diff --git a/.github/workflows/test-release.yml b/.github/workflows/test-release.yml
index 03cc470..3ab7678 100644
--- a/.github/workflows/test-release.yml
+++ b/.github/workflows/test-release.yml
@@ -40,7 +40,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]  # Focus on Linux for release testing
-        python-version: ['3.9', '3.11']  # Test on min and stable versions
+        python-version: ['3.10', '3.11']  # Test on min and stable versions
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 25dc581..0d113ac 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]  # Temporarily disable macOS due to mappy build issues
-        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
         include:
           # Add one macOS test with conda-based installation
           - os: macos-latest
@@ -54,7 +54,7 @@ jobs:
       env:
         # Force pytantan to build from sdist so all Python versions get the
         # same AVX2-off baseline. The published cp3x wheels have caused
-        # import-time failures on 3.9/3.10/3.11 in this matrix.
+        # import-time failures on 3.10/3.11 in this matrix.
         PIP_NO_BINARY: pytantan
       run: |
         if [[ "${{ matrix.use_conda }}" == "true" ]]; then
diff --git a/CITATION.cff b/CITATION.cff
index fa6a03b..4a692c5 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -1,4 +1,4 @@
-cff-version: version = "26.4.22"
+cff-version: version = "26.5.22"
 title: 'funannotate2: eukaryotic genome annotation'
 message: >-
   If you use this software, please cite it using the
@@ -17,5 +17,5 @@ keywords:
   - functional annotation
   - consensus gene models
 license: BSD-2-Clause
-version: version = "26.4.22"
-date-released: '2026-04-22'
+version: version = "26.5.22"
+date-released: '2026-05-23'
diff --git a/funannotate2/utilities.py b/funannotate2/utilities.py
index 9268ca6..4690ecd 100755
--- a/funannotate2/utilities.py
+++ b/funannotate2/utilities.py
@@ -774,13 +774,24 @@ def logoutput(logname, process_result):
                     from .memory import MemoryMonitor
 
                     monitor = MemoryMonitor()
-                    memory_stats = monitor.monitor_process(
-                        process, process_name or " ".join(cmd[:2])
-                    )
-                    process.wait()
+                    import threading
+                    def monitor_target():
+                        nonlocal memory_stats
+                        memory_stats = monitor.monitor_process(
+                            process, process_name or " ".join(cmd[:2])
+                        )
+
+                    t = threading.Thread(target=monitor_target)
+                    t.start()
+                    out, err = process.communicate()
+                    process.stdout = out
+                    process.stderr = err
+                    t.join()
                 except ImportError:
                     # Fallback if memory module not available
-                    process.communicate()
+                    out, err = process.communicate()
+                    process.stdout = out
+                    process.stderr = err
             else:
                 process = subprocess.run(
                     cmd,
@@ -806,13 +817,28 @@ def logoutput(logname, process_result):
                     from .memory import MemoryMonitor
 
