Build improvements and Go version update

- Update Go version from 1.25.0 to 1.26.1 in go.mod and go.work
- Fix Makefile: quote LDFLAGS to handle spaces safely in -ldflags
- Improve build error handling: on failure, cat log then cleanup and exit with error code
- Update install_obitools.sh: properly set GOROOT, GOPATH, and GOTOOLCHAIN; ensure GOPATH directory is created

.github/workflows/release.yml

@@ -62,6 +62,12 @@ jobs:
           TAG=${GITHUB_REF#refs/tags/Release_}
           echo "version=$TAG" >> $GITHUB_OUTPUT
 
+      - name: Install build tools (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update -q
+          sudo apt-get install -y musl-tools
+
       - name: Install build tools (macOS)
         if: runner.os == 'macOS'
         run: |
@@ -74,8 +80,13 @@ jobs:
           GOOS: ${{ matrix.goos }}
           GOARCH: ${{ matrix.goarch }}
           VERSION: ${{ steps.get_version.outputs.version }}
+          CC: ${{ matrix.goos == 'linux' && 'musl-gcc' || '' }}
         run: |
-          make obitools
+          if [ "$GOOS" = "linux" ]; then
+            make LDFLAGS='-linkmode=external -extldflags=-static' obitools
+          else
+            make obitools
+          fi
           mkdir -p artifacts
           # Create a single tar.gz with all binaries for this platform
           tar -czf artifacts/obitools4_${VERSION}_${{ matrix.output_name }}.tar.gz -C build .

Makefile

@@ -10,8 +10,9 @@ BLUE   := \033[0;34m
 NC     := \033[0m
 
 GOFLAGS=
+LDFLAGS=
 GOCMD=go
-GOBUILD=$(GOCMD) build $(GOFLAGS)
+GOBUILD=$(GOCMD) build $(GOFLAGS) $(if $(LDFLAGS),-ldflags="$(LDFLAGS)")
 GOGENERATE=$(GOCMD) generate
 GOCLEAN=$(GOCMD) clean
 GOTEST=$(GOCMD) test
@@ -50,7 +51,7 @@ $(OBITOOLS_PREFIX)$(notdir $(1)): $(BUILD_DIR) $(1) pkg/obioptions/version.go
 	@echo -n - Building obitool $(notdir $(1))...
 	@$(GOBUILD)  -o $(BUILD_DIR)/$(OBITOOLS_PREFIX)$(notdir $(1)) ./$(1) \
 	             2> $(OBITOOLS_PREFIX)$(notdir $(1)).log \
-				 || cat $(OBITOOLS_PREFIX)$(notdir $(1)).log
+				 || { cat $(OBITOOLS_PREFIX)$(notdir $(1)).log; rm -f $(OBITOOLS_PREFIX)$(notdir $(1)).log; exit 1; }
 	@rm -f $(OBITOOLS_PREFIX)$(notdir $(1)).log
 	@echo Done.
 endef

go.mod

@@ -1,35 +1,33 @@
 module git.metabarcoding.org/obitools/obitools4/obitools4
 
-go 1.23.4
+go 1.26.1
-
-toolchain go1.24.2
 
 require (
-	github.com/DavidGamba/go-getoptions v0.28.0
+	github.com/DavidGamba/go-getoptions v0.33.0
-	github.com/PaesslerAG/gval v1.2.2
+	github.com/PaesslerAG/gval v1.2.4
 	github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df
 	github.com/buger/jsonparser v1.1.1
 	github.com/chen3feng/stl4go v0.1.1
-	github.com/dlclark/regexp2 v1.11.4
+	github.com/dlclark/regexp2 v1.11.5
-	github.com/goccy/go-json v0.10.3
+	github.com/goccy/go-json v0.10.6
 	github.com/klauspost/pgzip v1.2.6
 	github.com/pbnjay/memory v0.0.0-20210728143218-7b4eea64cf58
 	github.com/pelletier/go-toml/v2 v2.2.4
 	github.com/rrethy/ahocorasick v1.0.0
-	github.com/schollz/progressbar/v3 v3.13.1
+	github.com/schollz/progressbar/v3 v3.19.0
-	github.com/sirupsen/logrus v1.9.3
+	github.com/sirupsen/logrus v1.9.4
-	github.com/stretchr/testify v1.8.4
+	github.com/stretchr/testify v1.10.0
 	github.com/tevino/abool/v2 v2.1.0
 	github.com/yuin/gopher-lua v1.1.1
-	golang.org/x/exp v0.0.0-20231110203233-9a3e6036ecaa
+	golang.org/x/exp v0.0.0-20260312153236-7ab1446f8b90
-	gonum.org/v1/gonum v0.14.0
+	gonum.org/v1/gonum v0.17.0
 	gopkg.in/yaml.v3 v3.0.1
 	scientificgo.org/special v0.0.0
 )
 
 require (
 	github.com/davecgh/go-spew v1.1.1 // indirect
-	github.com/goombaio/orderedmap v0.0.0-20180924084748-ba921b7e2419 // indirect
+	github.com/goombaio/orderedmap v0.0.0-20180925151256-3da0e2f905f9 // indirect
 	github.com/kr/pretty v0.3.1 // indirect
 	github.com/kr/text v0.2.0 // indirect
 	github.com/pmezard/go-difflib v1.0.0 // indirect
@@ -38,16 +36,15 @@ require (
 
