pandas error when scoring

[dtmvandenberg]

I get the following error when running carve on linux in a conda python=3.6 environment:

File "/home/dennis/miniconda3/envs/reframed/bin/carve", line 8, in sys.exit(main()) File "/home/dennis/miniconda3/envs/reframed/lib/python3.6/site-packages/carveme/cli/carve.py", line 358, in main ref_score=args.reference_score File "/home/dennis/miniconda3/envs/reframed/lib/python3.6/site-packages/carveme/cli/carve.py", line 160, in maincall scores = reaction_scoring(annotations, gprs, debug_output=debug_output) File "/home/dennis/miniconda3/envs/reframed/lib/python3.6/site-packages/carveme/reconstruction/scoring.py", line 105, in reaction_scoring .agg({'query_gene': merge_subunits, 'score': merge_subunit_scores}) File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/groupby/generic.py", line 940, in aggregate result, how = self._aggregate(func, *args, kwargs) File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/base.py", line 428, in _aggregate result = _agg(arg, _agg_1dim) File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/base.py", line 395, in _agg result[fname] = func(fname, agg_how) File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/base.py", line 379, in _agg_1dim return colg.aggregate(how) File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/groupby/generic.py", line 262, in aggregate return self._python_agg_general(func, *args, *kwargs) File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/groupby/groupby.py", line 936, in _python_agg_general result, counts = self.grouper.agg_series(obj, f) File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/groupby/ops.py", line 641, in agg_series return self._aggregate_series_fast(obj, func) File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/groupby/ops.py", line 666, in _aggregate_series_fast result, counts = grouper.get_result() File "pandas/_libs/reduction.pyx", line 376, in pandas._libs.reduction.SeriesGrouper.get_result File "pandas/_libs/reduction.pyx", line 193, in pandas._libs.reduction._BaseGrouper._apply_to_group File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/groupby/groupby.py", line 913, in f = lambda x: func(x, args, kwargs) File "/home/dennis/miniconda3/envs/reframed/lib/python3.6/site-packages/carveme/reconstruction/scoring.py", line 38, in merge_subunit_scores return scores.fillna(0).mean() File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/series.py", line 4159, in fillna downcast=downcast, File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/generic.py", line 6216, in fillna value=value, limit=limit, inplace=inplace, downcast=downcast File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/internals/managers.py", line 576, in fillna return self.apply("fillna", kwargs) File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/internals/managers.py", line 442, in apply applied = getattr(b, f)(kwargs) File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/internals/blocks.py", line 426, in fillna blocks = self.putmask(mask, value, inplace=inplace) File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/internals/blocks.py", line 1041, in putmask return [self.make_block(new_values)] File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/internals/blocks.py", line 273, in make_block return make_block(values, placement=placement, ndim=self.ndim) File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/internals/blocks.py", line 3041, in make_block return klass(values, ndim=ndim, placement=placement) File "/home/dennis/.local/lib/python3.6/site-packages/pandas/core/internals/blocks.py", line 125, in init f"Wrong number of items passed {len(self.values)}, " ValueError: Wrong number of items passed 2, placement implies 1

conda environment:

