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Unable to replicate the mouse hippocampus tutorial #74

Open
oieretxezarreta opened this issue Dec 31, 2024 · 1 comment
Open

Unable to replicate the mouse hippocampus tutorial #74

oieretxezarreta opened this issue Dec 31, 2024 · 1 comment
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bug Something isn't working

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@oieretxezarreta
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Hi,
I am unable to successfully run the "Preprocessing transcriptomic library" step of the adult mouse hippocampus tutorial. The error that I get is as follows, where I only manage to get the AnnData object of one of the tiles:

File "/home/labs/nyosef/oier/mambaforge/envs/spacemake/lib/python3.10/site-packages/squidpy/gr/_nhood.py", line 86, in _create_function
raise ValueError(f"Expected at least 2 clusters, found {n_cls}.")
ValueError: Expected at least 2 clusters, found 1.
[Wed Dec 11 09:22:01 2024]
Error in rule run_automated_analysis:
jobid: 206
output: projects/openst_demo/processed_data/openst_demo_adult_mouse/illumina/complete_data/automated_analysis/openst/umi_cutoff_500/openst_demo_adult_mouse_fc_2_L3_tile_2360_results.h5ad

I would appreciate it if you could provide me assistance on this.

Thanks in advance.

Steps to reproduce the bug

spacemake init \
  --dropseq_tools /home/labs/nyosef/oier/Open_ST/openst_adult_demo/bins/Drop-seq_tools-2.5.1

spacemake config add_species \
   --name mouse \
   --reference genome \
   --sequence GRCm39vM30.genome.fa \
   --annotation gencodevM30.annotation.gtf

spacemake config add_species \
   --name mouse \
   --reference rRNA \
   --sequence mouse.rRNA.fa

spacemake config add_species \
   --name mouse \
   --reference phiX \
   --sequence phiX.fa

spacemake projects add_sample \
    --project_id openst_demo \
    --sample_id openst_demo_adult_mouse \
    --R1 /home/labs/nyosef/oier/Open_ST/openst_adult_demo/data/fastq/adult_mouse_hippocampus_R1_001.fastq.gz \
    --R2 /home/labs/nyosef/oier/Open_ST/openst_adult_demo/data/fastq/adult_mouse_hippocampus_R2_001.fastq.gz \
    --species mouse \
    --puck openst \
    --run_mode openst \
    --barcode_flavor openst \
    --puck_barcode_file /home/labs/nyosef/oier/Open_ST/openst_adult_demo/data/tiles/*.txt.gz \
    --map_strategy "bowtie2:phiX->bowtie2:rRNA->STAR:genome:final"

bsub -n 32 -R rusage[mem=5GB] -R span[hosts=1] spacemake run --cores 32

Environment info

  • Platform: linux-64
  • Python version: Python 3.10.14

channels:

