Conda ENV python isn't pinned correctly #52
Description
I was trying toulligQC on some custom data, and came across a warning, and then a python error. The error is likely due to the python version needing to be downgraded, but should I worry about the Warning?
wget -q http://outils.genomique.biologie.ens.fr/leburon/downloads/toulligqc-example/toulligqc_demo_data.tar.bz2
tar -xvjf toulligqc_demo_data.tar.bz2
cd toulligqc_demo_data
bash run-toulligqc.shThis is the output
Warning: Barcode 'B0C7' is non-standard custom arrangement.
ToulligQC version 2.8.3
* Initialize extractors
* Start Toulligqc info extractor
* End of Toulligqc info extractor (done in 0m0.00s)
* Start Sequencing telemetry extractor
* End of Sequencing telemetry extractor (done in 0m0.04s)
* Start Basecaller sequencing summary extractor
- Load sequencing summary file (67.13 MB used) in 0m26.38s
Traceback (most recent call last):
File "/home/eriny/miniconda3/envs/toulligQC/bin/toulligqc", line 10, in <module>
sys.exit(main())
^^^^^^
File "/home/eriny/miniconda3/envs/toulligQC/lib/python3.12/site-packages/toulligqc/toulligqc.py", line 433, in main
extractor.extract(result_dict)
File "/home/eriny/miniconda3/envs/toulligQC/lib/python3.12/site-packages/toulligqc/sequencing_summary_extractor.py", line 229, in extract
set_result_value(self, result_dict, "n50", compute_NXX(self.dataframe_dict, 50))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/eriny/miniconda3/envs/toulligQC/lib/python3.12/site-packages/toulligqc/common_statistics.py", line 30, in compute_NXX
data.sort()
ValueError: sort array is read-only
This is my conda environment
# packages in environment at /home/eriny/miniconda3/envs/toulligQC:
#
# Name Version Build Channel
_openmp_mutex 4.5 20_gnu conda-forge
_python_abi3_support 1.0 hd8ed1ab_2 conda-forge
aws-c-auth 0.9.6 hb9c0fe4_1 conda-forge
aws-c-cal 0.9.13 h2c9d079_1 conda-forge
aws-c-common 0.12.6 hb03c661_0 conda-forge
aws-c-compression 0.3.2 h8b1a151_0 conda-forge
aws-c-event-stream 0.5.9 h841be55_2 conda-forge
aws-c-http 0.10.10 hf621c6d_0 conda-forge
aws-c-io 0.26.1 h3ca20c3_1 conda-forge
aws-c-mqtt 0.14.0 ha25ca29_1 conda-forge
aws-c-s3 0.11.5 h9b5df67_3 conda-forge
aws-c-sdkutils 0.2.4 h8b1a151_4 conda-forge
aws-checksums 0.2.10 h8b1a151_0 conda-forge
aws-crt-cpp 0.37.3 hb153662_0 conda-forge
aws-sdk-cpp 1.11.747 h133b1ee_1 conda-forge
azure-core-cpp 1.16.2 h206d751_0 conda-forge
azure-identity-cpp 1.13.3 hed0cdb0_1 conda-forge
azure-storage-blobs-cpp 12.16.0 hdd73cc9_1 conda-forge
azure-storage-common-cpp 12.12.0 ha7a2c86_1 conda-forge
azure-storage-files-datalake-cpp 12.14.0 h52c5a47_1 conda-forge
brotli 1.2.0 hed03a55_1 conda-forge
brotli-bin 1.2.0 hb03c661_1 conda-forge
bzip2 1.0.8 hda65f42_9 conda-forge
c-ares 1.34.6 hb03c661_0 conda-forge
ca-certificates 2026.2.25 hbd8a1cb_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
contourpy 1.3.3 py312h0a2e395_4 conda-forge
cpython 3.12.13 py312hd8ed1ab_0 conda-forge
cycler 0.12.1 pyhcf101f3_2 conda-forge
deprecated 1.3.1 pyhd8ed1ab_1 conda-forge
flatbuffers 24.3.25 h59595ed_0 conda-forge
fonttools 4.61.1 py312h8a5da7c_0 conda-forge
freetype 2.14.2 ha770c72_0 conda-forge
gflags 2.2.2 h5888daf_1005 conda-forge
glog 0.7.1 hbabe93e_0 conda-forge
h5py 3.15.1 nompi_py312ha4f8f14_101 conda-forge
hdf5 1.14.6 nompi_h19486de_106 conda-forge
icu 78.2 h33c6efd_0 conda-forge
iso8601 2.1.0 pyhd8ed1ab_1 conda-forge
joblib 1.5.3 pyhd8ed1ab_0 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
kiwisolver 1.5.0 py312h0a2e395_0 conda-forge
krb5 1.22.2 ha1258a1_0 conda-forge
lcms2 2.18 h0c24ade_0 conda-forge
ld_impl_linux-64 2.45.1 default_hbd61a6d_101 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
lib-pod5 0.3.33 py312h12fc78b_0 bioconda
libabseil 20260107.1 cxx17_h7b12aa8_0 conda-forge
libaec 1.1.5 h088129d_0 conda-forge
libarrow 20.0.0 h5f529fe_38_cpu conda-forge
libarrow-acero 20.0.0 h635bf11_38_cpu conda-forge
libarrow-dataset 20.0.0 h635bf11_38_cpu conda-forge
libarrow-substrait 20.0.0 hb4dd7c2_38_cpu conda-forge