                     monitor = MemoryMonitor()
-                    memory_stats = monitor.monitor_process(
-                        process, process_name or " ".join(cmd[:2])
-                    )
+                    import threading
+                    def monitor_target():
+                        nonlocal memory_stats
+                        memory_stats = monitor.monitor_process(
+                            process, process_name or " ".join(cmd[:2])
+                        )
+
+                    t = threading.Thread(target=monitor_target)
+                    t.start()
+                    out, err = process.communicate()
+                    process.stdout = out
+                    process.stderr = err
+                    t.join()
                 except ImportError:
                     # Fallback if memory module not available
-                    pass
-            process.communicate()
+                    out, err = process.communicate()
+                    process.stdout = out
+                    process.stderr = err
+            else:
+                out, err = process.communicate()
+                process.stdout = out
+                process.stderr = err
     try:
         # Handle return code checking for both subprocess.run and subprocess.Popen
         if hasattr(process, "check_returncode"):
diff --git a/pixi.lock b/pixi.lock
index 3c36f81..ace7639 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -12,22 +12,22 @@ environments:
       linux-64:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/absl-py-2.4.0-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/aiohappyeyeballs-2.6.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/aiohappyeyeballs-2.6.2-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.13.5-py311h55b9665_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/aiosignal-1.4.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/astunparse-1.6.3-pyhd8ed1ab_3.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/bioconda/linux-64/augustus-3.5.0-pl5321h9716f88_9.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.10.1-h2d2dd48_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.10.1-ha62d5e7_3.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.9.13-h2c9d079_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.12.6-hb03c661_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.3.2-h8b1a151_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.10.12-h4bacb7b_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.26.3-hc87160b_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.11.5-h6d69fc9_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.10.13-h4bacb7b_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.26.3-hb18f61d_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.12.2-he6ee468_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.2.4-h8b1a151_4.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.2.10-h8b1a151_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/backports.zstd-1.3.0-py311h6b1f9c4_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/backports.zstd-1.5.0-py311h6b1f9c4_0.conda
       - conda: https://conda.anaconda.org/bioconda/linux-64/bamtools-2.5.3-he132191_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/biopython-1.87-py311h49ec1c0_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/blinker-1.9.0-pyhff2d567_0.conda
@@ -36,41 +36,43 @@ environments:
       - conda: https://conda.anaconda.org/bioconda/noarch/buscolite-26.4.22-pyhdfd78af_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.6-hb03c661_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.5.20-hbd8a1cb_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cached-property-1.5.2-hd8ed1ab_1.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/cached_property-1.5.2-pyha770c72_1.tar.bz2
       - conda: https://conda.anaconda.org/bioconda/linux-64/cdbtools-0.99-h077b44d_12.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.2.25-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.5.20-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-2.0.0-py311h03d9500_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/click-8.3.2-pyhc90fa1f_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/cryptography-46.0.7-py311h2005dd1_0.conda
-      - conda: https://conda.anaconda.org/bioconda/linux-64/diamond-2.1.24-hf93d47f_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/click-8.4.0-pyhc90fa1f_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/cryptography-48.0.0-py311h2005dd1_0.conda
+      - conda: https://conda.anaconda.org/bioconda/linux-64/diamond-2.2.0-he361c42_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/flatbuffers-23.5.26-h59595ed_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/frozenlist-1.7.0-py311h52bc045_0.conda
-      - conda: https://conda.anaconda.org/bioconda/noarch/gapmm2-25.8.12-pyhdfd78af_0.conda
+      - conda: https://conda.anaconda.org/bioconda/noarch/gapmm2-26.5.22-pyhdfd78af_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/gast-0.7.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/bioconda/linux-64/gb-io-0.4.0-py311h5e00ca1_0.conda
-      - conda: https://conda.anaconda.org/bioconda/noarch/gfftk-26.2.12-pyh1f0d9b5_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.2-hd590300_0.conda
       - conda: https://conda.anaconda.org/bioconda/linux-64/glimmerhmm-3.0.4-pl5321h503566f_10.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/gmp-6.3.0-hac33072_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/google-auth-2.49.2-pyhcf101f3_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/google-auth-oauthlib-1.3.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/google-auth-2.53.0-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/google-auth-oauthlib-1.4.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/google-pasta-0.2.0-pyhd8ed1ab_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/grpcio-1.59.3-py311ha6695c7_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/gsl-2.8-hbf7d49c_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/h2-4.3.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/h5py-3.16.0-nompi_py311hfef529e_102.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/hdf5-2.1.0-nompi_hd4fcb43_104.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/hdf5-2.1.0-nompi_h87a9417_105.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/hpack-4.1.0-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/bioconda/linux-64/htslib-1.22.1-h566b1c6_0.tar.bz2
+      - conda: https://conda.anaconda.org/bioconda/linux-64/htslib-1.23.1-h633afcb_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.11-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.15-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/bioconda/linux-64/infernal-1.1.5-pl5321h7b50bb2_4.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/noarch/json-repair-0.59.4-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.3.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/json-repair-0.59.10-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/jsoncpp-1.9.6-hf42df4d_1.conda
       - conda: https://conda.anaconda.org/bioconda/linux-64/k8-1.2-he8db53b_6.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/keras-2.15.0-pyhd8ed1ab_0.conda
@@ -81,39 +83,39 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libabseil-20230802.1-cxx17_h59595ed_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.5-h088129d_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libamd-3.3.3-h456b2da_7100101.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-6_h4a7cf45_openblas.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-7_h4a7cf45_openblas.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libboost-1.85.0-hba137d9_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libboost-devel-1.85.0-h00ab1b0_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libboost-headers-1.85.0-ha770c72_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libbtf-2.3.2-hf02c80a_7100101.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libcamd-3.3.3-hf02c80a_7100101.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-6_h0358290_openblas.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-7_h0358290_openblas.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libccolamd-3.3.4-hf02c80a_7100101.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libcholmod-5.3.1-h9cf07ce_7100101.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libcolamd-3.3.4-hf02c80a_7100101.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.19.0-hcf29cc6_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.20.0-hcf29cc6_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libcxsparse-4.4.1-hf02c80a_7100101.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.25-h17f619e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.5-hecca717_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.8.1-hecca717_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_18.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_18.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-h68bc16d_18.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_19.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_19.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_19.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-h68bc16d_19.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_19.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgrpc-1.59.3-hd6c4280_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.18-h3b78370_2.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.4.1-hb03c661_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libklu-2.3.5-h95ff59c_7100101.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-6_h47877c9_openblas.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-7_h47877c9_openblas.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libldl-3.3.2-hf02c80a_7100101.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.3-hb03c661_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.68.1-h877daf1_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.32-pthreads_h94d23a6_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.33-pthreads_h94d23a6_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libopenssl-static-3.6.2-hb03c661_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libparu-1.0.0-hc6afc67_7100101.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.58-h421ea60_0.conda
@@ -122,13 +124,13 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libre2-11-2023.09.01-h7a70373_1.conda
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+  md5: 02d0e89dc3950aa2522aee60e0cf3adb
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+  - gast >=0.2.1,!=0.5.0,!=0.5.1,!=0.5.2
+  - giflib >=5.2.1,<5.3.0a0
+  - google-pasta >=0.1.1
+  - grpcio 1.59.*
+  - h5py >=2.9.0
+  - icu >=73.2,<74.0a0
+  - keras >=2.15,<2.16
+  - libabseil * cxx17*
+  - libabseil >=20230802.1,<20230803.0a0
+  - libcurl >=8.5.0,<9.0a0
+  - libcxx >=15
+  - libgrpc >=1.59.3,<1.60.0a0
+  - libjpeg-turbo >=3.0.0,<4.0a0
+  - libpng >=1.6.39,<1.7.0a0
+  - libprotobuf >=4.24.4,<4.24.5.0a0
+  - libsqlite >=3.44.2,<4.0a0
+  - libzlib >=1.2.13,<2.0.0a0
+  - ml_dtypes 0.2.0.*
+  - numpy >=1.22,<2.0a0
+  - numpy >=1.23.5,<2.0a0
+  - openssl >=3.2.0,<4.0a0
+  - opt_einsum >=2.3.2
+  - packaging
+  - protobuf >=3.20.3,<5,!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5
+  - python >=3.11,<3.12.0a0
+  - python-flatbuffers >=23.5.26
+  - python_abi 3.11.* *_cp311
+  - six >=1.12
+  - snappy >=1.1.10,<1.2.0a0
+  - tensorboard >=2.15,<2.16
+  - termcolor >=1.1.0
+  - typing_extensions >=3.6.6
+  - wrapt >=1.11.0,<1.15
+  track_features:
+  - tensorflow-cpu
+  license: Apache-2.0
+  license_family: Apache
+  purls:
+  - pkg:pypi/tensorflow?source=hash-mapping
+  size: 136364803
+  timestamp: 1705701142894
 - conda: https://conda.anaconda.org/conda-forge/linux-64/tensorflow-estimator-2.15.0-cpu_py311ha26c8b9_2.conda
   sha256: 8f859aedb4d7595e442ba01c160920cc2610e64a43526f95b0e858f6b98fca1f
   md5: a02a2e580dc884808bcad87c8136c653
@@ -3162,6 +5775,21 @@ packages:
   - pkg:pypi/tensorflow-estimator?source=hash-mapping
   size: 715426
   timestamp: 1705355904606
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/tensorflow-estimator-2.15.0-cpu_py311hcceb7c1_2.conda
+  sha256: ec1f65e55752dde531b8b86a8691254bd97bad5710fbe9a0ce5080431d149fa7
+  md5: fb71af2d74e735281c6121ba9168d140
+  depends:
+  - libcxx >=15
+  - openssl >=3.2.0,<4.0a0
+  - python >=3.11,<3.12.0a0
+  - python_abi 3.11.* *_cp311
+  - tensorflow-base 2.15.0 cpu_py311he034567_2
+  license: Apache-2.0
+  license_family: Apache
+  purls:
+  - pkg:pypi/tensorflow-estimator?source=hash-mapping
+  size: 715777
+  timestamp: 1705701523667
 - conda: https://conda.anaconda.org/conda-forge/noarch/termcolor-3.3.0-pyhd8ed1ab_0.conda
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   md5: bc6228906129e420c74a5ebaf0d63936
@@ -3202,6 +5830,29 @@ packages:
   purls: []
   size: 3301196
   timestamp: 1769460227866
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/tk-8.6.13-h010d191_3.conda
+  sha256: 799cab4b6cde62f91f750149995d149bc9db525ec12595e8a1d91b9317f038b3
+  md5: a9d86bc62f39b94c4661716624eb21b0
+  depends:
+  - __osx >=11.0
+  - libzlib >=1.3.1,<2.0a0
+  license: TCL
+  license_family: BSD
+  purls: []
+  size: 3127137
+  timestamp: 1769460817696
+- conda: https://conda.anaconda.org/conda-forge/noarch/tomli-2.4.1-pyhcf101f3_0.conda
+  sha256: 91cafdb64268e43e0e10d30bd1bef5af392e69f00edd34dfaf909f69ab2da6bd
+  md5: b5325cf06a000c5b14970462ff5e4d58
+  depends:
+  - python >=3.10
+  - python
+  license: MIT
+  license_family: MIT
+  purls:
+  - pkg:pypi/tomli?source=hash-mapping
+  size: 21561
+  timestamp: 1774492402955
 - conda: https://conda.anaconda.org/bioconda/linux-64/trnascan-se-2.0.12-pl5321h7b50bb2_2.tar.bz2
   sha256: 7e32f5727dfbf989466d8bc285215ab32d6f675d830ff2988b0a82a4d2f440f4
   md5: 785199e6cbd7260af9203c22ddbdacab
@@ -3214,6 +5865,17 @@ packages:
   purls: []
   size: 3271182
   timestamp: 1734214903046
+- conda: https://conda.anaconda.org/bioconda/osx-arm64/trnascan-se-2.0.12-pl5321hbdacb55_2.tar.bz2
+  sha256: 602242ef498986814582f33e4847b16124191f54f7705020b60ca9d003685cdb
+  md5: ad3f04cad4c34a8afb1f248fe807e3ad
+  depends:
+  - infernal >=1.1.4
+  - perl >=5.32.1,<5.33.0a0 *_perl5
+  license: GPL-3.0-or-later
+  license_family: GPL3
+  purls: []
+  size: 3379559
+  timestamp: 1733980716028
 - pypi: https://files.pythonhosted.org/packages/9a/bb/d43e5c75054e53efce310e79d63df0ac3f25e34c926be5dffb7d283fb2a8/typeguard-2.13.3-py3-none-any.whl
   name: typeguard
   version: 2.13.3
@@ -3225,16 +5887,6 @@ packages:
   - typing-extensions ; extra == 'test'
   - mypy ; platform_python_implementation != 'PyPy' and extra == 'test'
   requires_python: '>=3.5.3'
-- conda: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda
-  sha256: 7c2df5721c742c2a47b2c8f960e718c930031663ac1174da67c1ed5999f7938c
-  md5: edd329d7d3a4ab45dcf905899a7a6115
-  depends:
-  - typing_extensions ==4.15.0 pyhcf101f3_0
-  license: PSF-2.0
-  license_family: PSF
-  purls: []
-  size: 91383
-  timestamp: 1756220668932
 - conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda
   sha256: 032271135bca55aeb156cee361c81350c6f3fb203f57d024d7e5a1fc9ef18731
   md5: 0caa1af407ecff61170c9437a808404d
@@ -3270,6 +5922,20 @@ packages:
   purls: []
   size: 383232
   timestamp: 1750330214400
+- conda: https://conda.anaconda.org/bioconda/osx-arm64/ucsc-fatotwobit-482-h1643cc5_0.tar.bz2
+  sha256: 2c83e8d936ab4b3383099bd21b22743be9ed4abe4a656fe968e91b2895fdb570
+  md5: 597d147c0ce6ad35ab6921e515e973c9
+  depends:
+  - bzip2 >=1.0.8,<2.0a0
+  - liblzma >=5.8.1,<6.0a0
+  - libopenssl-static
+  - libpng >=1.6.49,<1.7.0a0
+  - libuuid >=2.38.1,<3.0a0
+  - libzlib >=1.3.1,<2.0a0
+  license: Varies; see https://genome.ucsc.edu/license
+  purls: []
+  size: 2644986
+  timestamp: 1750330026218
 - conda: https://conda.anaconda.org/bioconda/linux-64/ucsc-twobitinfo-482-hdc0a859_0.tar.bz2
   sha256: 113321fb70d6cd6b75c04dbd0925cb7a2f4aabfd138d0206af82f899412a1bb6
   md5: 91466585cc720548e4e4c105686fecb8
@@ -3286,9 +5952,23 @@ packages:
   purls: []
   size: 378240
   timestamp: 1750330740699
-- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda
-  sha256: af641ca7ab0c64525a96fd9ad3081b0f5bcf5d1cbb091afb3f6ed5a9eee6111a
-  md5: 9272daa869e03efe68833e3dc7a02130
+- conda: https://conda.anaconda.org/bioconda/osx-arm64/ucsc-twobitinfo-482-h1643cc5_0.tar.bz2
+  sha256: 8943954273712677c4ab5d64d9e5d6355f75b9cc1526cbafeadb1e887202df55
+  md5: ff94bf36f11af9fea2de167dee3bc83c
+  depends:
+  - bzip2 >=1.0.8,<2.0a0
+  - liblzma >=5.8.1,<6.0a0
+  - libopenssl-static
+  - libpng >=1.6.49,<1.7.0a0
+  - libuuid >=2.38.1,<3.0a0
+  - libzlib >=1.3.1,<2.0a0
+  license: Varies; see https://genome.ucsc.edu/license
+  purls: []
+  size: 2635760
+  timestamp: 1750330531460
+- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.7.0-pyhd8ed1ab_0.conda
+  sha256: feff959a816f7988a0893201aa9727bbb7ee1e9cec2c4f0428269b489eb93fb4
+  md5: cbb88288f74dbe6ada1c6c7d0a97223e
   depends:
   - backports.zstd >=1.0.0
   - brotli-python >=1.2.0
@@ -3299,8 +5979,8 @@ packages:
   license_family: MIT
   purls:
   - pkg:pypi/urllib3?source=hash-mapping
-  size: 103172
-  timestamp: 1767817860341
+  size: 103560
+  timestamp: 1778188657149
 - conda: https://conda.anaconda.org/conda-forge/noarch/werkzeug-3.1.8-pyhcf101f3_0.conda
   sha256: 5108c1bf2f0512e5c9dc8191e31b144c23b7cf0e73423a246173006002368d79
   md5: 3eeca039e7316268627f4116da9df64c
@@ -3311,12 +5991,12 @@ packages:
   license: BSD-3-Clause
   license_family: BSD
   purls:
-  - pkg:pypi/werkzeug?source=compressed-mapping
+  - pkg:pypi/werkzeug?source=hash-mapping
   size: 258232
   timestamp: 1775160081069
-- conda: https://conda.anaconda.org/conda-forge/noarch/wheel-0.46.3-pyhd8ed1ab_0.conda
-  sha256: d6cf2f0ebd5e09120c28ecba450556ce553752652d91795442f0e70f837126ae
-  md5: bdbd7385b4a67025ac2dba4ef8cb6a8f
+- conda: https://conda.anaconda.org/conda-forge/noarch/wheel-0.47.0-pyhd8ed1ab_0.conda
+  sha256: 9e156ffaefb8463437144326ada4b85d1de17961b9997ac5f1cbbaf747bd8bed
+  md5: d0e3b2f0030cf4fca58bde71d246e94c
   depends:
   - packaging >=24.0
   - python >=3.10
@@ -3324,8 +6004,8 @@ packages:
   license_family: MIT
   purls:
   - pkg:pypi/wheel?source=hash-mapping
-  size: 31858
-  timestamp: 1769139207397
+  size: 33491
+  timestamp: 1776878563806
 - conda: https://conda.anaconda.org/conda-forge/linux-64/wrapt-1.14.1-py311hd4cff14_1.tar.bz2
   sha256: 5b18cc1b4dd1cca104f69a4d9281d4845f8221b9bb32bca3fc83e90d3e0c9bed
   md5: f195e35cb733b64c8f7c2912f7bfa640
@@ -3339,6 +6019,19 @@ packages:
   - pkg:pypi/wrapt?source=hash-mapping
   size: 60524
   timestamp: 1666806220610
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/wrapt-1.14.1-py311he2be06e_1.tar.bz2
+  sha256: cede5d6f35a51b1e691ce3645c9aeb616e76d5eeebc36ff1178e96c5b83346e4
+  md5: 44ec6ead92d57df96dcb3ec33a9cc2c9
+  depends:
+  - python >=3.11,<3.12.0a0
+  - python >=3.11,<3.12.0a0 *_cpython
+  - python_abi 3.11.* *_cp311
+  license: BSD-2-Clause
+  license_family: BSD
+  purls:
+  - pkg:pypi/wrapt?source=hash-mapping
+  size: 57374
+  timestamp: 1666806555178
 - conda: https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.3-ha02ee65_0.conda
   sha256: 2553fd3ec0a1020b2ca05ca10b0036a596cb0d4bf3645922fcf69dacce0e6679
   md5: 6a1b6af49a334e4e06b9f103367762bf
@@ -3353,6 +6046,19 @@ packages:
   purls: []
   size: 24360
   timestamp: 1775825568523
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/xz-5.8.3-hd0f0c4f_0.conda
+  sha256: d5bb880876336f625523c022aa9bdc6be76a85df721d9e7b33c352f528619185
+  md5: 4df12be699991b97b66a85cc46ea75b5
+  depends:
+  - __osx >=11.0
+  - liblzma 5.8.3 h8088a28_0
+  - liblzma-devel 5.8.3 h8088a28_0
+  - xz-gpl-tools 5.8.3 hd0f0c4f_0
+  - xz-tools 5.8.3 h8088a28_0
+  license: 0BSD AND LGPL-2.1-or-later AND GPL-2.0-or-later
+  purls: []
+  size: 24348
+  timestamp: 1775825911109
 - conda: https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.3-ha02ee65_0.conda
   sha256: 8f139666ea18dc8340a44a54056627dd4e89e242e8cd136ab2467d6dc2c192ba
   md5: 8f5e2c6726c1339287a3c76a2c138ac7
@@ -3366,6 +6072,18 @@ packages:
   purls: []
   size: 34213
   timestamp: 1775825548743
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/xz-gpl-tools-5.8.3-hd0f0c4f_0.conda
+  sha256: 0864d53202f618b4c8a5f2c38b7029f14b900b852e99b6248813303f69ccfdee
+  md5: 43d168a8c95a8fcdcc44c2a0a7887653
+  depends:
+  - __osx >=11.0
+  - liblzma 5.8.3 h8088a28_0
+  constrains:
+  - xz 5.8.3.*
+  license: 0BSD AND LGPL-2.1-or-later AND GPL-2.0-or-later
+  purls: []
+  size: 34224
+  timestamp: 1775825884830
 - conda: https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.3-hb03c661_0.conda
   sha256: 162ebd76803464b8c8ebc7d45df32edf0ec717b3bf369a437ae3b0254f22dc2e
   md5: b62b615caa60812640f24db3a8d0fc87
@@ -3379,9 +6097,21 @@ packages:
   purls: []
   size: 95955
   timestamp: 1775825530484
-- conda: https://conda.anaconda.org/conda-forge/linux-64/yarl-1.23.0-py311h3778330_0.conda
-  sha256: 747a43142325b1bdf4184912aac043e23152062f54f5bdc43d7054373a4cf6ad
-  md5: 27ea2409d68cca4b0d02599c217bdb2d
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/xz-tools-5.8.3-h8088a28_0.conda
+  sha256: beb7fb34d5517cce06f5f89710de7108a8ca65ed9c0324269fc0446807bcbd91
+  md5: b8c47eab4e58fe7015a12ceb9d5b114c
+  depends:
+  - __osx >=11.0
+  - liblzma 5.8.3 h8088a28_0
+  constrains:
+  - xz 5.8.3.*
+  license: 0BSD AND LGPL-2.1-or-later
+  purls: []
+  size: 85931
+  timestamp: 1775825857949
+- conda: https://conda.anaconda.org/conda-forge/linux-64/yarl-1.24.2-py311h3778330_0.conda
+  sha256: c6e934bfe8bed3f0330980ea5faf3e33f3794584f293e5af3a26e849cda3474c
+  md5: 23874825495e4caaf4fdc36767a5d683
   depends:
   - __glibc >=2.17,<3.0.a0
   - idna >=2.0
@@ -3393,12 +6123,29 @@ packages:
   license: Apache-2.0
   license_family: Apache
   purls:
+  - pkg:pypi/yarl?source=compressed-mapping
+  size: 157353
+  timestamp: 1779246164758
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/yarl-1.24.2-py311hc290fe0_0.conda
+  sha256: 618f10ba92f8c2e1e269059d055009aa4d6a25abc66e4fd40c5d0d8f9557a59a
+  md5: 59bf735a79ec0190c0638ddb563d6e74
+  depends:
+  - __osx >=11.0
+  - idna >=2.0
+  - multidict >=4.0
+  - propcache >=0.2.1
+  - python >=3.11,<3.12.0a0
+  - python >=3.11,<3.12.0a0 *_cpython
+  - python_abi 3.11.* *_cp311
+  license: Apache-2.0
+  license_family: Apache
+  purls:
   - pkg:pypi/yarl?source=hash-mapping
-  size: 149070
-  timestamp: 1772409506948
-- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.1-pyhcf101f3_0.conda
-  sha256: 523616c0530d305d2216c2b4a8dfd3872628b60083255b89c5e0d8c42e738cca
-  md5: e1c36c6121a7c9c76f2f148f1e83b983
+  size: 149687
+  timestamp: 1779246852767
+- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda
+  sha256: 210bd31c22bb88f5e2a167df24c95bb5f152b2ada7502f9b8c49d1f5366db423
+  md5: ba3dcdc8584155c97c648ae9c044b7a3
   depends:
   - python >=3.10
   - python
@@ -3406,8 +6153,8 @@ packages:
   license_family: MIT
   purls:
   - pkg:pypi/zipp?source=compressed-mapping
-  size: 24461
-  timestamp: 1776131454755
+  size: 24190
+  timestamp: 1779159948016
 - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
   sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7
   md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829
@@ -3419,3 +6166,14 @@ packages:
   purls: []
   size: 601375
   timestamp: 1764777111296
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.7-hbf9d68e_6.conda
+  sha256: 9485ba49e8f47d2b597dd399e88f4802e100851b27c21d7525625b0b4025a5d9
+  md5: ab136e4c34e97f34fb621d2592a393d8
+  depends:
+  - __osx >=11.0
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  purls: []
+  size: 433413
+  timestamp: 1764777166076
diff --git a/pixi.toml b/pixi.toml
index 62f36e8..9303601 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -4,7 +4,7 @@ version = "0.1.0"
 description = "funannotate2 runtime (Docker/HPC) — assembled with pixi"
 authors = ["Jon Palmer <nextgenusfs@gmail.com>"]
 channels = ["conda-forge", "bioconda"]
-platforms = ["linux-64"]
+platforms = ["linux-64", "osx-arm64"]
 