  • bioconda
  • bih-cubi
  • conda-forge
    dependencies:
  • _libgcc_mutex=0.1=conda_forge
  • _openmp_mutex=4.5=2_gnu
  • _r-mutex=1.0.1=anacondar_1
  • _sysroot_linux-64_curr_repodata_hack=3=h69a702a_16
  • aioeasywebdav=2.4.0=pyha770c72_0
  • aiohappyeyeballs=2.4.0=pyhd8ed1ab_0
  • aiohttp=3.10.5=py310h5b4e0ec_0
  • aiosignal=1.3.1=pyhd8ed1ab_0
  • alsa-lib=1.2.12=h4ab18f5_0
  • amply=0.1.6=pyhd8ed1ab_0
  • appdirs=1.4.4=pyh9f0ad1d_0
  • async-timeout=4.0.3=pyhd8ed1ab_0
  • atk-1.0=2.38.0=hd4edc92_1
  • attmap=0.13.2=pyhd8ed1ab_0
  • attrs=24.2.0=pyh71513ae_0
  • bcl2fastq2=2.20.0.422=2
  • bcrypt=4.2.0=py310h505e2c1_1
  • binutils_impl_linux-64=2.40=ha1999f0_7
  • boto3=1.35.16=pyhd8ed1ab_0
  • bowtie2=2.5.4=h7071971_4
  • brotli=1.1.0=hb9d3cd8_2
  • brotli-bin=1.1.0=hb9d3cd8_2
  • brotli-python=1.1.0=py310hf71b8c6_2
  • bwidget=1.9.14=ha770c72_1
  • bzip2=1.0.8=h4bc722e_7
  • c-ares=1.33.1=heb4867d_0
  • ca-certificates=2024.8.30=hbcca054_0
  • cachetools=5.5.0=pyhd8ed1ab_0
  • cairo=1.18.0=h3faef2a_0
  • certifi=2024.8.30=pyhd8ed1ab_0
  • cffi=1.17.1=py310h8deb56e_0
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  • coin-or-cgl=0.60.7=h516709c_0
  • coin-or-clp=1.17.8=h1ee7a9c_0
  • coin-or-osi=0.108.10=haf5fa05_0
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  • coincbc=2.10.12=1_metapackage
  • colorama=0.4.6=pyhd8ed1ab_0
  • configargparse=1.7=pyhd8ed1ab_0
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  • cryptography=43.0.1=py310h6c63255_0
  • curl=8.8.0=he654da7_1
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  • expat=2.6.3=h5888daf_0
  • fastqc=0.12.1=hdfd78af_0
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  • filechunkio=1.8=py_2
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  • google-auth-httplib2=0.2.0=pyhd8ed1ab_0
  • google-cloud-core=2.4.1=pyhd8ed1ab_0
  • google-cloud-storage=2.18.2=pyhff2d567_0
  • google-crc32c=1.1.2=py310hc5c09a0_5
  • google-resumable-media=2.7.2=pyhd8ed1ab_1
  • googleapis-common-protos=1.65.0=pyhd8ed1ab_0
  • graphite2=1.3.13=h59595ed_1003
  • graphviz=8.1.0=h28d9a01_0
  • grpcio=1.62.2=py310h1b8f574_0
  • gtk2=2.24.33=h90689f9_2
  • gts=0.7.6=h977cf35_4
  • gxx_impl_linux-64=14.1.0=h8d00ecb_1
  • h2=4.1.0=pyhd8ed1ab_0
  • harfbuzz=8.3.0=h3d44ed6_0
  • hpack=4.0.0=pyh9f0ad1d_0
  • htslib=1.20=h81da01d_0
  • httplib2=0.22.0=pyhd8ed1ab_0
  • hyperframe=6.0.1=pyhd8ed1ab_0
  • icu=73.2=h59595ed_0
  • idna=3.8=pyhd8ed1ab_0
  • imagemagick=7.1.1_19=pl5321h7e74ff9_0
  • importlib_resources=6.4.5=pyhd8ed1ab_0
  • iniconfig=2.0.0=pyhd8ed1ab_0
  • jbig=2.1=h7f98852_2003
  • jinja2=3.1.4=pyhd8ed1ab_0
  • jmespath=1.0.1=pyhd8ed1ab_0
  • jsonschema=4.23.0=pyhd8ed1ab_0
  • jsonschema-specifications=2023.12.1=pyhd8ed1ab_0
  • jupyter_core=5.7.2=py310hff52083_0
  • kernel-headers_linux-64=3.10.0=h4a8ded7_16
  • keyutils=1.6.1=h166bdaf_0
  • kiwisolver=1.4.7=py310h3788b33_0
  • krb5=1.21.3=h659f571_0
  • lcms2=2.15=h7f713cb_2
  • ld_impl_linux-64=2.40=hf3520f5_7
  • lerc=4.0.0=h27087fc_0
  • libabseil=20240116.2=cxx17_he02047a_1
  • libasprintf=0.22.5=he8f35ee_3
  • libasprintf-devel=0.22.5=he8f35ee_3
