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vanheeringen-lab / gimmemotifs

Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples.
https://gimmemotifs.readthedocs.io/en/master
MIT License
109 stars 33 forks source link

Error while running tutorial #189

Closed fneuh closed 1 year ago

fneuh commented 3 years ago

Describe the bug I was following the tutorial (https://gimmemotifs.readthedocs.io/en/master/tutorials.html#find-de-novo-motifs). When searching for de-novo motifs I get the following error:

$ gimme motifs Gm12878.CTCF.top500.narrowPeak gimme.CTCF -g hg19 --denovo 2021-05-25 09:59:02,874 - INFO - creating background (matched GC%) Traceback (most recent call last): File "/home/neuhaus/miniconda3/envs/gimme/bin/gimme", line 11, in cli(sys.argv[1:]) File "/home/neuhaus/miniconda3/envs/gimme/lib/python3.9/site-packages/gimmemotifs/cli.py", line 661, in cli args.func(args) File "/home/neuhaus/miniconda3/envs/gimme/lib/python3.9/site-packages/gimmemotifs/commands/motifs.py", line 87, in motifs create_background_file( File "/home/neuhaus/miniconda3/envs/gimme/lib/python3.9/site-packages/gimmemotifs/background.py", line 121, in create_background_file m = MatchedGcFasta(inputfile, genome, number=number, size=size) File "/home/neuhaus/miniconda3/envs/gimme/lib/python3.9/site-packages/gimmemotifs/background.py", line 577, in init matched_gc_bedfile(tmpbed, matchfile, genome, number, size=size) File "/home/neuhaus/miniconda3/envs/gimme/lib/python3.9/site-packages/gimmemotifs/background.py", line 510, in matched_gc_bedfile fraction = number / len(gc) ZeroDivisionError: division by zero

$ tree gimme.CTCF/ gimme.CTCF/ ├── input.w200.bed └── motif_scan_results

The input.w200.bed looks alright, it contains 500 lines. $ head -n 5 gimme.CTCF/input.w200.bed chr11 190037 190237 1501.49835704239 chr14 106873577 106873777 1275.01449536283 chr14 106765204 106765404 1264.07667497398 chr15 22461178 22461378 1111.26912053378 chr14 107119996 107120196 996.90008265053

To Reproduce I pretty much followed the tutorial step-by-step, but for completness here are the commands:

$ conda create -n gimme python=3 gimmemotifs ... Executing transaction: \ For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default. To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before launching your MPI processes. Equivalently, you can set the MCA parameter in the command line: mpiexec --mca opal_cuda_support 1 ...

In addition, the UCX support is also built but disabled by default. To enable it, first install UCX (conda install -c conda-forge ucx). Then, set the environment variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes. Equivalently, you can set the MCA parameters in the command line: mpiexec --mca pml ucx --mca osc ucx ... Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX. Please consult UCX's documentation for detail. ... done

$ conda activate gimme $ conda env config vars set OMPI_MCA_opal_cuda_support=true $ conda install -c conda-forge ucx $ conda env config vars set OMPI_MCA_pml="ucx" $ conda env config vars set OMPI_MCA_osc="ucx" $ conda deactivate; conda activate gimme; conda env config vars list OMPI_MCA_opal_cuda_support = true OMPI_MCA_pml = ucx OMPI_MCA_osc = ucx

$ wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneGm12878CtcfStdAlnRep0_VS_wgEncodeBroadHistoneGm12878ControlStdAlnRep0.bb $ bigBedToBed spp.optimal.wgEncodeBroadHistoneGm12878CtcfStdAlnRep0_VS_wgEncodeBroadHistoneGm12878ControlStdAlnRep0.bb Gm12878.CTCF.narrowPeak $ sort -k7gr Gm12878.CTCF.narrowPeak | head -n 500 > Gm12878.CTCF.top500.narrowPeak $ genomepy install hg19 UCSC --annotation

