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IndexError with remove-background
See original GitHub issueHey! We are running into a weird indexing error when trying to run remove-background on our dataset.
We run the following command:
cellbender remove-background --input /path/to/filtered_feature_bc_matrix.h5 --output /path/to/filtered_feature_bc_matrix_Cellbender.h5 --expected-cells 13000 --total-droplets-included 20000 --fpr 0.01 --epochs 150
And get this error message:
cellbender:remove-background: 2022-07-22 15:38:16
cellbender:remove-background: Running remove-background
cellbender:remove-background: Loading data from file /path/to/filtered_feature_bc_matrix.h5
cellbender:remove-background: CellRanger v3 format
cellbender:remove-background: Trimming dataset for inference.
cellbender:remove-background: Including 21515 genes that have nonzero counts.
cellbender:remove-background: Prior on counts in empty droplets is 1479
cellbender:remove-background: Prior on counts for cells is 4829
cellbender:remove-background: Excluding barcodes with counts below 739
Traceback (most recent call last):
File "/home/user/anaconda3/envs/cellbender2/bin/cellbender", line 33, in <module>
sys.exit(load_entry_point('cellbender', 'console_scripts', 'cellbender')())
File "/mnt/c/Users/User/Karl/Python/Projects/CellBender/cellbender/base_cli.py", line 101, in main
cli_dict[args.tool].run(args)
File "/mnt/c/Users/User/Karl/Python/Projects/CellBender/cellbender/remove_background/cli.py", line 109, in run
main(args)
File "/mnt/c/Users/User/Karl/Python/Projects/CellBender/cellbender/remove_background/cli.py", line 204, in main
run_remove_background(args)
File "/mnt/c/Users/User/Karl/Python/Projects/CellBender/cellbender/remove_background/cli.py", line 159, in run_remove_background
fpr=args.fpr)
File "/mnt/c/Users/User/Karl/Python/Projects/CellBender/cellbender/remove_background/data/dataset.py", line 101, in __init__
gene_blacklist=gene_blacklist)
File "/mnt/c/Users/User/Karl/Python/Projects/CellBender/cellbender/remove_background/data/dataset.py", line 339, in _trim_dataset_for_analysis
[last_analyzed_bc])
IndexError: index 15845 is out of bounds for axis 0 with size 15845
The input file is the output we get from CellRanger and it opens without problems in Scanpy. Is there anything we could try to resolve the issue or are we missing something obvious?
Full list of installed packages
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_kmp_llvm conda-forge
alabaster 0.7.12 py_0 conda-forge
alsa-lib 1.2.6.1 h7f98852_0 conda-forge
anndata 0.8.0 pyhd8ed1ab_1 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py37h540881e_2 conda-forge
attr 2.5.1 h166bdaf_0 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
babel 2.10.3 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.11.1 pyha770c72_0 conda-forge
blas 2.115 mkl conda-forge
blas-devel 3.9.0 15_linux64_mkl conda-forge
bleach 5.0.1 pyhd8ed1ab_0 conda-forge
blosc 1.21.1 h83bc5f7_3 conda-forge
brotli 1.0.9 h166bdaf_7 conda-forge
brotli-bin 1.0.9 h166bdaf_7 conda-forge
brotlipy 0.7.0 py37h540881e_1004 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.6.15 ha878542_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cellbender 0.2.0 dev_0 <develop>
certifi 2022.6.15 py37h89c1867_0 conda-forge
cffi 1.15.1 py37h43b0acd_0 conda-forge
charset-normalizer 2.1.0 pyhd8ed1ab_0 conda-forge
click 8.1.3 py37h89c1867_0 conda-forge
colorama 0.4.5 pyhd8ed1ab_0 conda-forge
cryptography 37.0.4 py37h38fbfac_0 conda-forge
cudatoolkit 11.6.0 hecad31d_10 conda-forge
curl 7.83.1 h7bff187_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
debugpy 1.6.0 py37hd23a5d3_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
docutils 0.17.1 pypi_0 pypi
dunamai 1.12.0 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
expat 2.4.8 h27087fc_0 conda-forge
ffmpeg 4.3 hf484d3e_0 pytorch
fftw 3.3.10 nompi_h77c792f_102 conda-forge
flit-core 3.7.1 pyhd8ed1ab_0 conda-forge
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 hab24e00_0 conda-forge
fontconfig 2.14.0 h8e229c2_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.34.4 py37h540881e_0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
get_version 3.5.4 pyhd8ed1ab_0 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
git 2.37.1 pl5321h36853c3_0 conda-forge
glib 2.72.1 h6239696_0 conda-forge