 require (
 	github.com/dsnet/compress v0.0.1
-	github.com/gabriel-vasile/mimetype v1.4.3
+	github.com/gabriel-vasile/mimetype v1.4.13
 	github.com/goombaio/orderedset v0.0.0-20180925151225-8e67b20a9b77
-	github.com/klauspost/compress v1.17.2
+	github.com/klauspost/compress v1.18.4
-	github.com/mattn/go-runewidth v0.0.15 // indirect
+	github.com/mattn/go-runewidth v0.0.21 // indirect
 	github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
-	github.com/rivo/uniseg v0.4.4 // indirect
+	github.com/rivo/uniseg v0.4.7 // indirect
-	github.com/shopspring/decimal v1.3.1 // indirect
+	github.com/shopspring/decimal v1.4.0 // indirect
-	github.com/ulikunitz/xz v0.5.11
+	github.com/ulikunitz/xz v0.5.15
-	golang.org/x/net v0.35.0 // indirect
+	golang.org/x/sys v0.42.0 // indirect
-	golang.org/x/sys v0.30.0 // indirect
+	golang.org/x/term v0.41.0 // indirect
-	golang.org/x/term v0.29.0 // indirect
 	gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c
 )

go.sum

@@ -1,7 +1,7 @@
-github.com/DavidGamba/go-getoptions v0.28.0 h1:18wgEvfZdrlfIhVDGEBO3Dl0fkOyXqXLa0tLMCKxM1c=
+github.com/DavidGamba/go-getoptions v0.33.0 h1:8xCPH87Yy5avYenygyHVlqqm8RpymH0YFe4a7IWlarE=
-github.com/DavidGamba/go-getoptions v0.28.0/go.mod h1:zE97E3PR9P3BI/HKyNYgdMlYxodcuiC6W68KIgeYT84=
+github.com/DavidGamba/go-getoptions v0.33.0/go.mod h1:zE97E3PR9P3BI/HKyNYgdMlYxodcuiC6W68KIgeYT84=
-github.com/PaesslerAG/gval v1.2.2 h1:Y7iBzhgE09IGTt5QgGQ2IdaYYYOU134YGHBThD+wm9E=
+github.com/PaesslerAG/gval v1.2.4 h1:rhX7MpjJlcxYwL2eTTYIOBUyEKZ+A96T9vQySWkVUiU=
-github.com/PaesslerAG/gval v1.2.2/go.mod h1:XRFLwvmkTEdYziLdaCeCa5ImcGVrfQbeNUbVR+C6xac=
+github.com/PaesslerAG/gval v1.2.4/go.mod h1:XRFLwvmkTEdYziLdaCeCa5ImcGVrfQbeNUbVR+C6xac=
 github.com/PaesslerAG/jsonpath v0.1.0 h1:gADYeifvlqK3R3i2cR5B4DGgxLXIPb3TRTH1mGi0jPI=
 github.com/PaesslerAG/jsonpath v0.1.0/go.mod h1:4BzmtoM/PI8fPO4aQGIusjGxGir2BzcV0grWtFzq1Y8=
 github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df h1:GSoSVRLoBaFpOOds6QyY1L8AX7uoY+Ln3BHc22W40X0=
@@ -10,27 +10,32 @@ github.com/buger/jsonparser v1.1.1 h1:2PnMjfWD7wBILjqQbt530v576A/cAbQvEW9gGIpYMU
 github.com/buger/jsonparser v1.1.1/go.mod h1:6RYKKt7H4d4+iWqouImQ9R2FZql3VbhNgx27UK13J/0=
 github.com/chen3feng/stl4go v0.1.1 h1:0L1+mDw7pomftKDruM23f1mA7miavOj6C6MZeadzN2Q=
 github.com/chen3feng/stl4go v0.1.1/go.mod h1:5ml3psLgETJjRJnMbPE+JiHLrCpt+Ajc2weeTECXzWU=
+github.com/chengxilo/virtualterm v1.0.4 h1:Z6IpERbRVlfB8WkOmtbHiDbBANU7cimRIof7mk9/PwM=
+github.com/chengxilo/virtualterm v1.0.4/go.mod h1:DyxxBZz/x1iqJjFxTFcr6/x+jSpqN0iwWCOK1q10rlY=
+github.com/clipperhouse/uax29/v2 v2.2.0 h1:ChwIKnQN3kcZteTXMgb1wztSgaU+ZemkgWdohwgs8tY=
+github.com/clipperhouse/uax29/v2 v2.2.0/go.mod h1:EFJ2TJMRUaplDxHKj1qAEhCtQPW2tJSwu5BF98AuoVM=
 github.com/creack/pty v1.1.9/go.mod h1:oKZEueFk5CKHvIhNR5MUki03XCEU+Q6VDXinZuGJ33E=
-github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
-github.com/dlclark/regexp2 v1.11.4 h1:rPYF9/LECdNymJufQKmri9gV604RvvABwgOA8un7yAo=
+github.com/dlclark/regexp2 v1.11.5 h1:Q/sSnsKerHeCkc/jSTNq1oCm7KiVgUMZRDUoRu0JQZQ=
-github.com/dlclark/regexp2 v1.11.4/go.mod h1:DHkYz0B9wPfa6wondMfaivmHpzrQ3v9q8cnmRbL6yW8=
+github.com/dlclark/regexp2 v1.11.5/go.mod h1:DHkYz0B9wPfa6wondMfaivmHpzrQ3v9q8cnmRbL6yW8=
