Extremely Persistent Bug: `amptk database` incorrectly calls `amptk-extract_region.py` on a fresh install

[alicia960312]

Bug discription:
I have encountered a persistent and highly unusual bug where any amptk database command fails, incorrectly calling the amptk-extract_region.py script without the required arguments.

This error has survived every troubleshooting step, including a complete re-installation of Miniconda. This suggests a deep, system-specific incompatibility.

Error message:
/home/fancy/miniconda3/envs/amptk_final/lib/python3.9/site-packages/amptk/amptk.py:10: UserWarning: pkg_resources is deprecated as an API...
usage: amptk-extract_region.py [options] -f
amptk-extract_region.py: error: the following arguments are required: -i/--fasta

Troubleshooting steps taken:

• The error occurs on the latest version of AMPtk.
• The error persists when locking AMPtk to v1.5.4 and Python to v3.9.
• The error persisted even after a complete rm -rf ~/miniconda3 and a fresh re-installation of Miniconda.
• The final attempt was made in an environment created with Mamba on a fresh Miniconda install.

amptk --version
/home/fancy/miniconda3/envs/amptk_final/lib/python3.9/site-packages/amptk/amptk.py:10: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
from pkg_resources import get_distribution
AMPtk v1.5.4

uname -a and lsb_release -a
uname -a
Linux fancy-HP-Laptop-15-dw3xxx 6.11.0-21-generic #21-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 19 16:50:40 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux

lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 24.10
Release: 24.10
Codename: oracular

