diff --git a/Cargo.lock b/Cargo.lock
index c7a38495..018ac35a 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -606,6 +606,12 @@ version = "0.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80"
 
+[[package]]
+name = "fixedbitset"
+version = "0.5.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1d674e81391d1e1ab681a28d99df07927c6d4aa5b027d7da16ba32d1d21ecd99"
+
 [[package]]
 name = "flate2"
 version = "1.0.30"
@@ -646,9 +652,9 @@ dependencies = [
 
 [[package]]
 name = "getset"
-version = "0.1.3"
+version = "0.1.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f636605b743120a8d32ed92fc27b6cde1a769f8f936c065151eb66f88ded513c"
+checksum = "eded738faa0e88d3abc9d1a13cb11adc2073c400969eeb8793cf7132589959fc"
 dependencies = [
  "proc-macro-error2",
  "proc-macro2",
@@ -885,9 +891,9 @@ checksum = "78b3ae25bc7c8c38cec158d1f2757ee79e9b3740fbc7ccf0e59e4b08d793fa89"
 
 [[package]]
 name = "log"
-version = "0.4.22"
+version = "0.4.25"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a7a70ba024b9dc04c27ea2f0c0548feb474ec5c54bba33a7f72f873a39d07b24"
+checksum = "04cbf5b083de1c7e0222a7a51dbfdba1cbe1c6ab0b15e29fff3f6c077fd9cd9f"
 
 [[package]]
 name = "lz4-sys"
@@ -990,14 +996,16 @@ dependencies = [
 
 [[package]]
 name = "ndarray"
-version = "0.15.6"
+version = "0.16.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "adb12d4e967ec485a5f71c6311fe28158e9d6f4bc4a447b474184d0f91a8fa32"
+checksum = "882ed72dce9365842bf196bdeedf5055305f11fc8c03dee7bb0194a6cad34841"
 dependencies = [
  "matrixmultiply",
  "num-complex",
  "num-integer",
  "num-traits",
+ "portable-atomic",
+ "portable-atomic-util",
  "rawpointer",
  "rayon",
 ]
@@ -1163,11 +1171,11 @@ checksum = "57c0d7b74b563b49d38dae00a0c37d4d6de9b432382b2892f0574ddcae73fd0a"
 
 [[package]]
 name = "petgraph"
-version = "0.6.5"
+version = "0.7.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b4c5cc86750666a3ed20bdaf5ca2a0344f9c67674cae0515bec2da16fbaa47db"
+checksum = "3672b37090dbd86368a4145bc067582552b29c27377cad4e0a306c97f9bd7772"
 dependencies = [
- "fixedbitset",
+ "fixedbitset 0.5.7",
  "indexmap",
 ]
 
@@ -1199,6 +1207,15 @@ version = "1.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0"
 
+[[package]]
+name = "portable-atomic-util"
+version = "0.2.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d8a2f0d8d040d7848a709caf78912debcc3f33ee4b3cac47d73d1e1069e83507"
+dependencies = [
+ "portable-atomic",
+]
+
 [[package]]
 name = "ppv-lite86"
 version = "0.2.17"
@@ -1246,9 +1263,9 @@ dependencies = [
 
 [[package]]
 name = "priority-queue"
-version = "2.0.3"
+version = "2.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "70c501afe3a2e25c9bd219aa56ec1e04cdb3fcdd763055be268778c13fa82c1f"
+checksum = "714c75db297bc88a63783ffc6ab9f830698a6705aa0201416931759ef4c8183d"
 dependencies = [
  "autocfg",
  "equivalent",
@@ -1656,12 +1673,12 @@ dependencies = [
 
 [[package]]
 name = "rustworkx-core"
-version = "0.15.1"
+version = "0.16.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ef8108bdaf5b590d2ea261c6ca9b1795cbf253d0733b2e209b7990c95ed23843"
+checksum = "f8a4717d3df536ce531369b8c9a0c7f9624a51cf9c3948038ed3cb18e9a16c92"
 dependencies = [
  "ahash 0.8.11",
- "fixedbitset",
+ "fixedbitset 0.5.7",
  "hashbrown 0.14.5",
  "indexmap",
  "ndarray",
@@ -1717,9 +1734,9 @@ dependencies = [
 
 [[package]]
 name = "serde_json"
-version = "1.0.135"
+version = "1.0.137"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2b0d7ba2887406110130a978386c4e1befb98c674b4fba677954e4db976630d9"
+checksum = "930cfb6e6abf99298aaad7d29abbef7a9999a9a8806a40088f55f0dcec03146b"
 dependencies = [
  "itoa",
  "memchr",
@@ -1784,7 +1801,7 @@ dependencies = [
  "counter",
  "csv",
  "enum_dispatch",
- "fixedbitset",
+ "fixedbitset 0.4.2",
  "getrandom",
  "getset",
  "histogram",
diff --git a/Cargo.toml b/Cargo.toml
index e8b1c16b..56292d7d 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -13,9 +13,9 @@ pyo3 = { version = "0.23.4", features = ["extension-module", "anyhow"] }
 rayon = "1.10.0"
 serde = { version = "1.0.217", features = ["derive"] }
 sourmash = { version = "0.18.0", features = ["branchwater"] }
-serde_json = "1.0.135"
+serde_json = "1.0.137"
 niffler = "2.4.0"
-log = "0.4.22"
+log = "0.4.25"
 env_logger = { version = "0.11.6" }
 simple-error = "0.3.1"
 anyhow = "1.0.95"
@@ -25,7 +25,7 @@ needletail = "0.5.1"
 csv = "1.3.1"
 camino = "1.1.9"
 glob = "0.3.2"
-rustworkx-core = "0.15.1"
+rustworkx-core = "0.16.0"
 streaming-stats = "0.2.3"
 rust_decimal = { version = "1.36.0", features = ["maths"] }
 rust_decimal_macros = "1.36.0"