 [dependencies]
 python = "3.11.*"
@@ -18,11 +18,9 @@ snap = "*"
 glimmerhmm = "*"
 diamond = "*"
 trnascan-se = "*"
-table2asn = "*"
 
 # funannotate2 python deps available via bioconda / conda-forge
-gfftk = ">=26.2.12"
-gapmm2 = ">=25.8.12"
+gapmm2 = ">=26.5.22"
 buscolite = ">=26.4.22"
 pyhmmer = ">=0.12.0"
 pyfastx = ">=2.0.0"
@@ -39,10 +37,15 @@ h5py = "*"
 tensorflow = ">=2.10,<2.16"
 
 # runtime utilities
-tini = "*"
 ca-certificates = "*"
+pytest = "*"
+
+[target.linux-64.dependencies]
+tini = "*"
+table2asn = "*"
 
 [pypi-dependencies]
+gfftk = ">=26.5.22"
 # local funannotate2 source (built from repo)
 funannotate2 = { path = ".", editable = false }
 # pure-pypi packages
@@ -52,3 +55,6 @@ annorefine = ">=2026.2.9"
 # pytantan: bioconda lags at 0.1.3; pull 0.1.4+ from PyPI
 pytantan = ">=0.1.4"
 
+
+[tasks]
+install-mac-table2asn = "curl -O https://ftp.ncbi.nlm.nih.gov/asn1-converters/by_program/table2asn/mac.table2asn.gz && gunzip -f mac.table2asn.gz && mv mac.table2asn $CONDA_PREFIX/bin/table2asn && chmod 755 $CONDA_PREFIX/bin/table2asn"
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 6238813..400e2d1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,20 +4,20 @@ build-backend = "hatchling.build"
 
