Unable to run the pipeline with samples sequenced using the big tiles

[oieretxezarreta]

Hi,
I am unable to successfully run the Open-ST pipeline on samples sequenced using the big tiles. The error that I get is as follows, where I don't manage to get the dge folder as output:

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.base/java.util.Arrays.copyOf(Arrays.java:3720)
at java.base/java.util.Arrays.copyOf(Arrays.java:3689)
at java.base/java.util.ArrayList.grow(ArrayList.java:238)
at java.base/java.util.ArrayList.addAll(ArrayList.java:710)
at org.broadinstitute.dropseqrna.utils.ObjectCounter.getKeysOrderedByCount(ObjectCounter.java:183)
at org.broadinstitute.dropseqrna.metrics.BamTagHistogram.writeHistogram(BamTagHistogram.java:92)
at org.broadinstitute.dropseqrna.metrics.BamTagHistogram.doWork(BamTagHistogram.java:86)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at org.broadinstitute.dropseqrna.cmdline.DropSeqMain.main(DropSeqMain.java:42)
[Mon Jan 13 17:24:53 2025]
Error in rule get_barcode_readcounts_prealigned:
jobid: 14

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/spacemake/Drop-seq_tools-2.5.1

spacemake config add_species \
   --name Mouse \
   --reference genome \
   --sequence /home/labs/nyosef/oier/Open_ST/spacemake/species_data/mouse/mouse_genome.fa \
   --annotation /home/labs/nyosef/oier/Open_ST/spacemake/species_data/mouse/mouse_annotation.gtf

spacemake projects add_sample \
   --project_id Gut_IBD \
   --sample_id Naive_AT_9m \
   --R1 /home/labs/nyosef/Collaboration/OpenST_Data/Gut/Gut_25122024/li/lireich/20241225_LH00211_0214_B225MHKLT1/P7-F1_TCGCCTTA/P7-F1_TCGCCTTA_R1.fastq.gz \
   --R2 /home/labs/nyosef/Collaboration/OpenST_Data/Gut/Gut_25122024/li/lireich/20241225_LH00211_0214_B225MHKLT1/P7-F1_TCGCCTTA/P7-F1_TCGCCTTA_R2.fastq.gz \
   --species Mouse \
   --puck openst \
   --puck_barcode_file /home/labs/nyosef/Collaboration/OpenST_Data/Oier/fc_tiles/*.txt.gz \
   --run_mode openst \
   --barcode_flavor openst

bsub -n 30 -R rusage[mem=30GB] -R span[hosts=1] spacemake run --cores 30 --rerun-incomplete --keep-going

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
• charset-normalizer=3.3.2=pyhd8ed1ab_0
• coin-or-cbc=2.10.12=h8b142ea_1
• coin-or-cgl=0.60.7=h516709c_0
• coin-or-clp=1.17.8=h1ee7a9c_0
• coin-or-osi=0.108.10=haf5fa05_0
• coin-or-utils=2.11.11=hee58242_0
• coincbc=2.10.12=1_metapackage
• colorama=0.4.6=pyhd8ed1ab_0
• configargparse=1.7=pyhd8ed1ab_0
• contourpy=1.3.0=py310h3788b33_1
• cryptography=43.0.1=py310h6c63255_0
• curl=8.8.0=he654da7_1
• cycler=0.12.1=pyhd8ed1ab_0
• datrie=0.8.2=py310ha75aee5_8
• defusedxml=0.7.1=pyhd8ed1ab_0
• docutils=0.21.2=pyhd8ed1ab_0
• dropbox=12.0.2=pyhd8ed1ab_0
• exceptiongroup=1.2.2=pyhd8ed1ab_0
• expat=2.6.3=h5888daf_0
• fastqc=0.12.1=hdfd78af_0
• fftw=3.3.10=nompi_hf1063bd_110
• filechunkio=1.8=py_2
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• fontconfig=2.14.2=h14ed4e7_0
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• fonts-conda-forge=1=0
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• freetype=2.12.1=h267a509_2
• fribidi=1.0.10=h36c2ea0_0
• frozenlist=1.4.1=py310ha75aee5_1
• ftputil=5.1.0=pyhd8ed1ab_0
• gcc_impl_linux-64=14.1.0=h3c94d91_1
• gdk-pixbuf=2.42.10=h6c15284_3
• gettext=0.22.5=he02047a_3
• gettext-tools=0.22.5=he02047a_3
• gfortran_impl_linux-64=14.1.0=he4a1faa_1
• ghostscript=10.03.1=h59595ed_0
• giflib=5.2.2=hd590300_0
• gitdb=4.0.11=pyhd8ed1ab_0
• gitpython=3.1.43=pyhd8ed1ab_0
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• google-api-python-client=2.145.0=pyhd8ed1ab_0
• google-auth=2.34.0=pyhff2d567_0
• 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
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• 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
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• pcre2=10.40=hc3806b6_0
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• 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
• prettytable=3.11.0=pyhd8ed1ab_0
• proto-plus=1.23.0=pyhd8ed1ab_0
• protobuf=4.25.3=py310h0e2eeba_1
• psutil=6.0.0=py310ha75aee5_1
• pthread-stubs=0.4=h36c2ea0_1001
• pulp=2.7.0=py310hff52083_1
• pyasn1=0.6.1=pyhd8ed1ab_0
• pyasn1-modules=0.4.1=pyhd8ed1ab_0
• pycparser=2.22=pyhd8ed1ab_0
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• python-dateutil=2.9.0=pyhd8ed1ab_0
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• 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