MESSAGE: 'NoneType' object has no attribute 'startswith' (When using precomputed skani sketches) #687
Description
Environment
- Installed via pip (include the output of
pip list) - [ X ] Using a conda environment (include the output of
conda list && conda list --revisions) - Using a Docker container (include the
IMAGE IDof the container)
$ conda list && conda list --revisions
# packages in environment at /mnt/efs/miniforge3/envs/gtdbtk-2.6.1:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bzip2 1.0.8 hda65f42_8 conda-forge
ca-certificates 2026.1.4 hbd8a1cb_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
dendropy 5.0.8 pyhdfd78af_1 bioconda
fastani 1.34 hb66fcc3_7 bioconda
fasttree 2.2.0 h7b50bb2_1 bioconda
gsl 2.8 hbf7d49c_1 conda-forge
gtdbtk 2.6.1 pyh1f0d9b5_2 bioconda
hmmer 3.4 h503566f_3 bioconda
icu 78.2 h33c6efd_0 conda-forge
ld_impl_linux-64 2.45 default_hbd61a6d_105 conda-forge
libblas 3.11.0 5_h4a7cf45_openblas conda-forge
libcblas 3.11.0 5_h0358290_openblas conda-forge
libexpat 2.7.3 hecca717_0 conda-forge
libffi 3.5.2 h9ec8514_0 conda-forge
libgcc 15.2.0 he0feb66_16 conda-forge
libgfortran 15.2.0 h69a702a_16 conda-forge
libgfortran5 15.2.0 h68bc16d_16 conda-forge
libgomp 15.2.0 he0feb66_16 conda-forge
liblapack 3.11.0 5_h47877c9_openblas conda-forge
liblzma 5.8.2 hb03c661_0 conda-forge
libmpdec 4.0.0 hb9d3cd8_0 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_4 conda-forge
libsqlite 3.51.2 hf4e2dac_0 conda-forge
libstdcxx 15.2.0 h934c35e_16 conda-forge
libuuid 2.41.3 h5347b49_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
numpy 2.4.1 py313hf6604e3_0 conda-forge
openssl 3.6.0 h26f9b46_0 conda-forge
pip 25.3 pyh145f28c_0 conda-forge
pplacer 1.1.alpha19 h9ee0642_2 bioconda
prodigal 2.6.3 h577a1d6_11 bioconda
pydantic 1.10.22 pyh3cfb1c2_0 conda-forge
python 3.13.11 hc97d973_100_cp313 conda-forge
python_abi 3.13 8_cp313 conda-forge
readline 8.3 h853b02a_0 conda-forge
skani 0.3.1 ha6fb395_0 bioconda
tk 8.6.13 noxft_ha0e22de_103 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
typing_extensions 4.15.0 pyhcf101f3_0 conda-forge
tzdata 2025c hc9c84f9_1 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forge
2026-01-21 19:22:33 (rev 0)
+_libgcc_mutex-0.1 (conda-forge)
+_openmp_mutex-4.5 (conda-forge)
+bzip2-1.0.8 (conda-forge)
+ca-certificates-2026.1.4 (conda-forge)
+colorama-0.4.6 (conda-forge)
+dendropy-5.0.8 (bioconda)
+fastani-1.34 (bioconda)
+fasttree-2.2.0 (bioconda)
+gsl-2.8 (conda-forge)
+gtdbtk-2.6.1 (bioconda)
+hmmer-3.4 (bioconda)
+icu-78.2 (conda-forge)
+ld_impl_linux-64-2.45 (conda-forge)
+libblas-3.11.0 (conda-forge)
+libcblas-3.11.0 (conda-forge)
+libexpat-2.7.3 (conda-forge)
+libffi-3.5.2 (conda-forge)
+libgcc-15.2.0 (conda-forge)
+libgfortran-15.2.0 (conda-forge)
+libgfortran5-15.2.0 (conda-forge)
+libgomp-15.2.0 (conda-forge)
+liblapack-3.11.0 (conda-forge)
+liblzma-5.8.2 (conda-forge)
+libmpdec-4.0.0 (conda-forge)
+libopenblas-0.3.30 (conda-forge)
+libsqlite-3.51.2 (conda-forge)
+libstdcxx-15.2.0 (conda-forge)
+libuuid-2.41.3 (conda-forge)
+libzlib-1.3.1 (conda-forge)
+ncurses-6.5 (conda-forge)
+numpy-2.4.1 (conda-forge)
+openssl-3.6.0 (conda-forge)
+pip-25.3 (conda-forge)
+pplacer-1.1.alpha19 (bioconda)
+prodigal-2.6.3 (bioconda)
+pydantic-1.10.22 (conda-forge)
+python-3.13.11 (conda-forge)
+python_abi-3.13 (conda-forge)
+readline-8.3 (conda-forge)
+skani-0.3.1 (bioconda)
+tk-8.6.13 (conda-forge)
+tqdm-4.67.1 (conda-forge)
+typing_extensions-4.15.0 (conda-forge)
+tzdata-2025c (conda-forge)