 [project]
 name = "funannotate2"
-version = "26.4.22"
+version = "26.5.22"
 description = "Funannotate2: eukarytoic genome annotation pipeline"
 readme = {file = "README.md", content-type = "text/markdown"}
 authors = [
     {name = "Jon Palmer", email = "nextgenusfs@gmail.com"}
 ]
-requires-python = ">=3.9.0,<3.14"
+requires-python = ">=3.10.0,<3.14"
 dependencies = [
     "natsort",
     "numpy",
     "mappy",
-    "gfftk>=26.2.12",
+    "gfftk>=26.5.22",
     "buscolite>=26.4.22",
-    "gapmm2>=25.8.12",
+    "gapmm2>=26.5.22",
     "pyhmmer>=0.12.0",
     "pyfastx>=2.0.0",
     "requests",
diff --git a/tests/data/test_invalid.fasta.fxi b/tests/data/test_invalid.fasta.fxi
index f732a08..f4c9735 100644
Binary files a/tests/data/test_invalid.fasta.fxi and b/tests/data/test_invalid.fasta.fxi differ
diff --git a/tests/data/test_valid.fasta.fxi b/tests/data/test_valid.fasta.fxi
index 7955f8c..db7f531 100644
Binary files a/tests/data/test_valid.fasta.fxi and b/tests/data/test_valid.fasta.fxi differ
diff --git a/tests/integration/data/mock_lineage/hmms/busco1.hmm b/tests/integration/data/mock_lineage/hmms/busco1.hmm
index d2248e3..81581e5 100644
--- a/tests/integration/data/mock_lineage/hmms/busco1.hmm
+++ b/tests/integration/data/mock_lineage/hmms/busco1.hmm
@@ -1,7 +1,81 @@
-HMMER3/f [3.1b2 | February 2015]
+HMMER3/f [3.4 | Aug 2023]
 NAME  busco1
-ACC   PF00001.1
-DESC  Test BUSCO HMM
-LENG  300
+LENG  20
 ALPH  amino
+RF    no
+MM    no
+CONS  yes
+CS    no
+MAP   no
+DATE  Sat May 23 08:09:23 2026
+COM   [1] generate_hmms.py
+NSEQ  1
+STATS LOCAL MSV       -7.5203  0.80217
+STATS LOCAL VITERBI   -8.2197  0.80217
+STATS LOCAL FORWARD   -2.4528  0.80217
+HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.63972  3.73943  2.95908  2.71288  3.15345  2.80504  3.47799  2.92902  2.84823  2.44993  3.70203  3.13380  3.04237  3.19612  2.97300  2.71429  2.95006  2.77821  3.60501  3.24619
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      1   1.27959  4.19958  3.57405  3.03404  3.87264  2.67681  4.42214  3.15850  3.15119  2.66797  4.06769  3.82993  3.35896  3.55827  3.24540  2.37585  2.92798  2.70846  5.43730  4.13926      - a - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      2   2.34737  1.13399  3.68797  3.78387  3.66861  3.42664  4.53606  2.95447  3.58306  2.46394  3.86366  3.94385  3.79083  3.99015  3.67727  2.80772  3.04191  2.82238  4.91532  3.93523      - c - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      3   3.20437  5.17050  1.04751  2.09726  4.20766  3.01183  4.12126  3.81147  3.16826  3.63889  4.72066  2.89315  3.37603  3.25739  3.58042  2.71087  3.26301  3.67938  5.77232  4.47428      - d - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      4   2.94385  5.54588  2.37674  1.20083  4.26509  3.38721  3.86074  3.86890  2.58978  3.37837  4.46014  3.26853  3.43346  2.67892  3.00195  2.76830  3.32043  3.41886  5.51180  4.21376      - e - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      5   3.05258  4.70076  3.75727  3.53522  1.19430  3.49594  3.96947  2.70582  3.65237  2.21529  3.61502  4.01316  4.17809  4.05945  3.74658  3.19498  3.42916  2.89169  4.03077  2.41478      - f - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      6   2.53706  5.13910  3.24176  3.33766  4.17625  0.75477  4.40781  4.09802  3.45481  3.60749  4.68926  3.17969  3.66258  3.86189  3.54902  2.67946  3.54955  3.64798  5.10501  4.44288      - g - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      7   3.14672  5.11285  3.21551  2.67551  3.51410  3.27213  1.20205  3.75382  3.11061  3.26329  4.34506  2.83549  3.63633  3.19974  2.88687  2.97117  3.52331  3.62173  5.07876  2.82688      - h - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      8   2.83697  4.48516  3.85962  3.63757  3.20436  3.91624  4.70772  1.53637  3.75471  1.68174  3.39941  4.11551  3.96249  4.16180  3.84893  3.29732  3.21356  1.72223  5.40492  3.78894      - i - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      9   2.90017  5.18426  3.28692  2.42896  4.22141  3.34354  4.13501  3.82522  1.27430  3.01674  4.09851  3.22485  3.38978  2.95319  2.32237  2.72462  3.27676  3.37519  5.46812  4.17009      - k - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     10   2.84795  4.49614  4.18856  3.64855  3.21534  3.92722  4.71870  2.18325  3.44775  1.05682  3.09244  4.12649  3.97347  3.85483  3.54196  3.30831  3.22454  2.36912  5.09795  3.79992      - l - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     11   2.82260  4.47078  3.84525  3.30524  3.18998  3.58392  4.37539  2.47585  3.10444  1.66736  2.11323  3.78318  3.63016  3.19357  3.19865  2.96500  3.19919  2.34376  4.75465  3.77456      - m - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     12   3.20423  5.17036  2.63712  2.73302  4.20752  2.69374  3.48522  3.81133  2.85017  3.32080  4.40257  1.30325  3.69384  3.25725  2.94438  2.39278  2.94491  3.67924  5.77218  4.15619      - n - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     13   2.85151  5.13559  3.23825  3.01620  4.49070  3.29487  4.40430  3.77656  3.13335  3.28603  4.36780  3.81209  0.79751  3.54043  3.54551  2.99391  3.22810  3.32652  5.73741  4.43937      - p - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     14   2.87233  5.15641  2.94112  2.08317  4.19356  3.31569  3.78922  3.79738  2.51826  2.98890  3.75272  3.19701  3.36194  1.65354  2.61247  2.69678  3.24891  3.34734  5.12232  3.82429      - q - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     15   2.81678  5.10087  3.52148  2.66353  4.13802  3.26015  3.73367  3.74184  2.14477  2.93335  4.01513  3.14146  3.62434  2.86981  1.28512  2.95918  3.19337  3.60975  5.38473  4.08670      - r - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     16   2.27283  4.55692  2.97753  2.75548  3.91202  2.71620  4.14358  3.51584  2.87262  3.02531  4.10708  2.91546  3.39835  3.27971  3.28479  1.46138  2.64942  3.38375  5.47669  4.17865      - s - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     17   2.55499  4.52112  3.25968  3.03763  3.87623  3.31630  4.42573  3.16209  3.15478  2.67156  4.07128  3.19762  3.36255  3.56186  3.24899  2.37944  1.34182  2.71205  5.12294  4.14285      - t - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     18   2.54132  4.50746  3.88192  3.34192  3.54461  3.62059  4.73002  1.87662  3.45906  2.02199  3.42171  4.13781  3.66684  3.86615  3.87123  3.31963  2.91791  1.42658  5.42722  3.81124      - v - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     19   3.36566  4.69589  4.07036  3.53035  2.77919  3.17312  4.28255  3.65481  3.64750  2.84633  3.92810  4.32624  4.17322  3.73664  3.74171  3.50806  3.42430  3.52272  0.84639  2.72787      - w - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     20   3.13147  4.77965  3.83617  3.29616  2.22705  3.57483  3.09451  3.10267  3.41331  2.61214  4.01186  3.77410  3.93903  3.50244  3.50752  3.27387  3.50806  2.97058  3.79171  1.22187      - y - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.02020  3.91202        *  0.51083  0.91629  0.00000        *
 //
diff --git a/tests/integration/data/mock_lineage/hmms/busco2.hmm b/tests/integration/data/mock_lineage/hmms/busco2.hmm
index 4cf2a01..56ae723 100644
--- a/tests/integration/data/mock_lineage/hmms/busco2.hmm
+++ b/tests/integration/data/mock_lineage/hmms/busco2.hmm
@@ -1,7 +1,141 @@
-HMMER3/f [3.1b2 | February 2015]
+HMMER3/f [3.4 | Aug 2023]
 NAME  busco2
-ACC   PF00002.1
-DESC  Test BUSCO HMM
-LENG  400
+LENG  40
 ALPH  amino
+RF    no
+MM    no
+CONS  yes
+CS    no
+MAP   no
+DATE  Sat May 23 08:09:23 2026
+COM   [1] generate_hmms.py
+NSEQ  1
+STATS LOCAL MSV       -9.0185  0.74766
+STATS LOCAL VITERBI   -9.7638  0.74766
+STATS LOCAL FORWARD   -3.0030  0.74766
+HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.64071  3.74041  2.95917  2.71282  3.15319  2.80515  3.47748  2.92901  2.84810  2.44992  3.70185  3.13355  3.04221  3.19594  2.97289  2.71442  2.95006  2.77826  3.60412  3.24573
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      1   1.27959  4.19958  3.57405  3.03404  3.87264  2.67681  4.42214  3.15850  3.15119  2.66797  4.06769  3.82993  3.35896  3.55827  3.24540  2.37585  2.92798  2.70846  5.43730  4.13926      - a - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      2   2.34737  1.13399  3.68797  3.78387  3.66861  3.42664  4.53606  2.95447  3.58306  2.46394  3.86366  3.94385  3.79083  3.99015  3.67727  2.80772  3.04191  2.82238  4.91532  3.93523      - c - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      3   3.20437  5.17050  1.04751  2.09726  4.20766  3.01183  4.12126  3.81147  3.16826  3.63889  4.72066  2.89315  3.37603  3.25739  3.58042  2.71087  3.26301  3.67938  5.77232  4.47428      - d - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      4   2.94385  5.54588  2.37674  1.20083  4.26509  3.38721  3.86074  3.86890  2.58978  3.37837  4.46014  3.26853  3.43346  2.67892  3.00195  2.76830  3.32043  3.41886  5.51180  4.21376      - e - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      5   3.05258  4.70076  3.75727  3.53522  1.19430  3.49594  3.96947  2.70582  3.65237  2.21529  3.61502  4.01316  4.17809  4.05945  3.74658  3.19498  3.42916  2.89169  4.03077  2.41478      - f - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      6   2.53706  5.13910  3.24176  3.33766  4.17625  0.75477  4.40781  4.09802  3.45481  3.60749  4.68926  3.17969  