error when running scsnvmisc

[Qirong-Lin]

Hi!

Thanks for providing this great tool for mutation phasing! I was trying to run scsnvmisc but it returned the error as:

(scsnv) qirong@qirong-desktop:/media/run/tmp/20230331_cellline_scsnv/scsnv_output/SI-TT1$ scsnvmisc cells --skip-mt -o $SAMPLE_OUTPUT/$SAMPLE $SAMPLE_OUTPUT/$SAMPLE/${SAMPLE}summary.h5
Total Passed Cells 1536
(25988, 1536) (25988, 1536)
/home/qirong/anaconda3/envs/scsnv/lib/python3.8/site-packages/flammkuchen/hdf5io.py:253: PerformanceWarning: 
your performance may suffer as PyTables will pickle object types that it cannot
map directly to c-types [inferred_type->mixed,key->block0_values] [items->Index(['gene_id', 'gene_name'], dtype='object')]

  store.put(group._v_pathname + '/' + name, level)
ICE default IO error handler doing an exit(), pid = 533089, errno = 32

I searched around but was not sure how to fix the ICE default IO issue, do you have any suggestions to fix it?

Best, Qirong

conda environment:

``` # packages in environment at /home/qirong/anaconda3/envs/scsnv: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge alsa-lib 1.2.8 h166bdaf_0 conda-forge anndata 0.9.1 pyhd8ed1ab_0 conda-forge attr 2.5.1 h166bdaf_1 conda-forge blosc 1.21.3 hafa529b_0 conda-forge brotli 1.0.9 h166bdaf_8 conda-forge brotli-bin 1.0.9 h166bdaf_8 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge ca-certificates 2022.12.7 ha878542_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge click 8.1.3 unix_pyhd8ed1ab_2 conda-forge coloredlogs 15.0.1 pyhd8ed1ab_3 conda-forge contourpy 1.0.7 py38hfbd4bf9_0 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge cython 0.29.34 py38h8dc9893_0 conda-forge cyvcf2 0.30.16 py38h79e5e23_1 bioconda dbus 1.13.6 h5008d03_3 conda-forge expat 2.5.0 hcb278e6_1 conda-forge fftw 3.3.10 nompi_hc118613_107 conda-forge flammkuchen 0.9.2 py_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 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.39.3 py38h1de0b5d_0 conda-forge freetype 2.12.1 hca18f0e_1 conda-forge gettext 0.21.1 h27087fc_0 conda-forge glib 2.76.1 h3eb15da_0 conda-forge glib-tools 2.76.1 h3eb15da_0 conda-forge gst-plugins-base 1.21.3 h4243ec0_1 conda-forge gstreamer 1.21.3 h25f0c4b_1 conda-forge gstreamer-orc 0.4.33 h166bdaf_0 conda-forge h5py 3.7.0 nompi_py38h045baee_101 conda-forge hdf5 1.12.2 nompi_h2386368_101 conda-forge htslib 1.15.1 h6bc39ce_1 bioconda humanfriendly 10.0 py38h578d9bd_4 conda-forge icu 70.1 h27087fc_0 conda-forge jack 1.9.22 h11f4161_0 conda-forge jpeg 9e h0b41bf4_3 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.4 py38h43d8883_1 conda-forge krb5 1.20.1 hf9c8cef_0 conda-forge lame 3.100 h166bdaf_1003 conda-forge lcms2 2.14 h6ed2654_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libaec 1.0.6 hcb278e6_1 conda-forge libblas 3.9.0 16_linux64_openblas conda-forge libbrotlicommon 1.0.9 h166bdaf_8 conda-forge libbrotlidec 1.0.9 h166bdaf_8 conda-forge libbrotlienc 1.0.9 h166bdaf_8 conda-forge libcap 2.66 ha37c62d_0 conda-forge libcblas 3.9.0 16_linux64_openblas conda-forge libclang 15.0.7 default_had23c3d_1 conda-forge libclang13 15.0.7 default_h3e3d535_1 conda-forge libcups 2.3.3 h36d4200_3 conda-forge libcurl 7.87.0 h6312ad2_0 conda-forge libdb 6.2.32 h9c3ff4c_0 conda-forge libdeflate 1.13 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 libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libflac 1.4.2 h27087fc_0 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgcrypt 1.10.1 h166bdaf_0 conda-forge libgfortran-ng 12.2.0 h69a702a_19 conda-forge libgfortran5 12.2.0 h337968e_19 conda-forge libglib 2.76.1 ha491796_0 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libgpg-error 1.46 h620e276_0 conda-forge libiconv 1.17 h166bdaf_0 conda-forge liblapack 3.9.0 16_linux64_openblas conda-forge libllvm15 15.0.7 hadd5161_1 conda-forge libnghttp2 1.51.0 hdcd2b5c_0 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libogg 