pbbioconda
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Published
20 hours ago •
PacificBiosciences
PacificBiosciences
snakemake --reason deprecated
Snakemake 8.0 has been released. This removes the snakemake option '--reason', and causes ipa to fail.
Operating system Ubuntu 22.04.3 LTS
Package name ipa (wrapper) version=1.8.0
Conda environment
# packages in environment at /some/path/.snakemake/conda/6c6b6775dbae66b01cf772b931baaebc_:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
amply 0.1.6 pyhd8ed1ab_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
argparse-dataclass 2.0.0 pyhd8ed1ab_0 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
brotli-python 1.1.0 py312h30efb56_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.24.0 hd590300_0 conda-forge
ca-certificates 2023.11.17 hbcca054_0 conda-forge
certifi 2023.11.17 pyhd8ed1ab_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
coin-or-cbc 2.10.10 h9002f0b_0 conda-forge
coin-or-cgl 0.60.7 h516709c_0 conda-forge
coin-or-clp 1.17.8 h1ee7a9c_0 conda-forge
coin-or-osi 0.108.8 ha2443b9_0 conda-forge
coin-or-utils 2.11.9 hee58242_0 conda-forge
coincbc 2.10.10 0_metapackage conda-forge
conda-inject 1.3.1 pyhd8ed1ab_0 conda-forge
configargparse 1.7 pyhd8ed1ab_0 conda-forge
connection_pool 0.0.3 pyhd3deb0d_0 conda-forge
datrie 0.8.2 py312h98912ed_7 conda-forge
docutils 0.20.1 py312h7900ff3_3 conda-forge
dpath 2.1.6 pyha770c72_0 conda-forge
gitdb 4.0.11 pyhd8ed1ab_0 conda-forge
gitpython 3.1.40 pyhd8ed1ab_0 conda-forge
htslib 1.19 h81da01d_0 bioconda
humanfriendly 10.0 pyhd8ed1ab_6 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
immutables 0.20 py312h98912ed_1 conda-forge
importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
jsonschema 4.20.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.11.2 pyhd8ed1ab_0 conda-forge
jupyter_core 5.5.1 py312h7900ff3_0 conda-forge
k8 0.2.5 hdcf5f25_4 bioconda
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libblas 3.9.0 20_linux64_openblas conda-forge
libcblas 3.9.0 20_linux64_openblas conda-forge
libcurl 8.5.0 hca28451_0 conda-forge
libdeflate 1.19 hd590300_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h807b86a_3 conda-forge
libgfortran-ng 13.2.0 h69a702a_3 conda-forge
libgfortran5 13.2.0 ha4646dd_3 conda-forge
libgomp 13.2.0 h807b86a_3 conda-forge
liblapack 3.9.0 20_linux64_openblas conda-forge
liblapacke 3.9.0 20_linux64_openblas conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge
libsqlite 3.44.2 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
markupsafe 2.1.3 py312h98912ed_1 conda-forge
minimap2 2.26 he4a0461_2 bioconda
nbformat 5.9.2 pyhd8ed1ab_0 conda-forge
ncurses 6.4 h59595ed_2 conda-forge
networkx 3.2.1 pyhd8ed1ab_0 conda-forge
openssl 3.2.0 hd590300_1 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
pb-falconc 1.15.0 haabb649_2 bioconda
pbipa 1.8.0 h6ead514_2 bioconda
pcre 8.45 h9c3ff4c_0 conda-forge
pip 23.3.2 pyhd8ed1ab_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
plac 1.4.2 pyhd8ed1ab_0 conda-forge
platformdirs 4.1.0 pyhd8ed1ab_0 conda-forge
psutil 5.9.7 py312h98912ed_0 conda-forge
pulp 2.7.0 py312h7900ff3_1 conda-forge
pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.12.0 hab00c5b_0_cpython conda-forge
python-fastjsonschema 2.19.0 pyhd8ed1ab_0 conda-forge
python_abi 3.12 4_cp312 conda-forge
pyyaml 6.0.1 py312h98912ed_1 conda-forge
racon 1.5.0 h21ec9f0_2 bioconda
readline 8.2 h8228510_1 conda-forge
referencing 0.32.0 pyhd8ed1ab_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
reretry 0.11.8 pyhd8ed1ab_0 conda-forge
rpds-py 0.15.2 py312h4b3b743_0 conda-forge
samtools 1.19 h50ea8bc_0 bioconda
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
smart_open 6.4.0 pyhd8ed1ab_0 conda-forge
smmap 5.0.0 pyhd8ed1ab_0 conda-forge
snakemake-interface-common 1.15.0 pyhdfd78af_1 bioconda
snakemake-interface-executor-plugins 8.1.3 pyhdfd78af_0 bioconda
snakemake-interface-storage-plugins 3.0.0 pyhdfd78af_0 bioconda
snakemake-minimal 8.0.1 pyhdfd78af_0 bioconda
stopit 1.1.2 py_0 conda-forge
tabulate 0.9.0 pyhd8ed1ab_1 conda-forge
throttler 1.2.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toposort 1.10 pyhd8ed1ab_0 conda-forge
traitlets 5.14.0 pyhd8ed1ab_0 conda-forge
typing_extensions 4.9.0 pyha770c72_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
urllib3 2.1.0 pyhd8ed1ab_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
wrapt 1.16.0 py312h98912ed_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yte 1.5.4 pyha770c72_0 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
Describe the bug ipa fails due to error with arguments to snakemake
Error message
__main__.py: error: unrecognized arguments: --reason
ERROR: Command '/some/path/.snakemake/conda/6c6b6775dbae66b01cf772b931baaebc_/bin/python3 -m snakemake -j 1 -d RUN -p -s /some/path/.snakemake/conda/6c6b6775dbae66b01cf772b931baaebc_/etc/ipa.snakefile --configfile RUN/config.yaml --reason' returned non-zero exit status 2.
Exiting.
To Reproduce ipa local --input-fn some_file.fastq.gz --njobs 1 --nthreads "8" --genome-size "200000" --coverage "400"
Expected behavior snakemake commands generated within ipa should only include valid arguments to snakemake.