Name Version Build Channel

_libgcc_mutex 0.1 main
argon2-cffi 20.1.0 py36h7b6447c_1
arrow-cpp 0.15.1 py36h7cd5009_5
async_generator 1.10 py36h28b3542_0
attrs 20.3.0 pyhd3eb1b0_0
backcall 0.2.0 py_0
beautifulsoup4 4.9.3 pyha847dfd_0
blas 1.0 mkl
bleach 1.4.2 py36_0 bioconda blosc 1.16.3 hd408876_0
boost-cpp 1.71.0 h7b6447c_0
bottleneck 1.3.2 py36heb32a55_1
brotli 1.0.9 he6710b0_2
brotlipy 0.7.0 py36h27cfd23_1003
bzip2 1.0.8 h7b6447c_0
c-ares 1.11.0 h470a237_1 bioconda ca-certificates 2021.1.19 h06a4308_0
carveme 1.4.1 pypi_0 pypi certifi 2019.9.11 pypi_0 pypi cffi 1.14.4 py36h261ae71_0
chardet 4.0.0 py36h06a4308_1003
cobra 0.4.0 py36_1 bioconda cplex 12.10.0.0 pypi_0 pypi cryptography 3.3.1 py36h3c74f83_0
cycler 0.10.0 py36_0
dbus 1.13.18 hb2f20db_0
decorator 4.4.2 py_0
defusedxml 0.6.0 py_0
diamond 0.9.14 h8b12597_3 bioconda docloud 1.0.375 pypi_0 pypi docplex 2.11.176 pypi_0 pypi double-conversion 3.1.5 he6710b0_1
entrypoints 0.3 py36_0
et_xmlfile 1.0.1 py_1001
expat 2.2.10 he6710b0_2
fontconfig 2.13.0 h9420a91_0
framed 0.5.0 pypi_0 pypi freetype 2.10.4 h5ab3b9f_0
gflags 2.2.2 he6710b0_0
glib 2.66.1 h92f7085_0
glog 0.4.0 he6710b0_0
glpk 4.57 0 bioconda grpc-cpp 1.26.0 hf8bcb03_0
gst-plugins-base 1.14.0 h8213a91_2
gstreamer 1.14.0 h28cd5cc_2
hdf5 1.10.4 hb1b8bf9_0
html5lib 1.1 py_0
icu 58.2 he6710b0_3
idna 2.10 pyhd3eb1b0_0
importlib-metadata 2.0.0 py_1
importlib_metadata 2.0.0 1
intel-openmp 2020.2 254
ipykernel 5.3.4 py36h5ca1d4c_0
ipython 7.16.1 py36h5ca1d4c_0
ipython_genutils 0.2.0 pyhd3eb1b0_1
jdcal 1.4.1 py_0
jedi 0.18.0 py36h06a4308_1
jinja2 2.11.2 pyhd3eb1b0_0
jpeg 9b h024ee3a_2
jsonschema 3.2.0 py_2
jupyter_client 6.1.7 py_0
jupyter_core 4.7.0 py36h06a4308_0
jupyterlab_pygments 0.1.2 py_0
kiwisolver 1.3.0 py36h2531618_0
lcms2 2.11 h396b838_0
ld_impl_linux-64 2.33.1 h53a641e_7
libboost 1.71.0 h97c9712_0
libedit 3.1.20191231 h14c3975_1
libevent 2.1.8 h1ba5d50_1
libffi 3.3 he6710b0_2
libgcc 7.2.0 h69d50b8_2
libgcc-ng 9.1.0 hdf63c60_0
libgfortran-ng 7.3.0 hdf63c60_0
libpng 1.6.37 hbc83047_0
libprotobuf 3.11.2 hd408876_0
libsodium 1.0.18 h7b6447c_0
libstdcxx-ng 9.1.0 hdf63c60_0
libtiff 4.1.0 h2733197_0
libuuid 1.0.3 h1bed415_2
libxcb 1.14 h7b6447c_0
libxml2 2.9.10 hb55368b_3
libxslt 1.1.34 hc22bd24_0
lxml 4.6.2 py36h9120a33_0
lz4-c 1.8.1.2 h14c3975_0
lzo 2.10 h7b6447c_2
markupsafe 1.1.1 py36h7b6447c_0
matplotlib 3.3.2 h06a4308_0
matplotlib-base 3.3.2 py36h817c723_0
mistune 0.8.4 py36h7b6447c_0
mkl 2020.2 256
mkl-service 2.3.0 py36he8ac12f_0
mkl_fft 1.2.0 py36h23d657b_0
mkl_random 1.1.1 py36h0573a6f_0
mock 4.0.3 pyhd3eb1b0_0
nbclient 0.5.1 py_0
nbconvert 6.0.7 py36_0
nbformat 5.1.2 pyhd3eb1b0_1
ncurses 6.2 he6710b0_1
nest-asyncio 1.4.3 pyhd3eb1b0_0
notebook 6.2.0 py36h06a4308_0
numexpr 2.7.2 py36hb2eb853_0
numpy 1.19.2 py36h54aff64_0
numpy-base 1.19.2 py36hfa32c7d_0
olefile 0.46 py36_0
openpyxl 3.0.6 pyhd3eb1b0_0
openssl 1.1.1i h27cfd23_0
pandas 1.1.3 py36he6710b0_0
pandoc 2.11 hb0f4dca_0
pandocfilters 1.4.3 py36h06a4308_1
parso 0.8.1 pyhd3eb1b0_0
pcre 8.44 he6710b0_0
pexpect 4.8.0 pyhd3eb1b0_3
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 8.1.0 py36he98fc37_0
pip 21.0 pypi_0 pypi prometheus_client 0.9.0 pyhd3eb1b0_0
prompt-toolkit 3.0.8 py_0
ptyprocess 0.7.0 pyhd3eb1b0_2
pyarrow 0.15.1 py36h0573a6f_0
pycparser 2.20 py_2
pygments 2.7.4 pyhd3eb1b0_0
pyopenssl 20.0.1 pyhd3eb1b0_1
pyparsing 2.4.7 pyhd3eb1b0_0
pyqt 5.9.2 py36h05f1152_2
pyrsistent 0.17.3 py36h7b6447c_0
pysocks 1.7.1 py36h06a4308_0
pytables 3.6.1 py36h71ec239_0
python 3.6.12 hcff3b4d_2
python-dateutil 2.8.1 py_0
python-libsbml 5.18.0 py36hff43929_0 bioconda pytz 2020.5 pyhd3eb1b0_0
pyzmq 20.0.0 py36h2531618_1
qt 5.9.7 h5867ecd_1
re2 2020.11.01 h2531618_1
readline 8.1 h27cfd23_0
reframed 1.2.0 pypi_0 pypi requests 2.22.0 pypi_0 pypi scipy 1.5.2 py36h0b6359f_0
send2trash 1.5.0 pyhd3eb1b0_1
setuptools 52.0.0 py36h06a4308_0
sip 4.19.8 py36hf484d3e_0
six 1.12.0 pypi_0 pypi snappy 1.1.8 he6710b0_0
soupsieve 2.1 pyhd3eb1b0_0
sqlite 3.33.0 h62c20be_0
terminado 0.9.2 py36h06a4308_0
testpath 0.4.4 py_0
thrift-cpp 0.11.0 h02b749d_3
tk 8.6.10 hbc83047_0
tornado 6.1 py36h27cfd23_0
traitlets 4.3.3 py36_0
uriparser 0.9.3 he6710b0_1
urllib3 1.25.11 pypi_0 pypi wcwidth 0.2.5 py_0
webencodings 0.5.1 py36_1
wheel 0.36.2 pyhd3eb1b0_0
xarray 0.16.2 pyhd3eb1b0_0
xz 5.2.5 h7b6447c_0
zeromq 4.3.3 he6710b0_3
zipp 3.4.0 pyhd3eb1b0_0
zlib 1.2.11 h7b6447c_3
zstd 1.3.7 h0b5b093_0

Any idea what goes wrong?

[dtmvandenberg]

Fixed this issue by switching to python 3.7.9 and associated conda packages.

[cdanielmachado]

Thank you, and sorry for the lack of response, I have been super busy these last days.