  • libblas=3.9.0=23_linux64_openblas
  • libbrotlicommon=1.1.0=hb9d3cd8_2
  • libbrotlidec=1.1.0=hb9d3cd8_2
  • libbrotlienc=1.1.0=hb9d3cd8_2
  • libcblas=3.9.0=23_linux64_openblas
  • libcrc32c=1.1.2=h9c3ff4c_0
  • libcups=2.3.3=h4637d8d_4
  • libcurl=8.8.0=hca28451_1
  • libdeflate=1.19=hd590300_0
  • libedit=3.1.20191231=he28a2e2_2
  • libev=4.33=hd590300_2
  • libexpat=2.6.3=h5888daf_0
  • libffi=3.4.2=h7f98852_5
  • libgcc=14.1.0=h77fa898_1
  • libgcc-devel_linux-64=14.1.0=h5d3d1c9_101
  • libgcc-ng=14.1.0=h69a702a_1
  • libgd=2.3.3=he9388d3_8
  • libgettextpo=0.22.5=he02047a_3
  • libgettextpo-devel=0.22.5=he02047a_3
  • libgfortran=14.1.0=h69a702a_1
  • libgfortran-ng=14.1.0=h69a702a_1
  • libgfortran5=14.1.0=hc5f4f2c_1
  • libglib=2.78.1=hebfc3b9_0
  • libglu=9.0.0=hac7e632_1003
  • libgomp=14.1.0=h77fa898_1
  • libgrpc=1.62.2=h15f2491_0
  • libiconv=1.17=hd590300_2
  • libjpeg-turbo=2.1.5.1=hd590300_1
  • liblapack=3.9.0=23_linux64_openblas
  • liblapacke=3.9.0=23_linux64_openblas
  • libnghttp2=1.58.0=h47da74e_1
  • libnsl=2.0.1=hd590300_0
  • libopenblas=0.3.27=pthreads_hac2b453_1
  • libpng=1.6.43=h2797004_0
  • libprotobuf=4.25.3=h08a7969_0
  • libre2-11=2023.09.01=h5a48ba9_2
  • librsvg=2.56.3=he3f83f7_1
  • libsanitizer=14.1.0=hcba0ae0_1
  • libsodium=1.0.20=h4ab18f5_0
  • libsqlite=3.46.0=hde9e2c9_0
  • libssh2=1.11.0=h0841786_0
  • libstdcxx=14.1.0=hc0a3c3a_1
  • libstdcxx-devel_linux-64=14.1.0=h5d3d1c9_101
  • libstdcxx-ng=14.1.0=h4852527_1
  • libtiff=4.6.0=h29866fb_1
  • libtool=2.4.7=he02047a_1
  • libuuid=2.38.1=h0b41bf4_0
  • libwebp=1.3.2=hdffd6e0_0
  • libwebp-base=1.3.2=hd590300_1
  • libxcb=1.15=h0b41bf4_0
  • libxcrypt=4.4.36=hd590300_1
  • libxml2=2.12.7=hc051c1a_1
  • libzlib=1.2.13=h4ab18f5_6
  • logmuse=0.2.6=pyh8c360ce_0
  • lz4-c=1.9.4=hcb278e6_0
  • make=4.4.1=hb9d3cd8_1
  • markdown-it-py=3.0.0=pyhd8ed1ab_0
  • markupsafe=2.1.5=py310ha75aee5_1
  • matplotlib-base=3.9.2=py310hf02ac8c_0
  • mdurl=0.1.2=pyhd8ed1ab_0
  • multidict=6.1.0=py310ha75aee5_0
  • munkres=1.1.4=pyh9f0ad1d_0
  • nbformat=5.10.4=pyhd8ed1ab_0
  • ncurses=6.5=he02047a_1
  • networkx=3.3=pyhd8ed1ab_1
  • oauth2client=4.1.3=py_0
  • openjdk=11.0.15=hfea2f88_7
  • openjpeg=2.5.2=h488ebb8_0
  • openssl=3.3.2=hb9d3cd8_0
  • packaging=24.1=pyhd8ed1ab_0
  • pandoc=3.4=ha770c72_0
  • pango=1.50.14=ha41ecd1_2
  • paramiko=3.4.1=pyhd8ed1ab_0
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  • peppy=0.40.6=pyhd8ed1ab_0
  • perl=5.32.1=7_hd590300_perl5
  • pigz=2.8=h2797004_0
  • pillow=10.0.1=py310h29da1c1_1
  • pip=24.2=pyh8b19718_1
  • pixman=0.43.2=h59595ed_0
  • pkg-config=0.29.2=h4bc722e_1009
  • pkgutil-resolve-name=1.3.10=pyhd8ed1ab_1
  • platformdirs=4.3.2=pyhd8ed1ab_0
  • pluggy=1.5.0=pyhd8ed1ab_0
  • ply=3.11=pyhd8ed1ab_2
  • pot=0.9.4=py310hf9f9076_0
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  • python-dateutil=2.9.0=pyhd8ed1ab_0
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  • r-rematch=2.0.0=r43hc72bb7e_1
  • r-rematch2=2.1.2=r43hc72bb7e_4
  • r-reprex=2.1.1=r43hc72bb7e_1
  • r-rgl=1.3.1=r43h2184249_2