3.66258  3.86189  3.54902  2.67946  3.54955  3.64798  5.10501  4.44288      - g - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      7   3.14672  5.11285  3.21551  2.67551  3.51410  3.27213  1.20205  3.75382  3.11061  3.26329  4.34506  2.83549  3.63633  3.19974  2.88687  2.97117  3.52331  3.62173  5.07876  2.82688      - h - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      8   2.83697  4.48516  3.85962  3.63757  3.20436  3.91624  4.70772  1.53637  3.75471  1.68174  3.39941  4.11551  3.96249  4.16180  3.84893  3.29732  3.21356  1.72223  5.40492  3.78894      - i - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+      9   2.90017  5.18426  3.28692  2.42896  4.22141  3.34354  4.13501  3.82522  1.27430  3.01674  4.09851  3.22485  3.38978  2.95319  2.32237  2.72462  3.27676  3.37519  5.46812  4.17009      - k - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     10   2.84795  4.49614  4.18856  3.64855  3.21534  3.92722  4.71870  2.18325  3.44775  1.05682  3.09244  4.12649  3.97347  3.85483  3.54196  3.30831  3.22454  2.36912  5.09795  3.79992      - l - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     11   2.82260  4.47078  3.84525  3.30524  3.18998  3.58392  4.37539  2.47585  3.10444  1.66736  2.11323  3.78318  3.63016  3.19357  3.19865  2.96500  3.19919  2.34376  4.75465  3.77456      - m - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     12   3.20423  5.17036  2.63712  2.73302  4.20752  2.69374  3.48522  3.81133  2.85017  3.32080  4.40257  1.30325  3.69384  3.25725  2.94438  2.39278  2.94491  3.67924  5.77218  4.15619      - n - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     13   2.85151  5.13559  3.23825  3.01620  4.49070  3.29487  4.40430  3.77656  3.13335  3.28603  4.36780  3.81209  0.79751  3.54043  3.54551  2.99391  3.22810  3.32652  5.73741  4.43937      - p - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     14   2.87233  5.15641  2.94112  2.08317  4.19356  3.31569  3.78922  3.79738  2.51826  2.98890  3.75272  3.19701  3.36194  1.65354  2.61247  2.69678  3.24891  3.34734  5.12232  3.82429      - q - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     15   2.81678  5.10087  3.52148  2.66353  4.13802  3.26015  3.73367  3.74184  2.14477  2.93335  4.01513  3.14146  3.62434  2.86981  1.28512  2.95918  3.19337  3.60975  5.38473  4.08670      - r - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     16   2.27283  4.55692  2.97753  2.75548  3.91202  2.71620  4.14358  3.51584  2.87262  3.02531  4.10708  2.91546  3.39835  3.27971  3.28479  1.46138  2.64942  3.38375  5.47669  4.17865      - s - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     17   2.55499  4.52112  3.25968  3.03763  3.87623  3.31630  4.42573  3.16209  3.15478  2.67156  4.07128  3.19762  3.36255  3.56186  3.24899  2.37944  1.34182  2.71205  5.12294  4.14285      - t - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     18   2.54132  4.50746  3.88192  3.34192  3.54461  3.62059  4.73002  1.87662  3.45906  2.02199  3.42171  4.13781  3.66684  3.86615  3.87123  3.31963  2.91791  1.42658  5.42722  3.81124      - v - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     19   3.36566  4.69589  4.07036  3.53035  2.77919  3.17312  4.28255  3.65481  3.64750  2.84633  3.92810  4.32624  4.17322  3.73664  3.74171  3.50806  3.42430  3.52272  0.84639  2.72787      - w - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     20   3.13147  4.77965  3.83617  3.29616  2.22705  3.57483  3.09451  3.10267  3.41331  2.61214  4.01186  3.77410  3.93903  3.50244  3.50752  3.27387  3.50806  2.97058  3.79171  1.22187      - y - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     21   1.27959  4.19958  3.57405  3.03404  3.87264  2.67681  4.42214  3.15850  3.15119  2.66797  4.06769  3.82993  3.35896  3.55827  3.24540  2.37585  2.92798  2.70846  5.43730  4.13926      - a - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     22   2.34737  1.13399  3.68797  3.78387  3.66861  3.42664  4.53606  2.95447  3.58306  2.46394  3.86366  3.94385  3.79083  3.99015  3.67727  2.80772  3.04191  2.82238  4.91532  3.93523      - c - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     23   3.20437  5.17050  1.04751  2.09726  4.20766  3.01183  4.12126  3.81147  3.16826  3.63889  4.72066  2.89315  3.37603  3.25739  3.58042  2.71087  3.26301  3.67938  5.77232  4.47428      - d - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     24   2.94385  5.54588  2.37674  1.20083  4.26509  3.38721  3.86074  3.86890  2.58978  3.37837  4.46014  3.26853  3.43346  2.67892  3.00195  2.76830  3.32043  3.41886  5.51180  4.21376      - e - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     25   3.05258  4.70076  3.75727  3.53522  1.19430  3.49594  3.96947  2.70582  3.65237  2.21529  3.61502  4.01316  4.17809  4.05945  3.74658  3.19498  3.42916  2.89169  4.03077  2.41478      - f - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     26   2.53706  5.13910  3.24176  3.33766  4.17625  0.75477  4.40781  4.09802  3.45481  3.60749  4.68926  3.17969  3.66258  3.86189  3.54902  2.67946  3.54955  3.64798  5.10501  4.44288      - g - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     27   3.14672  5.11285  3.21551  2.67551  3.51410  3.27213  1.20205  3.75382  3.11061  3.26329  4.34506  2.83549  3.63633  3.19974  2.88687  2.97117  3.52331  3.62173  5.07876  2.82688      - h - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     28   2.83697  4.48516  3.85962  3.63757  3.20436  3.91624  4.70772  1.53637  3.75471  1.68174  3.39941  4.11551  3.96249  4.16180  3.84893  3.29732  3.21356  1.72223  5.40492  3.78894      - i - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     29   2.90017  5.18426  3.28692  2.42896  4.22141  3.34354  4.13501  3.82522  1.27430  3.01674  4.09851  3.22485  3.38978  2.95319  2.32237  2.72462  3.27676  3.37519  5.46812  4.17009      - k - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     30   2.84795  4.49614  4.18856  3.64855  3.21534  3.92722  4.71870  2.18325  3.44775  1.05682  3.09244  4.12649  3.97347  3.85483  3.54196  3.30831  3.22454  2.36912  5.09795  3.79992      - l - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     31   2.82260  4.47078  3.84525  3.30524  3.18998  3.58392  4.37539  2.47585  3.10444  1.66736  2.11323  3.78318  3.63016  3.19357  3.19865  2.96500  3.19919  2.34376  4.75465  3.77456      - m - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     32   3.20423  5.17036  2.63712  2.73302  4.20752  2.69374  3.48522  3.81133  2.85017  3.32080  4.40257  1.30325  3.69384  3.25725  2.94438  2.39278  2.94491  3.67924  5.77218  4.15619      - n - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     33   2.85151  5.13559  3.23825  3.01620  4.49070  3.29487  4.40430  3.77656  3.13335  3.28603  4.36780  3.81209  0.79751  3.54043  3.54551  2.99391  3.22810  3.32652  5.73741  4.43937      - p - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     34   2.87233  5.15641  2.94112  2.08317  4.19356  3.31569  3.78922  3.79738  2.51826  2.98890  3.75272  3.19701  3.36194  1.65354  2.61247  2.69678  3.24891  3.34734  5.12232  3.82429      - q - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     35   2.81678  5.10087  3.52148  2.66353  4.13802  3.26015  3.73367  3.74184  2.14477  2.93335  4.01513  3.14146  3.62434  2.86981  1.28512  2.95918  3.19337  3.60975  5.38473  4.08670      - r - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     36   2.27283  4.55692  2.97753  2.75548  3.91202  2.71620  4.14358  3.51584  2.87262  3.02531  4.10708  2.91546  3.39835  3.27971  3.28479  1.46138  2.64942  3.38375  5.47669  4.17865      - s - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     37   2.55499  4.52112  3.25968  3.03763  3.87623  3.31630  4.42573  3.16209  3.15478  2.67156  4.07128  3.19762  3.36255  3.56186  3.24899  2.37944  1.34182  2.71205  5.12294  4.14285      - t - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     38   2.54132  4.50746  3.88192  3.34192  3.54461  3.62059  4.73002  1.87662  3.45906  2.02199  3.42171  4.13781  3.66684  3.86615  3.87123  3.31963  2.91791  1.42658  5.42722  3.81124      - v - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     39   3.36566  4.69589  4.07036  3.53035  2.77919  3.17312  4.28255  3.65481  3.64750  2.84633  3.92810  4.32624  4.17322  3.73664  3.74171  3.50806  3.42430  3.52272  0.84639  2.72787      - w - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.04082  3.91202  3.91202  0.51083  0.91629  0.51083  0.91629
+     40   3.13147  4.77965  3.83617  3.29616  2.22705  3.57483  3.09451  3.10267  3.41331  2.61214  4.01186  3.77410  3.93903  3.50244  3.50752  3.27387  3.50806  2.97058  3.79171  1.22187      - y - - -
+          2.54091  4.18910  2.92766  2.70561  3.22625  2.66633  3.77575  2.83006  2.82275  2.33953  3.73926  3.18354  3.03052  3.22984  2.91696  2.68331  2.91750  2.69798  4.47296  3.49288
+          0.02020  3.91202        *  0.51083  0.91629  0.00000        *
 //
diff --git a/tests/integration/test_buscolite_api.py b/tests/integration/test_buscolite_api.py
index acac20e..fa8c346 100644
--- a/tests/integration/test_buscolite_api.py
+++ b/tests/integration/test_buscolite_api.py
@@ -55,7 +55,7 @@ def test_load_cutoffs(self, test_data_dir):
         assert cutoffs["busco1"]["sigma"] == 1.5
         assert cutoffs["busco2"]["sigma"] == 1.0  # Default value when 0.0 is provided
 
