {sample}/reverse.fastq.gz.
final_answer/02_alignment_stages/{sample}/
BAM + native text/TSV reports
Aligned, selected and deduplicated BAMs; alignment summary, chromosome idxstats, coordinate-duplicate library metrics and a headerless two-column insert-length/frequency histogram through 500 bp. Files: {sample}/aligned.bam, {sample}/deduplicated.bam, {sample}/duplicates.txt, {sample}/filtered.bam, {sample}/idxstats.tsv, {sample}/insert_lengths.tsv, {sample}/mapping.txt.
final_answer/03_peaks/{sample}/
narrowPeak + BED + TSV
Ten-column narrowPeak, one-base summit BED and the complete peak-calling TSV report; retain sub-peak summits. Files: {sample}/peaks.narrowPeak, {sample}/report.tsv, {sample}/summits.bed.
final_answer/04_peak_windows/{sample}/
TSV + BED
Headerless windows.tsv: chromosome, start, end, summit label, score; union.bed: chromosome, start, end. Coordinates are zero-based half-open. Files: {sample}/union.bed, {sample}/windows.tsv.
final_answer/05_signal_scaling/{sample}/
text
One number in each of all_count.txt, union_count.txt, all_factor.txt and union_factor.txt. Files: {sample}/all_count.txt, {sample}/all_factor.txt, {sample}/union_count.txt, {sample}/union_factor.txt.
final_answer/06_raw_pileup/{sample}.bedgraph
bedGraph
Unscaled shifted/extended treatment pileup.
final_answer/07_signal_total/{sample}.bw
bigWig
50-bp profile scaled by the total retained-record count.
final_answer/08_signal_in_union/{sample}.bw
bigWig
50-bp profile scaled by the union-overlapping record count.

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 + JSON	Processed mate files and the complete native JSON quality/processing report. Files: {sample}/forward.fastq.gz, {sample}/qc.json, {sample}/reverse.fastq.gz.	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.
2	`02_alignment_stages/{sample}/` BAM + native text/TSV reports	Aligned, selected and deduplicated BAMs; alignment summary, chromosome idxstats, coordinate-duplicate library metrics and a headerless two-column insert-length/frequency histogram through 500 bp. Files: {sample}/aligned.bam, {sample}/deduplicated.bam, {sample}/duplicates.txt, {sample}/filtered.bam, {sample}/idxstats.tsv, {sample}/insert_lengths.tsv, {sample}/mapping.txt.	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) 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_peaks/{sample}/` narrowPeak + BED + TSV	Ten-column narrowPeak, one-base summit BED and the complete peak-calling TSV report; retain sub-peak summits. Files: {sample}/peaks.narrowPeak, {sample}/report.tsv, {sample}/summits.bed.	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.
4	`04_peak_windows/{sample}/` TSV + BED	Headerless windows.tsv: chromosome, start, end, summit label, score; union.bed: chromosome, start, end. Coordinates are zero-based half-open. Files: {sample}/union.bed, {sample}/windows.tsv.	the same rows or records as the reference (F1 of their identifiers) Scored for each of the 2 samples and averaged.
5	`05_signal_scaling/{sample}/` text	One number in each of all_count.txt, union_count.txt, all_factor.txt and union_factor.txt. Files: {sample}/all_count.txt, {sample}/all_factor.txt, {sample}/union_count.txt, {sample}/union_factor.txt.	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.
6	`06_raw_pileup/{sample}.bedgraph` bedGraph	Unscaled shifted/extended treatment pileup.	the signal covers the same bases with agreeing values (F1 and concordance correlation) Scored for each of the 2 samples and averaged.
7	`07_signal_total/{sample}.bw` bigWig	50-bp profile scaled by the total retained-record count.	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.
8	`08_signal_in_union/{sample}.bw` bigWig	50-bp profile scaled by the union-overlapping record count.	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.

Data updated 27 October 2026, 08:48 EDT.