 github.com/dsnet/compress v0.0.1 h1:PlZu0n3Tuv04TzpfPbrnI0HW/YwodEXDS+oPKahKF0Q=
 github.com/dsnet/compress v0.0.1/go.mod h1:Aw8dCMJ7RioblQeTqt88akK31OvO8Dhf5JflhBbQEHo=
 github.com/dsnet/golib v0.0.0-20171103203638-1ea166775780/go.mod h1:Lj+Z9rebOhdfkVLjJ8T6VcRQv3SXugXy999NBtR9aFY=
-github.com/gabriel-vasile/mimetype v1.4.3 h1:in2uUcidCuFcDKtdcBxlR0rJ1+fsokWf+uqxgUFjbI0=
+github.com/gabriel-vasile/mimetype v1.4.13 h1:46nXokslUBsAJE/wMsp5gtO500a4F3Nkz9Ufpk2AcUM=
-github.com/gabriel-vasile/mimetype v1.4.3/go.mod h1:d8uq/6HKRL6CGdk+aubisF/M5GcPfT7nKyLpA0lbSSk=
+github.com/gabriel-vasile/mimetype v1.4.13/go.mod h1:d+9Oxyo1wTzWdyVUPMmXFvp4F9tea18J8ufA774AB3s=
-github.com/goccy/go-json v0.10.3 h1:KZ5WoDbxAIgm2HNbYckL0se1fHD6rz5j4ywS6ebzDqA=
+github.com/goccy/go-json v0.10.6 h1:p8HrPJzOakx/mn/bQtjgNjdTcN+/S6FcG2CTtQOrHVU=
-github.com/goccy/go-json v0.10.3/go.mod h1:oq7eo15ShAhp70Anwd5lgX2pLfOS3QCiwU/PULtXL6M=
+github.com/goccy/go-json v0.10.6/go.mod h1:oq7eo15ShAhp70Anwd5lgX2pLfOS3QCiwU/PULtXL6M=
-github.com/goombaio/orderedmap v0.0.0-20180924084748-ba921b7e2419 h1:SajEQ6tktpF9SRIuzbiPOX9AEZZ53Bvw0k9Mzrts8Lg=
+github.com/google/go-cmp v0.6.0 h1:ofyhxvXcZhMsU5ulbFiLKl/XBFqE1GSq7atu8tAmTRI=
+github.com/google/go-cmp v0.6.0/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY=
 github.com/goombaio/orderedmap v0.0.0-20180924084748-ba921b7e2419/go.mod h1:YKu81H3RSd1cFh0d7NhvUoTtUC9IY/vBX0WUQb1/o4Y=
+github.com/goombaio/orderedmap v0.0.0-20180925151256-3da0e2f905f9 h1:vFjPvFavIiDY71bQ9HIxPQBANvNl1SmFC4fgg5xRkho=
+github.com/goombaio/orderedmap v0.0.0-20180925151256-3da0e2f905f9/go.mod h1:YKu81H3RSd1cFh0d7NhvUoTtUC9IY/vBX0WUQb1/o4Y=
 github.com/goombaio/orderedset v0.0.0-20180925151225-8e67b20a9b77 h1:4dvq1tGHn1Y9KSRY0OZ24Khki4+4U+ZrA//YYsdUlJU=
 github.com/goombaio/orderedset v0.0.0-20180925151225-8e67b20a9b77/go.mod h1:HPelMYpOyy0XvglpBbmZ3krZpwaHmszj/vQNlnETPTM=
-github.com/k0kubun/go-ansi v0.0.0-20180517002512-3bf9e2903213/go.mod h1:vNUNkEQ1e29fT/6vq2aBdFsgNPmy8qMdSay1npru+Sw=
 github.com/klauspost/compress v1.4.1/go.mod h1:RyIbtBH6LamlWaDj8nUwkbUhJ87Yi3uG0guNDohfE1A=
-github.com/klauspost/compress v1.17.2 h1:RlWWUY/Dr4fL8qk9YG7DTZ7PDgME2V4csBXA8L/ixi4=
+github.com/klauspost/compress v1.18.4 h1:RPhnKRAQ4Fh8zU2FY/6ZFDwTVTxgJ/EMydqSTzE9a2c=
-github.com/klauspost/compress v1.17.2/go.mod h1:ntbaceVETuRiXiv4DpjP66DpAtAGkEQskQzEyD//IeE=
+github.com/klauspost/compress v1.18.4/go.mod h1:R0h/fSBs8DE4ENlcrlib3PsXS61voFxhIs2DeRhCvJ4=
 github.com/klauspost/cpuid v1.2.0/go.mod h1:Pj4uuM528wm8OyEC2QMXAi2YiTZ96dNQPGgoMS4s3ek=
 github.com/klauspost/pgzip v1.2.6 h1:8RXeL5crjEUFnR2/Sn6GJNWtSQ3Dk8pq4CL3jvdDyjU=
 github.com/klauspost/pgzip v1.2.6/go.mod h1:Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQKQE9RUs=
@@ -41,10 +46,8 @@ github.com/kr/pty v1.1.1/go.mod h1:pFQYn66WHrOpPYNljwOMqo10TkYh1fy3cYio2l3bCsQ=
 github.com/kr/text v0.1.0/go.mod h1:4Jbv+DJW3UT/LiOwJeYQe1efqtUx/iVham/4vfdArNI=
 github.com/kr/text v0.2.0 h1:5Nx0Ya0ZqY2ygV366QzturHI13Jq95ApcVaJBhpS+AY=
 github.com/kr/text v0.2.0/go.mod h1:eLer722TekiGuMkidMxC/pM04lWEeraHUUmBw8l2grE=
-github.com/mattn/go-isatty v0.0.17/go.mod h1:kYGgaQfpe5nmfYZH+SKPsOc2e4SrIfOl2e/yFXSvRLM=
+github.com/mattn/go-runewidth v0.0.21 h1:jJKAZiQH+2mIinzCJIaIG9Be1+0NR+5sz/lYEEjdM8w=
-github.com/mattn/go-runewidth v0.0.14/go.mod h1:Jdepj2loyihRzMpdS35Xk/zdY8IAYHsh153qUoGf23w=