glib-tools 2.72.1 h6239696_0 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
gnutls 3.6.13 h85f3911_1 conda-forge
gst-plugins-base 1.20.3 hf6a322e_0 conda-forge
gstreamer 1.20.3 hd4edc92_0 conda-forge
h5py 3.6.0 nompi_py37hd308b1e_100 conda-forge
hdf5 1.12.1 nompi_h2386368_104 conda-forge
icu 70.1 h27087fc_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
imagesize 1.4.1 pyhd8ed1ab_0 conda-forge
importlib-metadata 4.11.4 py37h89c1867_0 conda-forge
importlib_metadata 4.11.4 hd8ed1ab_0 conda-forge
importlib_resources 5.8.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.15.1 pyh210e3f2_0 conda-forge
ipython 7.33.0 py37h89c1867_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.7.1 pyhd8ed1ab_0 conda-forge
jack 1.9.18 h8c3723f_1002 conda-forge
jedi 0.18.1 py37h89c1867_1 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.1.0 pyhd8ed1ab_0 conda-forge
jpeg 9e h166bdaf_2 conda-forge
jsonschema 4.7.2 pyhd8ed1ab_0 conda-forge
jupyter 1.0.0 py37h89c1867_7 conda-forge
jupyter_client 7.3.4 pyhd8ed1ab_0 conda-forge
jupyter_console 6.4.4 pyhd8ed1ab_0 conda-forge
jupyter_core 4.11.1 py37h89c1867_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 1.1.1 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.4 py37h7cecad7_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
lame 3.100 h7f98852_1001 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
legacy-api-wrap 1.2 py_0 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 15_linux64_mkl conda-forge
libbrotlicommon 1.0.9 h166bdaf_7 conda-forge
libbrotlidec 1.0.9 h166bdaf_7 conda-forge
libbrotlienc 1.0.9 h166bdaf_7 conda-forge
libcap 2.64 ha37c62d_0 conda-forge
libcblas 3.9.0 15_linux64_mkl conda-forge
libclang 14.0.6 default_h2e3cab8_0 conda-forge
libclang13 14.0.6 default_h3a83d3e_0 conda-forge
libcups 2.3.3 hf5a7f15_1 conda-forge
libcurl 7.83.1 h7bff187_0 conda-forge
libdb 6.2.32 h9c3ff4c_0 conda-forge
libdeflate 1.12 h166bdaf_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.10 h9b69904_4 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.3.4 h27087fc_0 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgfortran-ng 12.1.0 h69a702a_16 conda-forge
libgfortran5 12.1.0 hdcd56e2_16 conda-forge
libglib 2.72.1 h2d90d5f_0 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 15_linux64_mkl conda-forge
liblapacke 3.9.0 15_linux64_mkl conda-forge
libllvm11 11.1.0 hf817b99_3 conda-forge
libllvm14 14.0.6 he0ac6c6_0 conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.20 pthreads_h78a6416_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.37 h753d276_3 conda-forge
libpq 14.4 hd77ab85_0 conda-forge
libsndfile 1.0.31 h9c3ff4c_1 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libtiff 4.4.0 hc85c160_1 conda-forge
libtool 2.4.6 h9c3ff4c_1008 conda-forge
libudev1 249 h166bdaf_4 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp 1.2.3 h522a892_0 conda-forge
libwebp-base 1.2.3 h166bdaf_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.9.14 h22db469_3 conda-forge
libzlib 1.2.12 h166bdaf_2 conda-forge
llvm-openmp 14.0.4 he0ac6c6_0 conda-forge
llvmlite 0.38.1 py37h0761922_0 conda-forge
loompy 3.0.6 py_0 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
lzo 2.10 h516909a_1000 conda-forge
markupsafe 2.1.1 py37h540881e_1 conda-forge
matplotlib 3.5.2 py37h89c1867_0 conda-forge
matplotlib-base 3.5.2 py37hc347a89_0 conda-forge
matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge
mistune 0.8.4 py37h5e8e339_1005 conda-forge
mkl 2022.1.0 h84fe81f_915 conda-forge
mkl-devel 2022.1.0 ha770c72_916 conda-forge
mkl-include 2022.1.0 h84fe81f_915 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.29 haf5c9bc_1 conda-forge
mysql-libs 8.0.29 h28c427c_1 conda-forge
natsort 8.1.0 pyhd8ed1ab_0 conda-forge
nbclient 0.6.6 pyhd8ed1ab_0 conda-forge
nbconvert 6.5.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 6.5.0 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 6.5.0 pyhd8ed1ab_0 conda-forge
nbformat 5.4.0 pyhd8ed1ab_0 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
nest-asyncio 1.5.5 pyhd8ed1ab_0 conda-forge
nettle 3.6 he412f7d_0 conda-forge
networkx 2.7.1 pyhd8ed1ab_0 conda-forge
notebook 6.4.12 pyha770c72_0 conda-forge
nspr 4.32 h9c3ff4c_1 conda-forge
nss 3.78 h2350873_0 conda-forge
numba 0.55.2 py37h43839f2_0 conda-forge
numexpr 2.7.3 py37he8f5f7f_1 conda-forge
numpy 1.21.6 py37h976b520_0 conda-forge
numpy_groupies 0.9.17 pyhd8ed1ab_0 conda-forge