which python
/home/fancy/miniconda3/envs/amptk_final/bin/python

conda list

packages in environment at /home/fancy/miniconda3/envs/amptk_final:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
amptk 1.5.4 pyh5e36f6f_0 bioconda
argcomplete 3.6.2 pyhd8ed1ab_0 conda-forge
binutils_impl_linux-64 2.44 h4bf12b8_1 conda-forge
bioconductor-biobase 2.66.0 r44h3df3fcb_0 bioconda
bioconductor-biocgenerics 0.52.0 r44hdfd78af_3 bioconda
bioconductor-biocparallel 1.40.0 r44he5774e6_1 bioconda
bioconductor-biomformat 1.34.0 r44hdfd78af_0 bioconda
bioconductor-biostrings 2.74.0 r44h3df3fcb_1 bioconda
bioconductor-dada2 1.34.0 r44he5774e6_2 bioconda
bioconductor-data-packages 20250625 hdfd78af_0 bioconda
bioconductor-delayedarray 0.32.0 r44h3df3fcb_1 bioconda
bioconductor-genomeinfodb 1.42.0 r44hdfd78af_2 bioconda
bioconductor-genomeinfodbdata 1.2.13 r44hdfd78af_0 bioconda
bioconductor-genomicalignments 1.42.0 r44h3df3fcb_1 bioconda
bioconductor-genomicranges 1.58.0 r44h3df3fcb_2 bioconda
bioconductor-iranges 2.40.0 r44h3df3fcb_2 bioconda
bioconductor-matrixgenerics 1.18.0 r44hdfd78af_0 bioconda
bioconductor-multtest 2.62.0 r44h3df3fcb_1 bioconda
bioconductor-phyloseq 1.50.0 r44hdfd78af_0 bioconda
bioconductor-pwalign 1.2.0 r44h3df3fcb_0 bioconda
bioconductor-rhdf5 2.50.0 r44h77050f0_1 bioconda
bioconductor-rhdf5filters 1.18.0 r44h77050f0_1 bioconda
bioconductor-rhdf5lib 1.28.0 r44h15a9599_0 bioconda
bioconductor-rhtslib 3.2.0 r44h15a9599_2 bioconda
bioconductor-rsamtools 2.22.0 r44h77050f0_1 bioconda
bioconductor-s4arrays 1.6.0 r44h3df3fcb_1 bioconda
bioconductor-s4vectors 0.44.0 r44h3df3fcb_2 bioconda
bioconductor-shortread 1.64.0 r44h77050f0_1 bioconda
bioconductor-sparsearray 1.6.0 r44h3df3fcb_1 bioconda
bioconductor-summarizedexperiment 1.36.0 r44hdfd78af_0 bioconda
bioconductor-ucsc.utils 1.2.0 r44h9ee0642_1 bioconda
bioconductor-xvector 0.46.0 r44h15a9599_2 bioconda
bioconductor-zlibbioc 1.52.0 r44h3df3fcb_2 bioconda
biom-format 2.1.16 py39h8cd3c5a_2 conda-forge
biopython 1.85 py39h8cd3c5a_1 conda-forge
brotli 1.1.0 hb03c661_4 conda-forge
brotli-bin 1.1.0 hb03c661_4 conda-forge
brotli-python 1.0.9 py39h5a03fae_8 conda-forge
bwidget 1.10.1 ha770c72_1 conda-forge
bzip2 1.0.8 hda65f42_8 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.8.3 hbd8a1cb_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.18.4 h3394656_0 conda-forge
certifi 2025.8.3 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py39h15c3d72_0 conda-forge
charset-normalizer 3.4.3 pyhd8ed1ab_0 conda-forge
click 8.1.8 pyh707e725_0 conda-forge
contourpy 1.3.0 py39h74842e3_2 conda-forge
curl 8.14.1 h332b0f4_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
distro 1.9.0 pyhd8ed1ab_1 conda-forge
fasttree 2.2.0 h7b50bb2_0 bioconda
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_3 conda-forge
fontconfig 2.15.0 h7e30c49_1 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.59.1 py39heb7d2ae_0 conda-forge
freetype 2.14.0 ha770c72_1 conda-forge
fribidi 1.0.16 hb03c661_0 conda-forge
gawk 5.3.1 hcd3d067_0 conda-forge
gcc_impl_linux-64 15.1.0 h4393ad2_5 conda-forge
gfortran_impl_linux-64 15.1.0 h3b9cdf2_5 conda-forge
glpk 5.0 h445213a_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
graphite2 1.3.14 hecca717_2 conda-forge
gsl 2.7 he838d99_0 conda-forge
gxx_impl_linux-64 15.1.0 h6a1bac1_5 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
h5py 3.14.0 nompi_py39h63168ba_100 conda-forge
harfbuzz 11.4.5 h15599e2_0 conda-forge
hdf5 1.14.6 nompi_h6e4c0c1_103 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