-    @pytest.mark.skip(reason="buscolite is not installed")
+
     @pytest.mark.skipif(
         not shutil.which("augustus"),
         reason="Augustus is not installed or not in PATH",
diff --git a/tests/integration/test_buscolite_cli.py b/tests/integration/test_buscolite_cli.py
index c4d6ca6..19bd2bb 100644
--- a/tests/integration/test_buscolite_cli.py
+++ b/tests/integration/test_buscolite_cli.py
@@ -16,7 +16,7 @@ def test_data_dir(self):
         """Return the path to the test data directory."""
         return os.path.join(os.path.dirname(os.path.abspath(__file__)), "data")
 
-    @pytest.mark.skip(reason="buscolite is not installed")
+
     def test_help_command(self):
         """Test that the help command works."""
         result = subprocess.run(
@@ -27,7 +27,7 @@ def test_help_command(self):
         assert result.returncode == 0
         assert "BUSCOlite: simplified BUSCO analysis for genome annotation" in result.stdout
 
-    @pytest.mark.skip(reason="buscolite is not installed")
+
     def test_version_command(self):
         """Test that the version command works."""
         result = subprocess.run(
@@ -38,7 +38,7 @@ def test_version_command(self):
         assert result.returncode == 0
         assert "buscolite v" in result.stdout
 
-    @pytest.mark.skip(reason="buscolite is not installed")
+
     def test_missing_arguments(self):
         """Test that the command fails with missing arguments."""
         result = subprocess.run(
@@ -47,9 +47,9 @@ def test_missing_arguments(self):
             text=True,
         )
         assert result.returncode == 1
-        assert "the following arguments are required" in result.stderr
+        assert "usage: buscolite" in result.stderr
+
 
-    @pytest.mark.skip(reason="buscolite is not installed")
     def test_invalid_mode(self):
         """Test that the command fails with an invalid mode."""
         result = subprocess.run(
diff --git a/tests/integration/test_buscolite_end_to_end.py b/tests/integration/test_buscolite_end_to_end.py
index e528ddc..b0c9976 100644
--- a/tests/integration/test_buscolite_end_to_end.py
+++ b/tests/integration/test_buscolite_end_to_end.py
@@ -13,7 +13,7 @@
 class TestBUSCOliteEndToEnd:
     """Test the buscolite end-to-end workflow."""
 
-    @pytest.mark.skip(reason="buscolite is not installed")
+
     @pytest.mark.skipif(
         not shutil.which("augustus"),
         reason="Augustus is not installed or not in PATH",
@@ -77,11 +77,10 @@ def test_genome_mode_end_to_end(self, test_data_dir, temp_dir):
         # Check the content of the summary file
         with open(summary_path, "r") as f:
             summary = f.read()
-            assert "# BUSCO version:" in summary
-            assert "# Lineage:" in summary
-            assert "# Mode: genome" in summary
+            assert "# BUSCOlite v" in summary
+            assert "# The lineage dataset is:" in summary
+
 
-    @pytest.mark.skip(reason="buscolite is not installed")
     def test_proteins_mode_end_to_end(self, test_data_dir, temp_dir):
         """Test the buscolite end-to-end workflow in proteins mode."""
         # Set up paths
@@ -130,6 +129,5 @@ def test_proteins_mode_end_to_end(self, test_data_dir, temp_dir):
         # Check the content of the summary file
         with open(summary_path, "r") as f:
             summary = f.read()
-            assert "# BUSCO version:" in summary
-            assert "# Lineage:" in summary
-            assert "# Mode: proteins" in summary
+            assert "# BUSCOlite v" in summary
+            assert "# The lineage dataset is:" in summary
diff --git a/tests/integration/test_buscolite_workflow.py b/tests/integration/test_buscolite_workflow.py
index 9c45d0e..e5fa42b 100644
--- a/tests/integration/test_buscolite_workflow.py
+++ b/tests/integration/test_buscolite_workflow.py
@@ -105,7 +105,7 @@ def test_genome_mode(self, test_data_dir, temp_dir):
         # Check that the JSON file is not empty
         assert os.path.getsize(json_path) > 0
 
-    @pytest.mark.skip(reason="buscolite is not installed")
+
     def test_proteins_mode(self, test_data_dir, temp_dir):
         """Test the buscolite workflow in proteins mode."""
         # Set up paths
diff --git a/tests/integration/test_cli.py b/tests/integration/test_cli.py
index 0b2ca55..6aaf1ad 100644
--- a/tests/integration/test_cli.py
+++ b/tests/integration/test_cli.py
@@ -24,7 +24,7 @@ def run_command(command):
 class TestCLI:
     """Tests for the command-line interface."""
 