+github.com/mattn/go-runewidth v0.0.21/go.mod h1:XBkDxAl56ILZc9knddidhrOlY5R/pDhgLpndooCuJAs=
-github.com/mattn/go-runewidth v0.0.15 h1:UNAjwbU9l54TA3KzvqLGxwWjHmMgBUVhBiTjelZgg3U=
-github.com/mattn/go-runewidth v0.0.15/go.mod h1:Jdepj2loyihRzMpdS35Xk/zdY8IAYHsh153qUoGf23w=
 github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db h1:62I3jR2EmQ4l5rM/4FEfDWcRD+abF5XlKShorW5LRoQ=
 github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db/go.mod h1:l0dey0ia/Uv7NcFFVbCLtqEBQbrT4OCwCSKTEv6enCw=
 github.com/pbnjay/memory v0.0.0-20210728143218-7b4eea64cf58 h1:onHthvaw9LFnH4t2DcNVpwGmV9E1BkGknEliJkfwQj0=
@@ -54,50 +57,40 @@ github.com/pelletier/go-toml/v2 v2.2.4/go.mod h1:2gIqNv+qfxSVS7cM2xJQKtLSTLUE9V8
 github.com/pkg/diff v0.0.0-20210226163009-20ebb0f2a09e/go.mod h1:pJLUxLENpZxwdsKMEsNbx1VGcRFpLqf3715MtcvvzbA=
 github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
 github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
-github.com/rivo/uniseg v0.2.0/go.mod h1:J6wj4VEh+S6ZtnVlnTBMWIodfgj8LQOQFoIToxlJtxc=
+github.com/rivo/uniseg v0.4.7 h1:WUdvkW8uEhrYfLC4ZzdpI2ztxP1I582+49Oc5Mq64VQ=
-github.com/rivo/uniseg v0.4.4 h1:8TfxU8dW6PdqD27gjM8MVNuicgxIjxpm4K7x4jp8sis=
+github.com/rivo/uniseg v0.4.7/go.mod h1:FN3SvrM+Zdj16jyLfmOkMNblXMcoc8DfTHruCPUcx88=
-github.com/rivo/uniseg v0.4.4/go.mod h1:FN3SvrM+Zdj16jyLfmOkMNblXMcoc8DfTHruCPUcx88=
 github.com/rogpeppe/go-internal v1.9.0/go.mod h1:WtVeX8xhTBvf0smdhujwtBcq4Qrzq/fJaraNFVN+nFs=
 github.com/rogpeppe/go-internal v1.12.0 h1:exVL4IDcn6na9z1rAb56Vxr+CgyK3nn3O+epU5NdKM8=
 github.com/rogpeppe/go-internal v1.12.0/go.mod h1:E+RYuTGaKKdloAfM02xzb0FW3Paa99yedzYV+kq4uf4=
 github.com/rrethy/ahocorasick v1.0.0 h1:YKkCB+E5PXc0xmLfMrWbfNht8vG9Re97IHSWZk/Lk8E=
 github.com/rrethy/ahocorasick v1.0.0/go.mod h1:nq8oScE7Vy1rOppoQxpQiiDmPHuKCuk9rXrNcxUV3R0=
-github.com/schollz/progressbar/v3 v3.13.1 h1:o8rySDYiQ59Mwzy2FELeHY5ZARXZTVJC7iHD6PEFUiE=
+github.com/schollz/progressbar/v3 v3.19.0 h1:Ea18xuIRQXLAUidVDox3AbwfUhD0/1IvohyTutOIFoc=
-github.com/schollz/progressbar/v3 v3.13.1/go.mod h1:xvrbki8kfT1fzWzBT/UZd9L6GA+jdL7HAgq2RFnO6fQ=
+github.com/schollz/progressbar/v3 v3.19.0/go.mod h1:IsO3lpbaGuzh8zIMzgY3+J8l4C8GjO0Y9S69eFvNsec=
-github.com/shopspring/decimal v1.3.1 h1:2Usl1nmF/WZucqkFZhnfFYxxxu8LG21F6nPQBE5gKV8=
 github.com/shopspring/decimal v1.3.1/go.mod h1:DKyhrW/HYNuLGql+MJL6WCR6knT2jwCFRcu2hWCYk4o=
-github.com/sirupsen/logrus v1.9.3 h1:dueUQJ1C2q9oE3F7wvmSGAaVtTmUizReu6fjN8uqzbQ=
+github.com/shopspring/decimal v1.4.0 h1:bxl37RwXBklmTi0C79JfXCEBD1cqqHt0bbgBAGFp81k=
-github.com/sirupsen/logrus v1.9.3/go.mod h1:naHLuLoDiP4jHNo9R0sCBMtWGeIprob74mVsIT4qYEQ=
+github.com/shopspring/decimal v1.4.0/go.mod h1:gawqmDU56v4yIKSwfBSFip1HdCCXN8/+DMd9qYNcwME=
-github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
+github.com/sirupsen/logrus v1.9.4 h1:TsZE7l11zFCLZnZ+teH4Umoq5BhEIfIzfRDZ1Uzql2w=
-github.com/stretchr/testify v1.3.0/go.mod h1:M5WIy9Dh21IEIfnGCwXGc5bZfKNJtfHm1UVUgZn+9EI=
+github.com/sirupsen/logrus v1.9.4/go.mod h1:ftWc9WdOfJ0a92nsE2jF5u5ZwH8Bv2zdeOC42RjbV2g=
-github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
+github.com/stretchr/testify v1.10.0 h1:Xv5erBjTwe/5IxqUQTdXv5kgmIvbHo3QQyRwhJsOfJA=
-github.com/stretchr/testify v1.8.4 h1:CcVxjf3Q8PM0mHUKJCdn+eZZtm5yQwehR5yeSVQQcUk=