libblas 3.11.0 5_h4a7cf45_openblas conda-forge
libbrotlicommon 1.2.0 hb03c661_1 conda-forge
libbrotlidec 1.2.0 hb03c661_1 conda-forge
libbrotlienc 1.2.0 hb03c661_1 conda-forge
libcblas 3.11.0 5_h0358290_openblas conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcurl 8.18.0 hcf29cc6_1 conda-forge
libdeflate 1.25 h17f619e_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.7.4 hecca717_0 conda-forge
libffi 3.5.2 h3435931_0 conda-forge
libfreetype 2.14.2 ha770c72_0 conda-forge
libfreetype6 2.14.2 h73754d4_0 conda-forge
libgcc 15.2.0 he0feb66_18 conda-forge
libgcc-ng 15.2.0 h69a702a_18 conda-forge
libgfortran 15.2.0 h69a702a_18 conda-forge
libgfortran5 15.2.0 h68bc16d_18 conda-forge
libgomp 15.2.0 he0feb66_18 conda-forge
libgoogle-cloud 2.39.0 h9d11ab5_1 conda-forge
libgoogle-cloud-storage 2.39.0 hdbdcf42_1 conda-forge
libgrpc 1.78.0 h1d1128b_1 conda-forge
libiconv 1.18 h3b78370_2 conda-forge
libjpeg-turbo 3.1.2 hb03c661_0 conda-forge
liblapack 3.11.0 5_h47877c9_openblas conda-forge
liblzma 5.8.2 hb03c661_0 conda-forge
libnghttp2 1.67.0 had1ee68_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_4 conda-forge
libopentelemetry-cpp 1.21.0 h9692893_2 conda-forge
libopentelemetry-cpp-headers 1.21.0 ha770c72_2 conda-forge
libparquet 20.0.0 h7376487_38_cpu conda-forge
libpng 1.6.55 h421ea60_0 conda-forge
libprotobuf 6.33.5 h2b00c02_0 conda-forge
libre2-11 2025.11.05 h0dc7533_1 conda-forge
libsqlite 3.52.0 hf4e2dac_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.2.0 h934c35e_18 conda-forge
libstdcxx-ng 15.2.0 hdf11a46_18 conda-forge
libthrift 0.22.0 h454ac66_1 conda-forge
libtiff 4.7.1 h9d88235_1 conda-forge
libutf8proc 2.11.3 hfe17d71_0 conda-forge
libuuid 2.41.3 h5347b49_0 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 2.15.2 he237659_0 conda-forge
libxml2-16 2.15.2 hca6bf5a_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
lz4-c 1.10.0 h5888daf_1 conda-forge
matplotlib-base 3.10.8 py312he3d6523_0 conda-forge
more-itertools 10.8.0 pyhcf101f3_1 conda-forge
munkres 1.1.4 pyhd8ed1ab_1 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
nlohmann_json 3.12.0 h54a6638_1 conda-forge
numpy 2.4.2 py312h33ff503_1 conda-forge
openjpeg 2.5.4 h55fea9a_0 conda-forge
openssl 3.6.1 h35e630c_1 conda-forge
orc 2.2.2 hbb90d81_1 conda-forge
packaging 26.0 pyhcf101f3_0 conda-forge
pandas 3.0.1 py312h8ecdadd_0 conda-forge
pillow 12.1.1 py312h50c33e8_0 conda-forge
pip 26.0.1 pyh8b19718_0 conda-forge
plotly 5.24.1 pyhd8ed1ab_1 conda-forge
pod5 0.3.33 pyhdfd78af_0 bioconda
polars 1.38.1 pyh6a1acc5_0 conda-forge
polars-runtime-32 1.38.1 py310hffdcd12_0 conda-forge
prometheus-cpp 1.3.0 ha5d0236_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pyarrow 20.0.0 py312h7900ff3_2 conda-forge
pyarrow-core 20.0.0 py312hc195796_2_cpu conda-forge
pyparsing 3.3.2 pyhcf101f3_0 conda-forge
pysam 0.23.3 py312h8f9e533_2 bioconda
python 3.12.13 hd63d673_0_cpython conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-gil 3.12.13 hd8ed1ab_0 conda-forge
python_abi 3.12 8_cp312 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
qhull 2020.2 h434a139_5 conda-forge
re2 2025.11.05 h5301d42_1 conda-forge
readline 8.3 h853b02a_0 conda-forge
s2n 1.7.0 ha63dd3a_1 conda-forge
scikit-learn 1.8.0 np2py312h3226591_1 conda-forge
scipy 1.17.1 py312h54fa4ab_0 conda-forge
setuptools 82.0.0 pyh332efcf_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
snappy 1.2.2 h03e3b7b_1 conda-forge
tenacity 9.1.4 pyhcf101f3_0 conda-forge
threadpoolctl 3.6.0 pyhecae5ae_0 conda-forge
tk 8.6.13 noxft_h366c992_103 conda-forge
toulligqc 2.8.3 pyhdfd78af_0 bioconda
tqdm 4.67.3 pyh8f84b5b_0 conda-forge
tzdata 2025c hc9c84f9_1 conda-forge
unicodedata2 17.0.1 py312h4c3975b_0 conda-forge
vbz-h5py-plugin 1.0.1 pyhdfd78af_0 bioconda
wheel 0.46.3 pyhd8ed1ab_0 conda-forge
wrapt 2.1.2 py312h4c3975b_0 conda-forge
xorg-libxau 1.0.12 hb03c661_1 conda-forge
xorg-libxdmcp 1.1.5 hb03c661_1 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zlib-ng 2.3.3 hceb46e0_1 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forge