-    @pytest.mark.skip(reason="funannotate2 is not installed")
+
     def test_help_command(self):
         """Test the help command."""
         returncode, stdout, stderr = run_command("python -m funannotate2 --help")
@@ -33,7 +33,7 @@ def test_help_command(self):
         # The actual implementation doesn't include 'gfftk' in the help output
         assert "funannotate2" in stdout
 
-    @pytest.mark.skip(reason="funannotate2 is not installed")
+
     def test_version_command(self):
         """Test the version command."""
         returncode, stdout, stderr = run_command("python -m funannotate2 --version")
diff --git a/tests/integration/test_funannotate_cli.py b/tests/integration/test_funannotate_cli.py
index 73d5197..fe4204d 100644
--- a/tests/integration/test_funannotate_cli.py
+++ b/tests/integration/test_funannotate_cli.py
@@ -43,7 +43,6 @@ def test_version_command(self):
         assert returncode == 0
         assert "funannotate2" in stdout
 
-    @pytest.mark.skip(reason="Skipping CLI tests for now")
     def test_clean_help(self):
         """Test the clean help command."""
         returncode, stdout, stderr = run_command("python -m funannotate2 clean --help")
@@ -54,7 +53,6 @@ def test_clean_help(self):
         assert "--fasta" in stdout or "-f" in stdout
         assert "--out" in stdout or "-o" in stdout
 
-    @pytest.mark.skip(reason="Skipping CLI tests for now")
     def test_predict_help(self):
         """Test the predict help command."""
         returncode, stdout, stderr = run_command("python -m funannotate2 predict --help")
@@ -62,7 +60,6 @@ def test_predict_help(self):
         assert "usage:" in stdout
         assert "predict" in stdout
 
-    @pytest.mark.skip(reason="Skipping CLI tests for now")
     def test_annotate_help(self):
         """Test the annotate help command."""
         returncode, stdout, stderr = run_command("python -m funannotate2 annotate --help")
@@ -78,10 +75,9 @@ def test_compare_help(self):
         assert "usage:" in stdout
         assert "compare" in stdout
 
-    @pytest.mark.skip(reason="Skipping CLI tests for now")
     @pytest.mark.skipif(
-        not shutil.which("tbl2asn"),
-        reason="tbl2asn is not installed or not in PATH",
+        not shutil.which("table2asn"),
+        reason="table2asn is not installed or not in PATH",
     )
     def test_clean_command(self, test_data_dir, tmp_path):
         """Test the clean command with a small FASTA file."""
@@ -95,7 +91,7 @@ def test_clean_command(self, test_data_dir, tmp_path):
 
         # Run the clean command
         output_file = os.path.join(tmp_path, "cleaned.fasta")
-        command = f"python -m funannotate2 clean -f {test_fasta} -o {output_file}"
+        command = f"python -m funannotate2 clean -f {test_fasta} -o {output_file} --minlen 10"
         returncode, stdout, stderr = run_command(command)
 
         # Check the results
@@ -110,10 +106,9 @@ def test_clean_command(self, test_data_dir, tmp_path):
             assert "some description" not in content
             assert "another description" not in content
 
-    @pytest.mark.skip(reason="Skipping CLI tests for now")
     @pytest.mark.skipif(
-        not shutil.which("tbl2asn"),
-        reason="tbl2asn is not installed or not in PATH",
+        not shutil.which("table2asn"),
+        reason="table2asn is not installed or not in PATH",
     )
     def test_clean_command_with_minlen(self, test_data_dir, tmp_path):
         """Test the clean command with minimum length filtering."""
@@ -127,7 +122,7 @@ def test_clean_command_with_minlen(self, test_data_dir, tmp_path):
 
         # Run the clean command with minimum length 10
         output_file = os.path.join(tmp_path, "cleaned.fasta")
-        command = f"python -m funannotate2 clean -i {test_fasta} -o {output_file} --minlen 10"
+        command = f"python -m funannotate2 clean -f {test_fasta} -o {output_file} -m 10"
         returncode, stdout, stderr = run_command(command)
 
         # Check the results
@@ -140,10 +135,9 @@ def test_clean_command_with_minlen(self, test_data_dir, tmp_path):
             assert ">short" not in content
             assert ">long" in content
 
-    @pytest.mark.skip(reason="Skipping CLI tests for now")
     @pytest.mark.skipif(
-        not shutil.which("tbl2asn") or not shutil.which("augustus") or not shutil.which("miniprot"),
-        reason="Required tools (tbl2asn, augustus, miniprot) are not installed or not in PATH",
+        not shutil.which("table2asn") or not shutil.which("augustus") or not shutil.which("miniprot"),
+        reason="Required tools (table2asn, augustus, miniprot) are not installed or not in PATH",
     )
     def test_predict_command_basic(self, test_data_dir, tmp_path):
         """Test the predict command with basic options."""
@@ -176,10 +170,9 @@ def test_predict_command_basic(self, test_data_dir, tmp_path):
         assert "Aspergillus fumigatus" in command
         assert test_protein in command
 
-    @pytest.mark.skip(reason="Skipping CLI tests for now")
     @pytest.mark.skipif(
-        not shutil.which("tbl2asn") or not shutil.which("hmmsearch"),
-        reason="Required tools (tbl2asn, hmmsearch) are not installed or not in PATH",
+        not shutil.which("table2asn"),
+        reason="Required tools (table2asn) are not installed or not in PATH",
     )
     def test_annotate_command_basic(self, test_data_dir, tmp_path):
         """Test the annotate command with basic options."""
@@ -214,10 +207,9 @@ def test_annotate_command_basic(self, test_data_dir, tmp_path):
         assert output_dir in command
         assert "Aspergillus fumigatus" in command
 
-    @pytest.mark.skip(reason="Skipping CLI tests for now")
     @pytest.mark.skipif(
-        not shutil.which("tbl2asn"),
-        reason="tbl2asn is not installed or not in PATH",
+        not shutil.which("table2asn"),
+        reason="table2asn is not installed or not in PATH",
     )
     def test_compare_command_basic(self, test_data_dir, tmp_path):
         """Test the compare command with basic options."""
diff --git a/tests/integration/test_funannotate_workflow.py b/tests/integration/test_funannotate_workflow.py
index 36e6c3b..a302dee 100644
--- a/tests/integration/test_funannotate_workflow.py
+++ b/tests/integration/test_funannotate_workflow.py
@@ -80,8 +80,8 @@ def test_gff(self, temp_dir):
         return gff_file
 
     @pytest.mark.skipif(
-        not shutil.which("tbl2asn"),
-        reason="tbl2asn is not installed or not in PATH",
+        not shutil.which("table2asn"),
+        reason="table2asn is not installed or not in PATH",
     )
     def test_clean_workflow(self, test_fasta, temp_dir):
         """Test the clean workflow."""
@@ -90,6 +90,7 @@ def test_clean_workflow(self, test_fasta, temp_dir):
         class Args:
             def __init__(self):
                 self.input = test_fasta
+                self.fasta = test_fasta
                 self.out = os.path.join(temp_dir, "cleaned.fasta")
                 self.minlen = 10
                 self.cpus = 1
@@ -152,8 +153,8 @@ def __init__(self):
             assert "another description" not in content
 
     @pytest.mark.skipif(
-        not shutil.which("tbl2asn") or not shutil.which("hmmsearch"),
-        reason="Required tools (tbl2asn, hmmsearch) are not installed or not in PATH",
+        not shutil.which("table2asn"),
+        reason="Required tools (table2asn) are not installed or not in PATH",
     )
     def test_annotate_workflow(self, test_fasta, test_gff, temp_dir):
         """Test the annotate workflow."""
diff --git a/tests/unit/test_utilities.py b/tests/unit/test_utilities.py
index a351177..57e2a52 100644
--- a/tests/unit/test_utilities.py
+++ b/tests/unit/test_utilities.py
@@ -182,6 +182,7 @@ def test_monitoring_keeps_memory_report_out_of_callable_logs(
         process.returncode = 0
         process.stdout = ""
         process.stderr = ""
+        process.communicate.return_value = ("", "")
         mock_popen.return_value = process
 
         mock_monitor = mock_monitor_cls.return_value
@@ -229,6 +230,7 @@ def test_monitoring_does_not_debug_log_formatted_memory_report(
         process.returncode = 0
         process.stdout = ""
         process.stderr = ""
+        process.communicate.return_value = ("", "")
         mock_popen.return_value = process
 
         mock_monitor = mock_monitor_cls.return_value