1.3.4 h7f98852_1 conda-forge libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge libopus 1.3.1 h7f98852_1 conda-forge libpng 1.6.39 h753d276_0 conda-forge libpq 15.1 h2baec63_3 conda-forge libsndfile 1.2.0 hb75c966_0 conda-forge libsqlite 3.40.0 h753d276_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libsystemd0 252 h2a991cd_0 conda-forge libtiff 4.4.0 h0e0dad5_3 conda-forge libtool 2.4.7 h27087fc_0 conda-forge libudev1 253 h0b41bf4_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libwebp-base 1.3.0 h0b41bf4_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxkbcommon 1.5.0 h79f4944_1 conda-forge libxml2 2.10.3 hca2bb57_4 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge lzo 2.10 h516909a_1000 conda-forge matplotlib 3.6.2 py38h578d9bd_0 conda-forge matplotlib-base 3.6.2 py38h945d387_0 mpg123 1.31.3 hcb278e6_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge mysql-common 8.0.32 h14678bc_0 conda-forge mysql-libs 8.0.32 h54cf53e_0 conda-forge natsort 8.3.1 pyhd8ed1ab_0 conda-forge ncls 0.0.66 py38hbff2b2d_0 bioconda ncurses 6.3 h27087fc_1 conda-forge nomkl 1.0 h5ca1d4c_0 conda-forge nspr 4.35 h27087fc_0 conda-forge nss 3.89 he45b914_0 conda-forge numexpr 2.8.3 py38h97b1c41_100 conda-forge numpy 1.19.5 py38h8246c76_3 conda-forge openjpeg 2.5.0 h7d73246_1 conda-forge openssl 1.1.1t h0b41bf4_0 conda-forge packaging 23.1 pyhd8ed1ab_0 conda-forge pandas 1.4.4 py38h47df419_0 conda-forge patsy 0.5.3 pyhd8ed1ab_0 conda-forge pcre2 10.40 hc3806b6_0 conda-forge pillow 9.2.0 py38h9eb91d8_3 conda-forge pip 23.1 pyhd8ed1ab_0 conda-forge ply 3.11 py_1 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pulseaudio 16.1 h4ab2085_1 conda-forge pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge pyqt 5.15.7 py38ha0d8c90_3 conda-forge pyqt5-sip 12.11.0 py38h8dc9893_3 conda-forge pytables 3.7.0 py38hf632491_2 conda-forge python 3.8.15 h257c98d_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python_abi 3.8 3_cp38 conda-forge pytz 2023.3 pyhd8ed1ab_0 conda-forge qt-main 5.15.6 h62441b5_5 conda-forge readline 8.2 h8228510_1 conda-forge scipy 1.9.1 py38hea3f02b_0 conda-forge scsnvpy 1.0 pypi_0 pypi setuptools 67.6.1 pyhd8ed1ab_0 conda-forge sip 6.7.8 py38h8dc9893_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.1.10 h9fff704_0 conda-forge statsmodels 0.13.2 py38h71d37f0_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tornado 6.3 py38h1de0b5d_0 conda-forge unicodedata2 15.0.0 py38h0a891b7_0 conda-forge wheel 0.40.0 pyhd8ed1ab_0 conda-forge xcb-util 0.4.0 h166bdaf_0 conda-forge xcb-util-image 0.4.0 h166bdaf_0 conda-forge xcb-util-keysyms 0.4.0 h166bdaf_0 conda-forge xcb-util-renderutil 0.3.9 h166bdaf_0 conda-forge xcb-util-wm 0.4.1 h166bdaf_0 conda-forge xkeyboard-config 2.38 h0b41bf4_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge zstd 1.5.2 h3eb15da_6 conda-forge ```

[Alf-Kenz]

Not the author but I think I hit onto a similar error a while ago, on a different package, depending on how your graphics are set up, especially on linux

I think it has to do with the plotting - see https://stackoverflow.com/questions/39270988/ice-default-io-error-handler-doing-an-exit-pid-errno-32-when-running

[GWW]

Thanks for commenting @Alf-Kenz, I have not seen this error before but hopefully your comment helps @Qirong-Lin.

Gavin

[Qirong-Lin]

Hi!

Much appreciated for the quick reply! I have a unique use case as I will use xrdp to remotely log in to my ubuntu desktop, which might cause the graphic issue. I tried to delete the .Xauthority and .ICEauthority, logged out the remote desktop, and login through ssh to rerun it, then it worked without that ICE default IO issue. Thanks @Alf-Kenz for pointing out the solution!

Best, Qirong

[GWW]

I apologize, I tried searching for your issue as well and I cannot find a reason other than what @Alf-Kenz suggested.

[Qirong-Lin]

You've helped so much with your speedy reply :). Thanks again!