importlib-resources 6.5.2 pyhd8ed1ab_0 conda-forge
importlib_resources 6.5.2 pyhd8ed1ab_0 conda-forge
jq 1.5 0 bioconda
k8 1.2 he8db53b_6 bioconda
kernel-headers_linux-64 5.14.0 he073ed8_2 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
kiwisolver 1.4.7 py39h74842e3_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.17 h717163a_0 conda-forge
ld_impl_linux-64 2.44 h1423503_1 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
libaec 1.1.4 h3f801dc_0 conda-forge
libasprintf 0.25.1 h3f43e3d_1 conda-forge
libblas 3.9.0 35_h4a7cf45_openblas conda-forge
libbrotlicommon 1.1.0 hb03c661_4 conda-forge
libbrotlidec 1.1.0 hb03c661_4 conda-forge
libbrotlienc 1.1.0 hb03c661_4 conda-forge
libcblas 3.9.0 35_h0358290_openblas conda-forge
libcurl 8.14.1 h332b0f4_0 conda-forge
libdeflate 1.24 h86f0d12_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.1 hecca717_0 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libfreetype 2.14.0 ha770c72_1 conda-forge
libfreetype6 2.14.0 h73754d4_1 conda-forge
libgcc 15.1.0 h767d61c_5 conda-forge
libgcc-devel_linux-64 15.1.0 h4c094af_105 conda-forge
libgcc-ng 15.1.0 h69a702a_5 conda-forge
libgettextpo 0.25.1 h3f43e3d_1 conda-forge
libgfortran 15.1.0 h69a702a_5 conda-forge
libgfortran-ng 15.1.0 h69a702a_5 conda-forge
libgfortran5 15.1.0 hcea5267_5 conda-forge
libglib 2.84.3 hf39c6af_0 conda-forge
libgomp 15.1.0 h767d61c_5 conda-forge
libiconv 1.18 h3b78370_2 conda-forge
libjpeg-turbo 3.1.0 hb9d3cd8_0 conda-forge
liblapack 3.9.0 35_h47877c9_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
libnghttp2 1.67.0 had1ee68_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_2 conda-forge
libpng 1.6.50 h421ea60_1 conda-forge
libsanitizer 15.1.0 h97b714f_5 conda-forge
libsqlite 3.50.4 h0c1763c_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.1.0 h8f9b012_5 conda-forge
libstdcxx-devel_linux-64 15.1.0 h4c094af_105 conda-forge
libstdcxx-ng 15.1.0 h4852527_5 conda-forge
libtiff 4.7.0 h8261f1e_6 conda-forge
libuuid 2.41.1 he9a06e4_0 conda-forge
libuv 1.51.0 hb03c661_1 conda-forge
libwebp-base 1.6.0 hd42ef1d_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.13.8 h04c0eec_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
mafft 7.525 h031d066_1 bioconda
make 4.4.1 hb9d3cd8_2 conda-forge
matplotlib-base 3.9.4 py39h16632d1_0 conda-forge
minimap2 2.30 h577a1d6_0 bioconda
mpfr 4.2.1 h90cbb55_3 conda-forge
munkres 1.0.7 py_1 bioconda
natsort 8.4.0 pyh29332c3_1 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
numpy 2.0.2 py39h9cb892a_1 conda-forge
openjpeg 2.5.3 h55fea9a_1 conda-forge
openssl 3.5.2 h26f9b46_0 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.3.1 py39h1b6b32d_0 conda-forge
pandoc 3.8 ha770c72_0 conda-forge
pango 1.56.4 hadf4263_0 conda-forge
patsy 1.0.1 pyhd8ed1ab_1 conda-forge
pcre2 10.45 hc749103_0 conda-forge
pigz 2.8 hadc24fc_1 conda-forge
pillow 11.3.0 py39h15c0740_0 conda-forge
pip 25.2 pyh8b19718_0 conda-forge
pixman 0.46.4 h54a6638_1 conda-forge
psutil 7.0.0 py39h8cd3c5a_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pyfastx 2.2.0 py39h0699b22_1 bioconda
pyparsing 3.2.3 pyhe01879c_2 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
python 3.9.23 hc30ae73_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-edlib 1.3.9.post1 py39h2de1943_2 bioconda
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python_abi 3.9 8_cp39 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py39h9399b63_2 conda-forge
qhull 2020.2 h434a139_5 conda-forge
r-abind 1.4_8 r44hc72bb7e_1 conda-forge