+github.com/stretchr/testify v1.10.0/go.mod h1:r2ic/lqez/lEtzL7wO/rwa5dbSLXVDPFyf8C91i36aY=
-github.com/stretchr/testify v1.8.4/go.mod h1:sz/lmYIOXD/1dqDmKjjqLyZ2RngseejIcXlSw2iwfAo=
 github.com/tevino/abool/v2 v2.1.0 h1:7w+Vf9f/5gmKT4m4qkayb33/92M+Um45F2BkHOR+L/c=
 github.com/tevino/abool/v2 v2.1.0/go.mod h1:+Lmlqk6bHDWHqN1cbxqhwEAwMPXgc8I1SDEamtseuXY=
 github.com/ulikunitz/xz v0.5.6/go.mod h1:2bypXElzHzzJZwzH67Y6wb67pO62Rzfn7BSiF4ABRW8=
-github.com/ulikunitz/xz v0.5.11 h1:kpFauv27b6ynzBNT/Xy+1k+fK4WswhN/6PN5WhFAGw8=
+github.com/ulikunitz/xz v0.5.15 h1:9DNdB5s+SgV3bQ2ApL10xRc35ck0DuIX/isZvIk+ubY=
-github.com/ulikunitz/xz v0.5.11/go.mod h1:nbz6k7qbPmH4IRqmfOplQw/tblSgqTqBwxkY0oWt/14=
+github.com/ulikunitz/xz v0.5.15/go.mod h1:nbz6k7qbPmH4IRqmfOplQw/tblSgqTqBwxkY0oWt/14=
 github.com/yuin/gopher-lua v1.1.1 h1:kYKnWBjvbNP4XLT3+bPEwAXJx262OhaHDWDVOPjL46M=
 github.com/yuin/gopher-lua v1.1.1/go.mod h1:GBR0iDaNXjAgGg9zfCvksxSRnQx76gclCIb7kdAd1Pw=
-golang.org/x/exp v0.0.0-20231110203233-9a3e6036ecaa h1:FRnLl4eNAQl8hwxVVC17teOw8kdjVDVAiFMtgUdTSRQ=
+golang.org/x/exp v0.0.0-20260312153236-7ab1446f8b90 h1:jiDhWWeC7jfWqR9c/uplMOqJ0sbNlNWv0UkzE0vX1MA=
-golang.org/x/exp v0.0.0-20231110203233-9a3e6036ecaa/go.mod h1:zk2irFbV9DP96SEBUUAy67IdHUaZuSnrz1n472HUCLE=
+golang.org/x/exp v0.0.0-20260312153236-7ab1446f8b90/go.mod h1:xE1HEv6b+1SCZ5/uscMRjUBKtIxworgEcEi+/n9NQDQ=
-golang.org/x/net v0.35.0 h1:T5GQRQb2y08kTAByq9L4/bz8cipCdA8FbRTXewonqY8=
+golang.org/x/sys v0.42.0 h1:omrd2nAlyT5ESRdCLYdm3+fMfNFE/+Rf4bDIQImRJeo=
-golang.org/x/net v0.35.0/go.mod h1:EglIi67kWsHKlRzzVMUD93VMSWGFOMSZgxFjparz1Qk=
+golang.org/x/sys v0.42.0/go.mod h1:4GL1E5IUh+htKOUEOaiffhrAeqysfVGipDYzABqnCmw=
-golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
+golang.org/x/term v0.41.0 h1:QCgPso/Q3RTJx2Th4bDLqML4W6iJiaXFq2/ftQF13YU=
-golang.org/x/sys v0.0.0-20220811171246-fbc7d0a398ab/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
+golang.org/x/term v0.41.0/go.mod h1:3pfBgksrReYfZ5lvYM0kSO0LIkAl4Yl2bXOkKP7Ec2A=
-golang.org/x/sys v0.6.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
+gonum.org/v1/gonum v0.17.0 h1:VbpOemQlsSMrYmn7T2OUvQ4dqxQXU+ouZFQsZOx50z4=
-golang.org/x/sys v0.30.0 h1:QjkSwP/36a20jFYWkSue1YwXzLmsV5Gfq7Eiy72C1uc=
+gonum.org/v1/gonum v0.17.0/go.mod h1:El3tOrEuMpv2UdMrbNlKEh9vd86bmQ6vqIcDwxEOc1E=
-golang.org/x/sys v0.30.0/go.mod h1:/VUhepiaJMQUp4+oa/7Zr1D23ma6VTLIYjOOTFZPUcA=
-golang.org/x/term v0.6.0/go.mod h1:m6U89DPEgQRMq3DNkDClhWw02AUbt2daBVO4cn4Hv9U=
-golang.org/x/term v0.29.0 h1:L6pJp37ocefwRRtYPKSWOWzOtWSxVajvz2ldH/xi3iU=
-golang.org/x/term v0.29.0/go.mod h1:6bl4lRlvVuDgSf3179VpIxBF0o10JUpXWOnI7nErv7s=
-gonum.org/v1/gonum v0.14.0 h1:2NiG67LD1tEH0D7kM+ps2V+fXmsAnpUeec7n8tcr4S0=
-gonum.org/v1/gonum v0.14.0/go.mod h1:AoWeoz0becf9QMWtE8iWXNXc27fK4fNeHNf/oMejGfU=
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c h1:Hei/4ADfdWqJk1ZMxUNpqntNwaWcugrBjAiHlqqRiVk=
 gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c/go.mod h1:JHkPIbrfpd72SG/EVd6muEfDQjcINNoR0C8j2r3qZ4Q=
-gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
 gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA=
 gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
 scientificgo.org/special v0.0.0 h1:P6WJkECo6tgtvZAEfNXl+KEB9ReAatjKAeX8U07mjSc=