+zstd-1.5.7 (conda-forge)
Server information
- CPU:
grep -m 1 "^model name" /proc/cpuinfo && grep -c "^processor" /proc/cpuinfo - RAM:
grep "^MemTotal" /proc/meminfo - OS:
cat /etc/os-release
$ grep -m 1 "^model name" /proc/cpuinfo && grep -c "^processor" /proc/cpuinfo
model name : Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
16
$ grep "^MemTotal" /proc/meminfo
MemTotal: 129804256 kB
$ cat /etc/os-release
PRETTY_NAME="Ubuntu 24.04.3 LTS"
NAME="Ubuntu"
VERSION_ID="24.04"
VERSION="24.04.3 LTS (Noble Numbat)"
VERSION_CODENAME=noble
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=noble
LOGO=ubuntu-logo
Debugging information
- [ X ]
gtdbtk.loghas been included (drag and drop the file to upload). - [ X ] Genomes have been included (if possible, and there are few).
bins.zip
The 2 bins are model organisms (ecoli and hvolcanii) just for testing:
$ cat all_genomes/gtdbtk.log
[2026-01-21 22:20:07] INFO: GTDB-Tk v2.6.1
[2026-01-21 22:20:07] INFO: gtdbtk classify_wf --genome_dir bins --prefix all_genomes --out_dir all_genomes --cpus 8 --extension fa.gz --skani_sketch_dir sketches
[2026-01-21 22:20:07] INFO: Using GTDB-Tk reference data version r226: r226
[2026-01-21 22:20:08] INFO: Loading reference genomes.
[2026-01-21 22:20:09] INFO: Calculating all vs all ANI with skani v0.3.1.
[2026-01-21 22:20:09] INFO: Sketching refence genomes
[2026-01-21 22:20:09] INFO: Sketches already exist at sketches, skipping sketching step.
[2026-01-21 22:20:09] INFO: Done
[2026-01-21 22:22:25] INFO: Capturing skani results.
[2026-01-21 22:22:26] ERROR: Uncontrolled exit resulting from an unexpected error.
================================================================================
EXCEPTION: AttributeError
MESSAGE: 'NoneType' object has no attribute 'startswith'
________________________________________________________________________________
Traceback (most recent call last):
File "/usr/local/lib/python3.13/site-packages/gtdbtk/__main__.py", line 100, in main
gt_parser.parse_options(args)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
File "/usr/local/lib/python3.13/site-packages/gtdbtk/main.py", line 1132, in parse_options
all_classified_ani,classified_genomes = self.ani_screen(options)
~~~~~~~~~~~~~~~^^^^^^^^^
File "/usr/local/lib/python3.13/site-packages/gtdbtk/main.py", line 653, in ani_screen
classified_genomes,reports = aniscreener.run_aniscreen(
~~~~~~~~~~~~~~~~~~~~~~~~~^
genomes=genomes,
^^^^^^^^^^^^^^^^
out_dir=options.out_dir,
^^^^^^^^^^^^^^^^^^^^^^^^
prefix=options.prefix,
^^^^^^^^^^^^^^^^^^^^^^
skani_sketch_dir=options.skani_sketch_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.13/site-packages/gtdbtk/ani_screen.py", line 54, in run_aniscreen
skani_classified_user_genomes = self.sort_skani_ani_screen(
skani_results,taxonomy)
File "/usr/local/lib/python3.13/site-packages/gtdbtk/ani_screen.py", line 96, in sort_skani_ani_screen
canonical_gid(ref_gid))]
~~~~~~~~~~~~~^^^^^^^^^
File "/usr/local/lib/python3.13/site-packages/gtdbtk/biolib_lite/common.py", line 43, in canonical_gid
if gid.startswith('U'):
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'startswith'
================================================================================
[2026-01-21 22:34:36] INFO: GTDB-Tk v2.6.1
[2026-01-21 22:34:36] INFO: gtdbtk classify_wf --genome_dir bins --prefix all_genomes --out_dir all_genomes --cpus 8 --extension fa.gz --skani_sketch_dir sketches
[2026-01-21 22:34:36] ERROR: Controlled exit resulting from early termination.