r-ade4 1.7_23 r44h3704496_3 conda-forge
r-ape 5.8_1 r44h3704496_2 conda-forge
r-askpass 1.2.1 r44h2b5f3a1_0 conda-forge
r-base 4.4.3 h85845a0_2 conda-forge
r-base64enc 0.1_3 r44h54b55ab_1008 conda-forge
r-bh 1.87.0_1 r44hc72bb7e_1 conda-forge
r-bitops 1.0_9 r44h54b55ab_1 conda-forge
r-bslib 0.9.0 r44hc72bb7e_1 conda-forge
r-cachem 1.1.0 r44h54b55ab_2 conda-forge
r-cli 3.6.5 r44h3697838_1 conda-forge
r-cluster 2.1.8.1 r44heaba542_1 conda-forge
r-codetools 0.2_20 r44hc72bb7e_2 conda-forge
r-colorspace 2.1_1 r44h54b55ab_1 conda-forge
r-cpp11 0.5.2 r44h785f33e_2 conda-forge
r-crayon 1.5.3 r44hc72bb7e_2 conda-forge
r-crosstalk 1.2.2 r44hc72bb7e_1 conda-forge
r-curl 7.0.0 r44h10955f1_1 conda-forge
r-data.table 1.17.8 r44h1c8cec4_1 conda-forge
r-deldir 2.0_4 r44heaba542_2 conda-forge
r-digest 0.6.37 r44h3697838_1 conda-forge
r-dplyr 1.1.4 r44h3697838_2 conda-forge
r-dt 0.34.0 r44hc72bb7e_1 conda-forge
r-ellipsis 0.3.2 r44h54b55ab_4 conda-forge
r-evaluate 1.0.5 r44hc72bb7e_1 conda-forge
r-fansi 1.0.6 r44h54b55ab_2 conda-forge
r-farver 2.1.2 r44h3697838_2 conda-forge
r-fastmap 1.2.0 r44h3697838_2 conda-forge
r-fontawesome 0.5.3 r44hc72bb7e_1 conda-forge
r-foreach 1.5.2 r44hc72bb7e_4 conda-forge
r-formatr 1.14 r44hc72bb7e_3 conda-forge
r-fs 1.6.6 r44h3697838_1 conda-forge
r-futile.logger 1.4.3 r44hc72bb7e_1007 conda-forge
r-futile.options 1.0.1 r44hc72bb7e_1006 conda-forge
r-generics 0.1.4 r44hc72bb7e_1 conda-forge
r-ggplot2 4.0.0 r44h785f33e_0 conda-forge
r-glue 1.8.0 r44h54b55ab_1 conda-forge
r-gtable 0.3.6 r44hc72bb7e_1 conda-forge
r-hexbin 1.28.5 r44heaba542_1 conda-forge
r-highr 0.11 r44hc72bb7e_2 conda-forge
r-htmltools 0.5.8.1 r44h3697838_2 conda-forge
r-htmlwidgets 1.6.4 r44h785f33e_4 conda-forge
r-httpuv 1.6.16 r44h6d565e7_1 conda-forge
r-httr 1.4.7 r44hc72bb7e_1 conda-forge
r-hwriter 1.3.2.1 r44hc72bb7e_3 conda-forge
r-igraph 2.1.4 r44hadbbdbc_0 conda-forge
r-interp 1.1_6 r44ha36cffa_3 conda-forge
r-isoband 0.2.7 r44h3697838_4 conda-forge
r-iterators 1.0.14 r44hc72bb7e_4 conda-forge
r-jpeg 0.1_11 r44hd0206f1_1 conda-forge
r-jquerylib 0.1.4 r44hc72bb7e_4 conda-forge
r-jsonlite 2.0.0 r44h54b55ab_1 conda-forge
r-knitr 1.50 r44hc72bb7e_1 conda-forge
r-labeling 0.4.3 r44hc72bb7e_2 conda-forge
r-lambda.r 1.2.4 r44hc72bb7e_5 conda-forge
r-later 1.4.4 r44h3697838_1 conda-forge
r-lattice 0.22_7 r44h54b55ab_1 conda-forge
r-latticeextra 0.6_31 r44hc72bb7e_0 conda-forge
r-lazyeval 0.2.2 r44h54b55ab_6 conda-forge
r-lifecycle 1.0.4 r44hc72bb7e_2 conda-forge
r-magrittr 2.0.3 r44h54b55ab_4 conda-forge
r-mass 7.3_65 r44h54b55ab_0 conda-forge
r-matrix 1.7_4 r44h0e4624f_1 conda-forge
r-matrixstats 1.5.0 r44h54b55ab_1 conda-forge
r-memoise 2.0.1 r44hc72bb7e_4 conda-forge
r-mgcv 1.9_3 r44h0e4624f_1 conda-forge
r-mime 0.13 r44h54b55ab_1 conda-forge
r-munsell 0.5.1 r44hc72bb7e_2 conda-forge
r-nlme 3.1_168 r44heaba542_1 conda-forge
r-openssl 2.3.3 r44he8289e2_0 conda-forge
r-permute 0.9_8 r44hc72bb7e_1 conda-forge
r-pillar 1.11.0 r44hc72bb7e_1 conda-forge
r-pixmap 0.4_14 r44hc72bb7e_1 conda-forge
r-pkgconfig 2.0.3 r44hc72bb7e_5 conda-forge
r-plotly 4.11.0 r44hc72bb7e_0 conda-forge
r-plyr 1.8.9 r44h3697838_3 conda-forge
r-png 0.1_8 r44h6b2d295_3 conda-forge
r-promises 1.3.3 r44h3697838_1 conda-forge
r-purrr 1.1.0 r44h54b55ab_1 conda-forge
r-r6 2.6.1 r44hc72bb7e_1 conda-forge
r-rappdirs 0.3.3 r44h54b55ab_4 conda-forge
r-rcolorbrewer 1.1_3 r44h785f33e_4 conda-forge
r-rcpp 1.1.0 r44h3697838_1 conda-forge
r-rcppeigen 0.3.4.0.2 r44h3704496_1 conda-forge
r-rcppparallel 5.1.9 r44h93ab643_1 conda-forge