go.work

@@ -1,5 +1,3 @@
-go 1.23.4
+go 1.26.1
-
-toolchain go1.24.2
 
 use .

go.work.sum

@@ -52,6 +52,7 @@ golang.org/x/image v0.6.0/go.mod h1:MXLdDR43H7cDJq5GEGXEVeeNhPgi+YYEQ2pC1byI1x0=
 golang.org/x/mod v0.13.0 h1:I/DsJXRlw/8l/0c24sM9yb0T4z9liZTduXvdAWYiysY=
 golang.org/x/mod v0.13.0/go.mod h1:hTbmBsO62+eylJbnUtE2MGJUyE7QWk4xUqPFrRgJ+7c=
 golang.org/x/mod v0.14.0/go.mod h1:hTbmBsO62+eylJbnUtE2MGJUyE7QWk4xUqPFrRgJ+7c=
+golang.org/x/net v0.52.0/go.mod h1:R1MAz7uMZxVMualyPXb+VaqGSa3LIaUqk0eEt3w36Sw=
 golang.org/x/sync v0.0.0-20220722155255-886fb9371eb4 h1:uVc8UZUe6tr40fFVnUP5Oj+veunVezqYl9z7DYw9xzw=
 golang.org/x/text v0.13.0 h1:ablQoSUd0tRdKxZewP80B+BaqeKJuVhuRxj/dkrun3k=
 golang.org/x/text v0.13.0/go.mod h1:TvPlkZtksWOMsz7fbANvkp4WM8x/WCo/om8BMLbz+aE=

install_obitools.sh

@@ -183,22 +183,24 @@ GOURL=$(curl -s "${URL}${GOFILE}" \
 
 echo "Installing Go from: $GOURL" 1>&2
 
-curl -s "$GOURL" | tar zxf -
+curl --progress-bar "$GOURL" | tar zxf -
 
-PATH="$(pwd)/go/bin:$PATH"
+export GOROOT="$(pwd)/go"
+PATH="${GOROOT}/bin:$PATH"
 export PATH
-GOPATH="$(pwd)/go"
+export GOPATH="$(pwd)/gopath"
-export GOPATH
 export GOCACHE="$(pwd)/cache"
+export GOTOOLCHAIN=local
 
+echo "GOROOT=$GOROOT" 1>&2
 echo "GOCACHE=$GOCACHE" 1>&2
-mkdir -p "$GOCACHE"
+mkdir -p "$GOPATH" "$GOCACHE"
 
 # Download OBITools4 source
 echo "Downloading OBITools4 v${VERSION}..." 1>&2
 echo "Source URL: $OBIURL4" 1>&2
 
-if ! curl -sL "$OBIURL4" > obitools4.zip; then
+if ! curl --progress-bar -L "$OBIURL4" > obitools4.zip; then
   echo "Error: Could not download OBITools4 version ${VERSION}" 1>&2
   echo "Please check that this version exists with: $0 --list" 1>&2
   exit 1

pkg/obidefault/batch.go

@@ -1,6 +1,12 @@
 package obidefault
 
-var _BatchSize = 2000
+// _BatchSize is the minimum number of sequences per batch (floor).
+// Used as the minSeqs argument to RebatchBySize.
+var _BatchSize = 1
+
+// _BatchSizeMax is the maximum number of sequences per batch (ceiling).
+// A batch is flushed when this count is reached regardless of memory usage.
+var _BatchSizeMax = 2000
 
 // SetBatchSize sets the size of the sequence batches.
 //
@@ -24,3 +30,42 @@ func BatchSize() int {
 func BatchSizePtr() *int {
 	return &_BatchSize
 }
+
+// BatchSizeMax returns the maximum number of sequences per batch.
+func BatchSizeMax() int {
+	return _BatchSizeMax
+}
+
+func BatchSizeMaxPtr() *int {
+	return &_BatchSizeMax
+}
+
+// _BatchMem holds the maximum cumulative memory (in bytes) per batch when
+// memory-based batching is requested. A value of 0 disables memory-based
+// batching and falls back to count-based batching.
+var _BatchMem = 128 * 1024 * 1024 // 128 MB default; set to 0 to disable
+var _BatchMemStr = ""
+
+// SetBatchMem sets the memory budget per batch in bytes.
+func SetBatchMem(n int) {
+	_BatchMem = n
+}
+
+// BatchMem returns the current memory budget per batch in bytes.
+// A value of 0 means memory-based batching is disabled.
+func BatchMem() int {
+	return _BatchMem
+}
+
+func BatchMemPtr() *int {
+	return &_BatchMem
+}
+
+// BatchMemStr returns the raw --batch-mem string value as provided on the CLI.
+func BatchMemStr() string {
+	return _BatchMemStr
+}
+
+func BatchMemStrPtr() *string {
+	return &_BatchMemStr
+}

pkg/obiiter/batchiterator.go

@@ -444,6 +444,67 @@ func (iterator IBioSequence) Rebatch(size int) IBioSequence {
 	return newIter
 }
 