[2026-01-21 22:34:59] INFO: GTDB-Tk v2.6.1
[2026-01-21 22:34:59] INFO: gtdbtk classify_wf --genome_dir bins --prefix all_genomes --out_dir all_genomes --cpus 8 --extension fa.gz --skani_sketch_dir sketches
[2026-01-21 22:34:59] INFO: Using GTDB-Tk reference data version r226: r226
[2026-01-21 22:34:59] INFO: Loading reference genomes.
[2026-01-21 22:35:00] INFO: Calculating all vs all ANI with skani v0.3.1.
[2026-01-21 22:35:00] INFO: Sketching refence genomes
[2026-01-21 22:35:00] INFO: Sketches already exist at sketches, skipping sketching step.
[2026-01-21 22:35:00] INFO: Done
[2026-01-21 22:35:27] INFO: Capturing skani results.
[2026-01-21 22:35:27] ERROR: Uncontrolled exit resulting from an unexpected error.
================================================================================
EXCEPTION: AttributeError
MESSAGE: 'NoneType' object has no attribute 'startswith'
________________________________________________________________________________
Traceback (most recent call last):
File "/mnt/efs/miniforge3/envs/gtdbtk-2.6.1/lib/python3.13/site-packages/gtdbtk/__main__.py", line 100, in main
gt_parser.parse_options(args)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
File "/mnt/efs/miniforge3/envs/gtdbtk-2.6.1/lib/python3.13/site-packages/gtdbtk/main.py", line 1132, in parse_options
all_classified_ani,classified_genomes = self.ani_screen(options)
~~~~~~~~~~~~~~~^^^^^^^^^
File "/mnt/efs/miniforge3/envs/gtdbtk-2.6.1/lib/python3.13/site-packages/gtdbtk/main.py", line 653, in ani_screen
classified_genomes,reports = aniscreener.run_aniscreen(
~~~~~~~~~~~~~~~~~~~~~~~~~^
genomes=genomes,
^^^^^^^^^^^^^^^^
out_dir=options.out_dir,
^^^^^^^^^^^^^^^^^^^^^^^^
prefix=options.prefix,
^^^^^^^^^^^^^^^^^^^^^^
skani_sketch_dir=options.skani_sketch_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/efs/miniforge3/envs/gtdbtk-2.6.1/lib/python3.13/site-packages/gtdbtk/ani_screen.py", line 54, in run_aniscreen
skani_classified_user_genomes = self.sort_skani_ani_screen(
skani_results,taxonomy)
File "/mnt/efs/miniforge3/envs/gtdbtk-2.6.1/lib/python3.13/site-packages/gtdbtk/ani_screen.py", line 96, in sort_skani_ani_screen
canonical_gid(ref_gid))]
~~~~~~~~~~~~~^^^^^^^^^
File "/mnt/efs/miniforge3/envs/gtdbtk-2.6.1/lib/python3.13/site-packages/gtdbtk/biolib_lite/common.py", line 43, in canonical_gid
if gid.startswith('U'):
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'startswith'
================================================================================
Here's the md5 for the sketches:
$ md5sum sketches/*
51d02c8bc639d112bdccc5b8a5867f3b sketches/index.db
ff39f41044e147b8933956ab2bc5ec56 sketches/markers.bin
512f74d1ef69a1487aeb8c30c4bd0bad sketches/sketches.db