r-reshape2 1.4.4 r44h3697838_6 conda-forge
r-rlang 1.1.6 r44h3697838_1 conda-forge
r-rmarkdown 2.29 r44hc72bb7e_1 conda-forge
r-s7 0.2.0 r44h54b55ab_1 conda-forge
r-sass 0.4.10 r44h3697838_1 conda-forge
r-scales 1.4.0 r44hc72bb7e_1 conda-forge
r-snow 0.4_4 r44hc72bb7e_4 conda-forge
r-sp 2.2_0 r44h54b55ab_1 conda-forge
r-stringi 1.8.7 r44h2dae267_1 conda-forge
r-stringr 1.5.2 r44h785f33e_1 conda-forge
r-survival 3.8_3 r44h54b55ab_1 conda-forge
r-sys 3.4.3 r44h54b55ab_1 conda-forge
r-tibble 3.3.0 r44h54b55ab_1 conda-forge
r-tidyr 1.3.1 r44h3697838_2 conda-forge
r-tidyselect 1.2.1 r44hc72bb7e_2 conda-forge
r-tinytex 0.57 r44hc72bb7e_1 conda-forge
r-utf8 1.2.6 r44h54b55ab_1 conda-forge
r-vctrs 0.6.5 r44h3697838_2 conda-forge
r-vegan 2.7_1 r44h11cdb10_1 conda-forge
r-viridislite 0.4.2 r44hc72bb7e_3 conda-forge
r-withr 3.0.2 r44hc72bb7e_1 conda-forge
r-xfun 0.53 r44h3697838_1 conda-forge
r-yaml 2.3.10 r44h54b55ab_1 conda-forge
readline 8.2 h8c095d6_2 conda-forge
requests 2.32.5 pyhd8ed1ab_0 conda-forge
scipy 1.13.1 py39haf93ffa_0 conda-forge
seaborn 0.13.2 hd8ed1ab_3 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_3 conda-forge
sed 4.9 h6688a6e_0 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
statsmodels 0.14.5 py39h7c0b2d6_0 conda-forge
sysroot_linux-64 2.34 h087de78_2 conda-forge
tk 8.6.13 noxft_hd72426e_102 conda-forge
tktable 2.10 h8d826fa_7 conda-forge
toml 0.10.2 pyhd8ed1ab_1 conda-forge
tomlkit 0.13.3 pyha770c72_0 conda-forge
tzdata 2025b h78e105d_0 conda-forge
unicodedata2 16.0.0 py39h8cd3c5a_0 conda-forge
urllib3 2.5.0 pyhd8ed1ab_0 conda-forge
vsearch 2.30.0 hd6d6fdc_0 bioconda
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
xmltodict 0.14.2 pyhd8ed1ab_1 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.12 h4f16b4b_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
yaml 0.2.5 h280c20c_3 conda-forge
yq 3.4.3 pyhe01879c_2 conda-forge
zipp 3.23.0 pyhd8ed1ab_0 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstandard 0.23.0 py39hd399759_3 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge

[nextgenusfs]

I don't really see the error here. The warning you are getting is related to the python version, you could create the amptk environment in conda and pin "python==3.8" to get rid of that warning.

[alicia960312]

Hi
Thank you for the quick response.

I understand that the pkg_resources warning can be resolved by changing the Python version. However, that warning is not the issue preventing the program from running.

The critical problem is the error that occurs immediately after the warning: amptk-extract_region.py [options] -f
amptk-extract_region.py: error: the following arguments are required: -i/--fasta

This error happens every time I run amptk database --install, amptk database --clean, or even amptk --version in some cases. It seems the main amptk script is incorrectly calling amptk-extract_region.py for the database subcommand.

As you can see in the diagnostic information I provided, this error persisted even in a completely clean Miniconda installation with AMPtk v1.5.4 and Python 3.9.

Could you please look again at the error: line and my original report? The issue is not the warning, but the incorrect script call that causes the program to crash.

Thank you for your help.

[nextgenusfs]

I think a fasta file is required, what is output of amptk database -h, that command is to create a database new database and under the hood it uses the extract_regions script if my memory serves (admittedly it's been a long time since I've looked at the code)