+// RebatchBySize reorganises the stream into batches bounded by two independent
+// upper limits: maxCount (max number of sequences) and maxBytes (max cumulative
+// estimated memory). A batch is flushed as soon as either limit would be
+// exceeded. A single sequence larger than maxBytes is always emitted alone.
+// Passing 0 for a limit disables that constraint; if both are 0 it falls back
+// to Rebatch(obidefault.BatchSizeMax()).
+func (iterator IBioSequence) RebatchBySize(maxBytes int, maxCount int) IBioSequence {
+	if maxBytes <= 0 && maxCount <= 0 {
+		return iterator.Rebatch(obidefault.BatchSizeMax())
+	}
+
+	newIter := MakeIBioSequence()
+
+	newIter.Add(1)
+
+	go func() {
+		newIter.WaitAndClose()
+	}()
+
+	go func() {
+		order := 0
+		iterator = iterator.SortBatches()
+		buffer := obiseq.MakeBioSequenceSlice()
+		bufBytes := 0
+		source := ""
+
+		flush := func() {
+			if len(buffer) > 0 {
+				newIter.Push(MakeBioSequenceBatch(source, order, buffer))
+				order++
+				buffer = obiseq.MakeBioSequenceSlice()
+				bufBytes = 0
+			}
+		}
+
+		for iterator.Next() {
+			seqs := iterator.Get()
+			source = seqs.Source()
+			for _, s := range seqs.Slice() {
+				sz := s.MemorySize()
+				countFull := maxCount > 0 && len(buffer) >= maxCount
+				memFull := maxBytes > 0 && bufBytes+sz > maxBytes && len(buffer) > 0
+				if countFull || memFull {
+					flush()
+				}
+				buffer = append(buffer, s)
+				bufBytes += sz
+			}
+		}
+		flush()
+
+		newIter.Done()
+	}()
+
+	if iterator.IsPaired() {
+		newIter.MarkAsPaired()
+	}
+
+	return newIter
+}
+
 func (iterator IBioSequence) FilterEmpty() IBioSequence {
 
 	newIter := MakeIBioSequence()
@@ -638,7 +699,7 @@ func (iterator IBioSequence) FilterOn(predicate obiseq.SequencePredicate,
 		trueIter.MarkAsPaired()
 	}
 
-	return trueIter.Rebatch(size)
+	return trueIter.RebatchBySize(obidefault.BatchMem(), obidefault.BatchSizeMax())
 }
 
 func (iterator IBioSequence) FilterAnd(predicate obiseq.SequencePredicate,
@@ -694,7 +755,7 @@ func (iterator IBioSequence) FilterAnd(predicate obiseq.SequencePredicate,
 		trueIter.MarkAsPaired()
 	}
 
-	return trueIter.Rebatch(size)
+	return trueIter.RebatchBySize(obidefault.BatchMem(), obidefault.BatchSizeMax())
 }
 
 // Load all sequences availables from an IBioSequenceBatch iterator into

pkg/obiiter/fragment.go

@@ -3,6 +3,7 @@ package obiiter
 import (
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 )
 
@@ -70,7 +71,7 @@ func IFragments(minsize, length, overlap, size, nworkers int) Pipeable {
 		}
 		go f(iterator)
 
-		return newiter.SortBatches().Rebatch(size)
+		return newiter.SortBatches().RebatchBySize(obidefault.BatchMem(), obidefault.BatchSizeMax())
 	}
 
 	return ifrg

pkg/obioptions/options.go

@@ -8,6 +8,7 @@ import (
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 	log "github.com/sirupsen/logrus"
 
 	"github.com/DavidGamba/go-getoptions"
@@ -55,7 +56,15 @@ func RegisterGlobalOptions(options *getoptions.GetOpt) {
 
 	options.IntVar(obidefault.BatchSizePtr(), "batch-size", obidefault.BatchSize(),
 		options.GetEnv("OBIBATCHSIZE"),
-		options.Description("Number of sequence per batch for paralelle processing"))
+		options.Description("Minimum number of sequences per batch (floor, default 1)"))
+
+	options.IntVar(obidefault.BatchSizeMaxPtr(), "batch-size-max", obidefault.BatchSizeMax(),
+		options.GetEnv("OBIBATCHSIZEMAX"),
+		options.Description("Maximum number of sequences per batch (ceiling, default 2000)"))
+
+	options.StringVar(obidefault.BatchMemStrPtr(), "batch-mem", "",
+		options.GetEnv("OBIBATCHMEM"),
+		options.Description("Maximum memory per batch (e.g. 128K, 64M, 1G; default: 128M). Set to 0 to disable."))
 
 	options.Bool("solexa", false,
 		options.GetEnv("OBISOLEXA"),
@@ -157,6 +166,15 @@ func ProcessParsedOptions(options *getoptions.GetOpt, parseErr error) {
 	if options.Called("solexa") {
 		obidefault.SetReadQualitiesShift(64)
 	}
+
+	if options.Called("batch-mem") {
+		n, err := obiutils.ParseMemSize(obidefault.BatchMemStr())
+		if err != nil {
+			log.Fatalf("Invalid --batch-mem value %q: %v", obidefault.BatchMemStr(), err)
+		}
+		obidefault.SetBatchMem(n)
+		log.Printf("Memory-based batching enabled: %s per batch", obidefault.BatchMemStr())
+	}
 }
 
 func GenerateOptionParser(program string,

pkg/obioptions/version.go

@@ -3,7 +3,7 @@ package obioptions
 // Version is automatically updated by the Makefile from version.txt
 // The patch number (third digit) is incremented on each push to the repository
 
-var _Version = "Release 4.4.20"
+var _Version = "Release 4.4.22"
 
 // Version returns the version of the obitools package.
 //

pkg/obiseq/biosequence.go

@@ -273,6 +273,28 @@ func (s *BioSequence) Len() int {
 	return len(s.sequence)
 }
 