  • r-rlang=1.1.4=r43ha18555a_1
  • r-rmarkdown=2.28=r43hc72bb7e_0
  • r-rstudioapi=0.16.0=r43hc72bb7e_1
  • r-rvest=1.0.4=r43hc72bb7e_1
  • r-sass=0.4.9=r43ha18555a_1
  • r-scales=1.3.0=r43hc72bb7e_1
  • r-selectr=0.4_2=r43hc72bb7e_4
  • r-stringi=1.8.4=r43ha8ce623_2
  • r-stringr=1.5.1=r43h785f33e_1
  • r-svglite=2.1.3=r43h3d53355_1
  • r-sys=3.4.2=r43hb1dbf0f_2
  • r-systemfonts=1.1.0=r43h38d38ca_1
  • r-textshaping=0.3.7=r43hd87b9d6_0
  • r-tibble=3.2.1=r43hdb488b9_3
  • r-tidyr=1.3.1=r43h0d4f4ea_1
  • r-tidyselect=1.2.1=r43hc72bb7e_1
  • r-tidyverse=2.0.0=r43h785f33e_2
  • r-timechange=0.3.0=r43ha18555a_1
  • r-tinytex=0.52=r43hc72bb7e_0
  • r-tzdb=0.4.0=r43ha18555a_2
  • r-utf8=1.2.4=r43hb1dbf0f_1
  • r-uuid=1.2_1=r43hdb488b9_0
  • r-vctrs=0.6.5=r43h0d4f4ea_1
  • r-viridislite=0.4.2=r43hc72bb7e_2
  • r-vroom=1.6.5=r43h0d4f4ea_1
  • r-webshot=0.5.5=r43hc72bb7e_1
  • r-withr=3.0.1=r43hc72bb7e_0
  • r-xfun=0.47=r43h0d4f4ea_0
  • r-xml2=1.3.6=r43h8194278_2
  • r-yaml=2.3.10=r43hdb488b9_0
  • ratelimiter=1.2.0=pyhd8ed1ab_1003
  • re2=2023.09.01=h7f4b329_2
  • readline=8.2=h8228510_1
  • referencing=0.35.1=pyhd8ed1ab_0
  • requests=2.32.3=pyhd8ed1ab_0
  • rich=13.7.1=pyhd8ed1ab_0
  • rpds-py=0.20.0=py310h505e2c1_1
  • rsa=4.9=pyhd8ed1ab_0
  • s3transfer=0.10.2=pyhd8ed1ab_0
  • sambamba=1.0.1=h6f6fda4_2
  • samtools=1.20=h50ea8bc_1
  • scipy=1.14.1=py310ha3fb0e1_0
  • sed=4.8=he412f7d_0
  • setuptools=73.0.1=pyhd8ed1ab_0
  • setuptools-scm=8.1.0=pyhd8ed1ab_0
  • six=1.16.0=pyh6c4a22f_0
  • slacker=0.14.0=py_0
  • smart_open=7.0.4=pyhd8ed1ab_0
  • smmap=5.0.0=pyhd8ed1ab_0
  • snakemake=6.3.0=hdfd78af_0
  • snakemake-minimal=6.3.0=pyhdfd78af_0
  • star=2.7.11b=h43eeafb_2
  • stone=3.3.2=pyhd8ed1ab_0
  • stopit=1.1.2=py_0
  • sysroot_linux-64=2.17=h4a8ded7_16
  • tk=8.6.13=noxft_h4845f30_101
  • tktable=2.10=h8bc8fbc_6
  • tomli=2.0.1=pyhd8ed1ab_0
  • toposort=1.10=pyhd8ed1ab_0
  • traitlets=5.14.3=pyhd8ed1ab_0
  • typing-extensions=4.12.2=hd8ed1ab_0
  • typing_extensions=4.12.2=pyha770c72_0
  • tzdata=2024a=h8827d51_1
  • ubiquerg=0.8.0=pyhd8ed1ab_0
  • unicodedata2=15.1.0=py310h2372a71_0
  • uritemplate=4.1.1=pyhd8ed1ab_0
  • veracitools=0.1.3=py_0
  • wcwidth=0.2.13=pyhd8ed1ab_0
  • wheel=0.44.0=pyhd8ed1ab_0
  • wrapt=1.16.0=py310ha75aee5_1
  • xorg-fixesproto=5.0=h7f98852_1002
  • xorg-inputproto=2.3.2=h7f98852_1002
  • xorg-kbproto=1.0.7=h7f98852_1002
  • xorg-libice=1.1.1=hd590300_0
  • xorg-libsm=1.2.4=h7391055_0
  • xorg-libx11=1.8.9=h8ee46fc_0
  • xorg-libxau=1.0.11=hd590300_0
  • xorg-libxdmcp=1.1.3=h7f98852_0
  • xorg-libxext=1.3.4=h0b41bf4_2
  • xorg-libxfixes=5.0.3=h7f98852_1004
  • xorg-libxi=1.7.10=h4bc722e_1
  • xorg-libxrender=0.9.11=hd590300_0
  • xorg-libxt=1.3.0=hd590300_1
  • xorg-libxtst=1.2.5=h4bc722e_0
  • xorg-recordproto=1.14.2=h7f98852_1002
  • xorg-renderproto=0.11.1=h7f98852_1002
  • xorg-xextproto=7.3.0=h0b41bf4_1003
  • xorg-xproto=7.0.31=h7f98852_1007
  • xz=5.2.6=h166bdaf_0
  • yaml=0.2.5=h7f98852_2
  • yarl=1.11.1=py310ha75aee5_0
  • zipp=3.20.1=pyhd8ed1ab_0
  • zlib=1.2.13=h4ab18f5_6
  • zstandard=0.23.0=py310ha39cb0e_1
  • zstd=1.5.6=ha6fb4c9_0
