From 7c228210eed41b924a9ad30aa07a3f0c44b7f9ee Mon Sep 17 00:00:00 2001
From: Glenn Hickey <glenn.hickey@gmail.com>
Date: Thu, 15 Jan 2026 11:40:16 -0500
Subject: [PATCH 1/2] allow bigger mem for consolidated

---
 src/cactus/cactus_progressive_config.xml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/cactus/cactus_progressive_config.xml b/src/cactus/cactus_progressive_config.xml
index 427eae7ab..f9eb9b349 100644
--- a/src/cactus/cactus_progressive_config.xml
+++ b/src/cactus/cactus_progressive_config.xml
@@ -111,6 +111,7 @@
 		   dechunkBatchSize="1000"
 		   pickIngroupPrimaryAlignmentsSeparatelyToOutgroups="1"
 		   slurmChunkScale="3"
+		   bigGenomeChunkScale="2"
 		   >
 
 		<!-- The following are parametrised to produce the same results as the default settings,
@@ -550,6 +551,8 @@
 			seq_size_1000000000="128000000000"
 			seq_size_4000000000="256000000000"
 			seq_size_10000000000="512000000000"
+			seq_size_15000000000="999000000000"
+			seq_size_20000000000="1990000000000"
 	 	/>
 	</consolidated>
 	<consolidated2></consolidated2>

From b6f3977276eb8826c8c3efaec531c3c3d0b5838f Mon Sep 17 00:00:00 2001
From: Glenn Hickey <glenn.hickey@gmail.com>
Date: Thu, 15 Jan 2026 11:40:46 -0500
Subject: [PATCH 2/2] 11;rgb:3030/0a0a/2424# This is the 1st commit message:

cut headers uses linear memory for some reason
---
 src/cactus/preprocessor/cactus_preprocessor.py | 3 ++-
 src/cactus/preprocessor/cutHeaders.py          | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/cactus/preprocessor/cactus_preprocessor.py b/src/cactus/preprocessor/cactus_preprocessor.py
index a1d3253db..b4cfa18a3 100644
--- a/src/cactus/preprocessor/cactus_preprocessor.py
+++ b/src/cactus/preprocessor/cactus_preprocessor.py
@@ -90,7 +90,8 @@ class CheckUniqueHeaders(RoundedJob):
     """
     def __init__(self, prepOptions, inChunkID):
         disk = 2*inChunkID.size
-        RoundedJob.__init__(self, memory=prepOptions.memory, cores=prepOptions.cpu, disk=disk,
+        memory = max(prepOptions.memory, inChunkID.size)
+        RoundedJob.__init__(self, memory=memory, cores=prepOptions.cpu, disk=disk,
                      preemptable=True)
         self.prepOptions = prepOptions
         self.inChunkID = inChunkID
diff --git a/src/cactus/preprocessor/cutHeaders.py b/src/cactus/preprocessor/cutHeaders.py
index 1b857d7d2..6e2934b10 100644
--- a/src/cactus/preprocessor/cutHeaders.py
+++ b/src/cactus/preprocessor/cutHeaders.py
@@ -17,6 +17,7 @@
 class CutHeadersJob(RoundedJob):
     def __init__(self, fastaID, cutBefore, cutBeforeOcc, cutAfter):
         disk = 2*(fastaID.size)
+        memory = fastaID.size
         RoundedJob.__init__(self, disk=disk, preemptable=True)
         self.fastaID = fastaID
         self.cutBefore = cutBefore