+// MemorySize returns an estimate of the memory footprint of the BioSequence
+// in bytes. It accounts for the sequence, quality scores, feature data,
+// annotations, and fixed struct overhead. The estimate is conservative
+// (cap rather than len for byte slices) so it is suitable for memory-based
+// batching decisions.
+func (s *BioSequence) MemorySize() int {
+	if s == nil {
+		return 0
+	}
+	// fixed struct overhead (strings, pointers, mutex pointer)
+	const overhead = 128
+	n := overhead
+	n += cap(s.sequence)
+	n += cap(s.qualities)
+	n += cap(s.feature)
+	n += len(s.id)
+	n += len(s.source)
+	// rough annotation estimate: each key+value pair ~64 bytes on average
+	n += len(s.annotations) * 64
+	return n
+}
+
 // HasQualities checks if the BioSequence has sequence qualitiy scores.
 //
 // This function does not have any parameters.

pkg/obiseq/pool.go

@@ -1,13 +1,20 @@
 package obiseq
 
 import (
+	"runtime"
 	"sync"
+	"sync/atomic"
 
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
 )
 
+const _LargeSliceThreshold = 100 * 1024        // 100 kb — below: leave to GC, above: trigger explicit GC
+const _GCBytesBudget = int64(256 * 1024 * 1024) // trigger GC every 256 MB of large discards
+
+var _largeSliceDiscardedBytes = atomic.Int64{}
+
 var _BioSequenceByteSlicePool = sync.Pool{
 	New: func() interface{} {
 		bs := make([]byte, 0, 300)
@@ -34,6 +41,13 @@ func RecycleSlice(s *[]byte) {
 		}
 		if cap(*s) <= 1024 {
 			_BioSequenceByteSlicePool.Put(s)
+		} else if cap(*s) >= _LargeSliceThreshold {
+			n := int64(cap(*s))
+			*s = nil
+			prev := _largeSliceDiscardedBytes.Load()
+			if _largeSliceDiscardedBytes.Add(n)/_GCBytesBudget > prev/_GCBytesBudget {
+				runtime.GC()
+			}
 		}
 	}
 }

pkg/obitools/obiconvert/sequence_reader.go

@@ -214,6 +214,8 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 
 	iterator = iterator.Speed("Reading sequences")
 
+	iterator = iterator.RebatchBySize(obidefault.BatchMem(), obidefault.BatchSizeMax())
+
 	return iterator, nil
 }
 

pkg/obitools/obirefidx/obirefidx.go

@@ -291,5 +291,5 @@ func IndexReferenceDB(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 		go f()
 	}
 
-	return indexed.Rebatch(obidefault.BatchSize())
+	return indexed.RebatchBySize(obidefault.BatchMem(), obidefault.BatchSizeMax())
 }

pkg/obiutils/memsize.go

@@ -0,0 +1,85 @@
+package obiutils
+
+import (
+	"fmt"
+	"strconv"
+	"strings"
+	"unicode"
+)
+
+// ParseMemSize parses a human-readable memory size string and returns the
+// equivalent number of bytes. The value is a number optionally followed by a
+// unit suffix (case-insensitive):
+//
+//	B  or (no suffix) — bytes
+//	K  or KB           — kibibytes  (1 024)
+//	M  or MB           — mebibytes  (1 048 576)
+//	G  or GB           — gibibytes  (1 073 741 824)
+//	T  or TB           — tebibytes  (1 099 511 627 776)
+//
+// Examples: "512", "128K", "128k", "64M", "1G", "2GB"
+func ParseMemSize(s string) (int, error) {
+	s = strings.TrimSpace(s)
+	if s == "" {
+		return 0, fmt.Errorf("empty memory size string")
+	}
+
+	// split numeric prefix from unit suffix
+	i := 0
+	for i < len(s) && (unicode.IsDigit(rune(s[i])) || s[i] == '.') {
+		i++
+	}
+	numStr := s[:i]
+	unit := strings.ToUpper(strings.TrimSpace(s[i:]))
+	// strip trailing 'B' from two-letter units (KB→K, MB→M …)
+	if len(unit) == 2 && unit[1] == 'B' {
+		unit = unit[:1]
+	}
+
+	val, err := strconv.ParseFloat(numStr, 64)
+	if err != nil {
+		return 0, fmt.Errorf("invalid memory size %q: %w", s, err)
+	}
+
+	var multiplier float64
+	switch unit {
+	case "", "B":
+		multiplier = 1
+	case "K":
+		multiplier = 1024
+	case "M":
+		multiplier = 1024 * 1024
+	case "G":
+		multiplier = 1024 * 1024 * 1024
+	case "T":
+		multiplier = 1024 * 1024 * 1024 * 1024
+	default:
+		return 0, fmt.Errorf("unknown memory unit %q in %q", unit, s)
+	}
+
+	return int(val * multiplier), nil
+}
+
+// FormatMemSize formats a byte count as a human-readable string with the
+// largest unit that produces a value ≥ 1 (e.g. 1536 → "1.5K").
+func FormatMemSize(n int) string {
+	units := []struct {
+		suffix string
+		size   int
+	}{
+		{"T", 1024 * 1024 * 1024 * 1024},
+		{"G", 1024 * 1024 * 1024},
+		{"M", 1024 * 1024},
+		{"K", 1024},
+	}
+	for _, u := range units {
+		if n >= u.size {
+			v := float64(n) / float64(u.size)
+			if v == float64(int(v)) {
+				return fmt.Sprintf("%d%s", int(v), u.suffix)
+			}
+			return fmt.Sprintf("%.1f%s", v, u.suffix)
+		}
+	}
+	return fmt.Sprintf("%dB", n)
+}

version.txt

@@ -1 +1 @@
-4.4.20
+4.4.22