  • pip:
    • aiobotocore==2.5.4
    • aioitertools==0.12.0
    • alabaster==1.0.0
    • anndata==0.10.9
    • array-api-compat==1.8
    • asciitree==0.3.3
    • babel==2.16.0
    • biopython==1.84
    • botocore==1.31.17
    • click==8.1.7
    • cloudpickle==3.0.0
    • colorcet==3.1.0
    • commonmark==0.9.1
    • dask==2022.11.0
    • dask-image==2023.3.0
    • datashader==0.16.3
    • distributed==2024.8.2
    • docrep==0.3.2
    • fasteners==0.19
    • fsspec==2023.6.0
    • geopandas==1.0.1
    • h5py==3.11.0
    • igraph==0.11.6
    • imageio==2.35.1
    • imagesize==1.4.1
    • importlib-metadata==8.4.0
    • inflect==7.4.0
    • joblib==1.4.2
    • lazy-loader==0.4
    • legacy-api-wrap==1.4
    • leidenalg==0.10.2
    • llvmlite==0.43.0
    • locket==1.0.0
    • matplotlib-scalebar==0.8.1
    • more-itertools==10.5.0
    • msgpack==1.1.0
    • multipledispatch==1.0.0
    • multiscale-spatial-image==1.0.1
    • natsort==8.4.0
    • novosparc==0.4.4
    • numba==0.60.0
    • numcodecs==0.13.0
    • numpy==1.26.4
    • ome-zarr==0.9.0
    • omnipath==1.0.8
    • opencv-python==4.10.0.84
    • pandas==1.5.1
    • param==2.1.1
    • partd==1.4.2
    • patsy==0.5.6
    • pims==0.7
    • pooch==1.8.2
    • pyarrow==17.0.0
    • pyct==0.5.0
    • pynndescent==0.5.13
    • pyogrio==0.9.0
    • pyproj==3.6.1
    • pywavelets==1.7.0
    • recommonmark==0.7.1
    • s3fs==2023.6.0
    • scanpy==1.10.2
    • scikit-image==0.20.0
    • scikit-learn==1.5.1
    • scikit-misc==0.5.1
    • seaborn==0.13.2
    • session-info==1.0.0
    • shapely==2.0.6
    • slicerator==1.1.0
    • snowballstemmer==2.2.0
    • sortedcontainers==2.4.0
    • spacemake==0.7.9
    • spatial-image==1.1.0
    • spatialdata==0.2.2
    • sphinx==8.0.2
    • sphinxcontrib-applehelp==2.0.0
    • sphinxcontrib-devhelp==2.0.0
    • sphinxcontrib-htmlhelp==2.1.0
    • sphinxcontrib-jsmath==1.0.1
    • sphinxcontrib-qthelp==2.0.0
    • sphinxcontrib-serializinghtml==2.0.0
    • squidpy==1.3.0
    • statsmodels==0.14.2
    • stdlib-list==0.10.0
    • tblib==3.0.0
    • texttable==1.7.0
    • threadpoolctl==3.5.0
    • tifffile==2024.8.30
    • toolz==0.12.1
    • tornado==6.4.1
    • tqdm==4.66.5
    • typeguard==4.3.0
    • umap-learn==0.5.6
    • urllib3==1.26.20
    • validators==0.34.0
    • xarray==2024.3.0
    • xarray-dataclasses==1.8.0
    • xarray-datatree==0.0.14
    • xarray-schema==0.0.3
    • xarray-spatial==0.4.0
    • zarr==2.18.3
    • zict==3.0.0
@oieretxezarreta oieretxezarreta added the bug Something isn't working label Dec 31, 2024
@nukappa
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nukappa commented Jan 7, 2025

Hi @oieretxezarreta this is a spacemake error which we are actively working to address in one of the upcoming spacemake updates. The error shouldn't prevent you from working further though, as it only concerns the automated analysis, which is downstream of the processed data.

Try running spacemake run --your_params --keep-going --rerun-incomplete to get the rest of the tiles if the pipeline stopped.

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