From d97d6f6b82daf631b7a24e364fc2f7305cab1a29 Mon Sep 17 00:00:00 2001
From: Steven Weaver <weaverst@gmail.com>
Date: Sat, 25 Jul 2026 21:26:17 -0400
Subject: [PATCH] Raise max_sequences limits for larger alignments

Sizes derived from the DM3 timing calculator (power-law runtime fits,
timingEstimates.js) targeting a ~12h budget at 1000 sites on the
32-core backend config:

  base (fel/meme/slac)  5000 -> 10000
  fubar                10000 -> 25000
  contrast-fel          2000 -> 5000
  absrel                1000 -> 2500
  relax                 1000 -> 2000
  busted                1000 -> 2000
  bgm                   1000 -> 1500

GARD and multi-hit intentionally left at 1000 (runtime is superlinear
in taxa; they are the methods most prone to walltime timeouts).
max_sites (base 32000) unchanged; real uploads top out ~12k.
---
 app/models/absrel.js       | 2 +-
 app/models/analysis.js     | 2 +-
 app/models/bgm.js          | 2 +-
 app/models/busted.js       | 2 +-
 app/models/contrast-fel.js | 2 +-
 app/models/fubar.js        | 2 +-
 app/models/relax.js        | 2 +-
 7 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/app/models/absrel.js b/app/models/absrel.js
index 20a5c4ae..e5f54f2c 100644
--- a/app/models/absrel.js
+++ b/app/models/absrel.js
@@ -28,7 +28,7 @@ aBSREL.virtual("upload_redirect_path").get(function () {
 });
 
 aBSREL.virtual("max_sequences").get(function () {
-  return 1000;
+  return 2500;
 });
 
 /**
diff --git a/app/models/analysis.js b/app/models/analysis.js
index edaa2205..8e59e347 100644
--- a/app/models/analysis.js
+++ b/app/models/analysis.js
@@ -59,7 +59,7 @@ AnalysisSchema.virtual("max_sites").get(function () {
 });
 
 AnalysisSchema.virtual("max_sequences").get(function () {
-  return 5000;
+  return 10000;
 });
 
 AnalysisSchema.virtual("input_data").get(function () {
diff --git a/app/models/bgm.js b/app/models/bgm.js
index 41f719b4..7594158d 100644
--- a/app/models/bgm.js
+++ b/app/models/bgm.js
@@ -28,7 +28,7 @@ BGM.virtual("analysistype").get(function () {
 });
 
 BGM.virtual("max_sequences").get(function () {
-  return 1000;
+  return 1500;
 });
 
 BGM.virtual("upload_redirect_path").get(function () {
diff --git a/app/models/busted.js b/app/models/busted.js
index c9307249..89e11e62 100644
--- a/app/models/busted.js
+++ b/app/models/busted.js
@@ -25,7 +25,7 @@ Busted.virtual("pmid").get(function () {
 });
 
 Busted.virtual("max_sequences").get(function () {
-  return 1000;
+  return 2000;
 });
 
 /**
diff --git a/app/models/contrast-fel.js b/app/models/contrast-fel.js
index a7df171d..88f3ced0 100644
--- a/app/models/contrast-fel.js
+++ b/app/models/contrast-fel.js
@@ -29,7 +29,7 @@ ContrastFEL.virtual("upload_redirect_path").get(function () {
 });
 
 ContrastFEL.virtual("max_sequences").get(function () {
-  return 2000;
+  return 5000;
 });
 
 /**
diff --git a/app/models/fubar.js b/app/models/fubar.js
index e87d1926..956b789b 100644
--- a/app/models/fubar.js
+++ b/app/models/fubar.js
@@ -27,7 +27,7 @@ FUBAR.virtual("upload_redirect_path").get(function () {
 });
 
 FUBAR.virtual("max_sequences").get(function () {
-  return 10000;
+  return 25000;
 });
 
 /**
diff --git a/app/models/relax.js b/app/models/relax.js
index 641cfcdf..7f7cb738 100644
--- a/app/models/relax.js
+++ b/app/models/relax.js
@@ -24,7 +24,7 @@ Relax.virtual("pmid").get(function () {
 });
 
 Relax.virtual("max_sequences").get(function () {
-  return 1000;
+  return 2000;
 });
 
 /**