openh264 2.1.1 h780b84a_0 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openssl 1.1.1q h166bdaf_0 conda-forge
opt-einsum 3.3.0 pypi_0 pypi
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.3.5 py37he8f5f7f_0 conda-forge
pandoc 2.18 ha770c72_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
patsy 0.5.2 pyhd8ed1ab_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.37 h032f7d1_0 conda-forge
perl 5.32.1 2_h7f98852_perl5 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.2.0 py37h44f0d7a_0 conda-forge
pip 22.1.2 pyhd8ed1ab_0 conda-forge
ply 3.11 py_1 conda-forge
portaudio 19.6.0 h57a0ea0_5 conda-forge
prometheus_client 0.14.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.30 pyha770c72_0 conda-forge
prompt_toolkit 3.0.30 hd8ed1ab_0 conda-forge
psutil 5.9.1 py37h540881e_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pulseaudio 14.0 h7f54b18_8 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.12.0 pyhd8ed1ab_0 conda-forge
pynndescent 0.5.7 pyh6c4a22f_0 conda-forge
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pyqt 5.15.7 py37hf30b843_0 conda-forge
pyqt5-sip 12.11.0 py37hd23a5d3_0 conda-forge
pyro-api 0.1.2 pyhd8ed1ab_0 conda-forge
pyro-ppl 1.8.1 pypi_0 pypi
pyrsistent 0.18.1 py37h540881e_1 conda-forge
pysocks 1.7.1 py37h89c1867_5 conda-forge
pytables 3.7.0 py37h5dea08b_0 conda-forge
python 3.7.12 hb7a2778_100_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.16.1 pyhd8ed1ab_0 conda-forge
python_abi 3.7 2_cp37m conda-forge
pytorch 1.12.0 py3.7_cuda11.6_cudnn8.3.2_0 pytorch
pytorch-mutex 1.0 cuda pytorch
pytz 2022.1 pyhd8ed1ab_0 conda-forge
pyzmq 23.2.0 py37h0c0c2a8_0 conda-forge
qt-main 5.15.4 ha5833f6_2 conda-forge
qtconsole 5.3.1 pyhd8ed1ab_0 conda-forge
qtconsole-base 5.3.1 pyha770c72_0 conda-forge
qtpy 2.1.0 pyhd8ed1ab_0 conda-forge
readline 8.1.2 h0f457ee_0 conda-forge
requests 2.28.1 pyhd8ed1ab_0 conda-forge
scanpy 1.8.2 pyhd8ed1ab_0 conda-forge
scikit-learn 1.0.2 py37hf9e9bfc_0 conda-forge
scipy 1.7.3 py37hf2a6cf1_0 conda-forge
seaborn 0.11.2 hd8ed1ab_0 conda-forge
seaborn-base 0.11.2 pyhd8ed1ab_0 conda-forge
send2trash 1.8.0 pyhd8ed1ab_0 conda-forge
session-info 1.0.0 pyhd8ed1ab_0 conda-forge
setuptools 59.8.0 py37h89c1867_1 conda-forge
sinfo 0.3.1 py_0 conda-forge
sip 6.6.2 py37hd23a5d3_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.9 hbd366e4_1 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge
sphinx 5.0.2 pyh6c4a22f_0 conda-forge
sphinx-argparse 0.3.1 pypi_0 pypi
sphinx-autodoc-typehints 1.18.3 pypi_0 pypi
sphinx-rtd-theme 1.0.0 pypi_0 pypi
sphinxcontrib-applehelp 1.0.2 py_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 2.0.0 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-programoutput 0.17 pypi_0 pypi
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge
sqlite 3.39.1 h4ff8645_0 conda-forge
statsmodels 0.13.2 py37hda87dfa_0 conda-forge
stdlib-list 0.7.0 py_2 conda-forge
tbb 2021.5.0 h924138e_1 conda-forge
terminado 0.15.0 py37h89c1867_0 conda-forge
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tinycss2 1.1.1 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
torchaudio 0.12.0 py37_cu116 pytorch
torchvision 0.13.0 py37_cu116 pytorch
tornado 6.2 py37h540881e_0 conda-forge
tqdm 4.64.0 pyhd8ed1ab_0 conda-forge
traitlets 5.3.0 pyhd8ed1ab_0 conda-forge
typing-extensions 4.3.0 hd8ed1ab_0 conda-forge
typing_extensions 4.3.0 pyha770c72_0 conda-forge
umap-learn 0.5.3 py37h89c1867_0 conda-forge
unicodedata2 14.0.0 py37h540881e_1 conda-forge
urllib3 1.26.10 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
widgetsnbextension 3.6.1 pyha770c72_0 conda-forge
xcb-util 0.4.0 h516909a_0 conda-forge
xcb-util-image 0.4.0 h166bdaf_0 conda-forge
xcb-util-keysyms 0.4.0 h516909a_0 conda-forge
xcb-util-renderutil 0.3.9 h166bdaf_0 conda-forge
xcb-util-wm 0.4.1 h516909a_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zipp 3.8.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.12 h166bdaf_2 conda-forge
zstd 1.5.2 h8a70e8d_2 conda-forge
Thanks!
Issue Analytics
- State:
- Created a year ago
- Comments:6 (3 by maintainers)
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Hello @sjfleming, I have just sent an email sharing the file. And yes, we installed that CellBender version. Many thanks.
@vkartha how many total droplet barcodes are included in your
h5adfile? Do you include all the empty droplets?