$ gimme motifs Gm12878.CTCF.top500.narrowPeak gimme.CTCF -g hg19 --denovo

2021-05-25 09:59:02,874 - INFO - creating background (matched GC%) Traceback (most recent call last): File "/home/neuhaus/miniconda3/envs/gimme/bin/gimme", line 11, in cli(sys.argv[1:]) File "/home/neuhaus/miniconda3/envs/gimme/lib/python3.9/site-packages/gimmemotifs/cli.py", line 661, in cli args.func(args) File "/home/neuhaus/miniconda3/envs/gimme/lib/python3.9/site-packages/gimmemotifs/commands/motifs.py", line 87, in motifs create_background_file( File "/home/neuhaus/miniconda3/envs/gimme/lib/python3.9/site-packages/gimmemotifs/background.py", line 121, in create_background_file m = MatchedGcFasta(inputfile, genome, number=number, size=size) File "/home/neuhaus/miniconda3/envs/gimme/lib/python3.9/site-packages/gimmemotifs/background.py", line 577, in init matched_gc_bedfile(tmpbed, matchfile, genome, number, size=size) File "/home/neuhaus/miniconda3/envs/gimme/lib/python3.9/site-packages/gimmemotifs/background.py", line 510, in matched_gc_bedfile fraction = number / len(gc) ZeroDivisionError: division by zero

Installation information:

Thanks for your help, Florian

simonvh commented 3 years ago

Hi Florian,

I've checked and cannot reproduce the error, the tutorial seems to run fine on my side. Let's try to find the issue. Can you try:

1) Deleting ~/.cache/gimmemotifs/ and running the gimme command again. 2) Try running gimme background test.fa genomic -n 1 -s 10 -g hg19 -f fa. The output file test.fa should contain one sequence of length 10.

fneuh commented 3 years ago

  1. Deleting the cache and re-running didn't help, I got the same error

  2. This worked! $ cat test.fa

    chr14:41811982-41811992 ggcttgcaaa

simonvh commented 3 years ago

Hmm. The fact that 2 worked means your genome is installed and usable by GimmeMotifs.

Can you post the output of conda list, when run it inside the gimme conda environment?

fneuh commented 3 years ago

packages in environment at /home/neuhaus/miniconda3/envs/gimme:

Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge _py-xgboost-mutex 2.0 cpu_0 conda-forge abseil-cpp 20210324.1 h9c3ff4c_0 conda-forge alsa-lib 1.2.3 h516909a_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge arrow-cpp 4.0.0 py39h6ac3dd5_3_cpu conda-forge aws-c-cal 0.5.7 h3622835_1 conda-forge aws-c-common 0.5.11 h7f98852_0 conda-forge aws-c-event-stream 0.2.7 h5011166_5 conda-forge aws-c-io 0.9.12 h7aa3e40_2 conda-forge aws-checksums 0.1.11 hc0e0e8b_6 conda-forge aws-sdk-cpp 1.8.186 h9ad65fb_2 conda-forge bedtools 2.30.0 h7d7f7ad_1 bioconda biofluff 3.0.4 py_0 bioconda biopython 1.78 py39h3811e60_2 conda-forge boltons 20.2.1 pyh9f0ad1d_0 conda-forge boost-cpp 1.74.0 hc6e9bd1_3 conda-forge brotli 1.0.9 h9c3ff4c_4 conda-forge brotlipy 0.7.0 py39h3811e60_1001 conda-forge bucketcache 0.12.1 py39hde42818_2 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.17.1 h7f98852_1 conda-forge ca-certificates 2020.12.5 ha878542_0 conda-forge cairo 1.16.0 h6cf1ce9_1008 conda-forge certifi 2020.12.5 py39hf3d152e_1 conda-forge cffi 1.14.5 py39he32792d_0 conda-forge chardet 4.0.0 py39hf3d152e_1 conda-forge click 8.0.1 py39hf3d152e_0 conda-forge colorama 0.4.4 pyh9f0ad1d_0 conda-forge configparser 5.0.2 pyhd8ed1ab_0 conda-forge cryptography 3.4.7 py39hbca0aa6_0 conda-forge cycler 0.10.0 py_2 conda-forge dbus 1.13.6 hfdff14a_1 conda-forge decorator 5.0.9 pyhd8ed1ab_0 conda-forge dinamo 1.0 hee3b9ab_1 bioconda diskcache 5.2.1 pyh44b312d_0 conda-forge expat 2.2.10 h9c3ff4c_0 conda-forge feather-format 0.4.1 pyh9f0ad1d_0 conda-forge fontconfig 2.13.1 hba837de_1005 conda-forge freetype 2.10.4 h0708190_1 conda-forge future 0.18.2 py39hf3d152e_3 conda-forge gadem 1.3.1 h779adbc_3 bioconda genomepy 0.9.3 py_0 bioconda gettext 0.19.8.1 h0b5b191_1005 conda-forge gflags 2.2.2 he1b5a44_1004 conda-forge ghostscript 9.54.0 h9c3ff4c_1 conda-forge giflib 5.2.1 h36c2ea0_2 conda-forge gimmemotifs 0.15.3 py39h8f06ca0_0 bioconda glib 2.68.2 h9c3ff4c_0 conda-forge glib-tools 2.68.2 h9c3ff4c_0 conda-forge glog 0.5.0 h48cff8f_0 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge grpc-cpp 1.37.1 h2519f57_2 conda-forge gst-plugins-base 1.18.4 hf529b03_2 conda-forge gstreamer 1.18.4 h76c114f_2 conda-forge harfbuzz 2.8.1 h83ec7ef_0 conda-forge homer 4.11 pl5262h7d875b9_4 bioconda htseq 0.13.5 py39h70b41aa_1 bioconda htslib 1.12 h9093b5e_1 bioconda icu 68.1 h58526e2_0 conda-forge idna 2.10 pyh9f0ad1d_0 conda-forge jinja2 3.0.1 pyhd8ed1ab_0 conda-forge joblib 1.0.1 pyhd8ed1ab_0 conda-forge jpeg 9d h36c2ea0_0 conda-forge kiwisolver 1.3.1 py39h1a9c180_1 conda-forge krb5 1.19.1 hcc1bbae_0 conda-forge lcms2 2.12 hddcbb42_0 conda-forge ld_impl_linux-64 2.35.1 hea4e1c9_2 conda-forge libblas 3.9.0 9_openblas conda-forge libcblas 3.9.0 9_openblas conda-forge libclang 11.1.0 default_ha53f305_1 conda-forge libcurl 7.76.1 h2574ce0_2 conda-forge libdeflate 1.7 h7f98852_5 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libevent 2.1.10 hcdb4288_3 conda-forge libffi 3.3 h58526e2_2 conda-forge libgcc-ng 9.3.0 h2828fa1_19 conda-forge libgfortran-ng 9.3.0 hff62375_19 conda-forge libgfortran5 9.3.0 hff62375_19 conda-forge libglib 2.68.2 h3e27bee_0 conda-forge libgomp 9.3.0 h2828fa1_19 conda-forge libiconv 1.16 h516909a_0 conda-forge libidn2 2.3.1 h7f98852_0 conda-forge liblapack 3.9.0 9_openblas conda-forge libllvm10 10.0.1 he513fc3_3 conda-forge libllvm11 11.1.0 hf817b99_2 conda-forge libnghttp2 1.43.0 h812cca2_0 conda-forge libogg 1.3.4 h7f98852_1 conda-forge libopenblas 0.3.15 pthreads_h8fe5266_1 conda-forge libopus 1.3.1 h7f98852_1 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libpq 13.3 hd57d9b9_0 conda-forge libprotobuf 3.16.0 h780b84a_0 conda-forge libssh2 1.9.0 ha56f1ee_6 conda-forge libstdcxx-ng 9.3.0 h6de172a_19 conda-forge libthrift 0.14.1 he6d91bd_1 conda-forge libtiff 4.2.0 hbd63e13_2 conda-forge libunistring 0.9.10 h14c3975_0 conda-forge libutf8proc 2.6.1 h7f98852_0 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libwebp-base 1.2.0 h7f98852_2 conda-forge libxcb 1.13 h7f98852_1003 conda-forge libxgboost 1.4.0 h9c3ff4c_0 conda-forge libxkbcommon 1.0.3 he3ba5ed_0 conda-forge libxml2 2.9.12 h72842e0_0 conda-forge libxslt 1.1.33 h15afd5d_2 conda-forge llvmlite 0.36.0 py39h1bbdace_0 conda-forge logbook 1.5.3 py39h3811e60_4 conda-forge logomaker 0.8 pyh864c0ab_1 bioconda lz4-c 1.9.3 h9c3ff4c_0 conda-forge markupsafe 2.0.1 py39h3811e60_0 conda-forge matplotlib 3.4.2 py39hf3d152e_0 conda-forge matplotlib-base 3.4.2 py39h2fa2bec_0 conda-forge meme 5.3.0 py39pl5262heb7a276_2 bioconda mpi 1.0 openmpi conda-forge mysql-common 8.0.23 ha770c72_2 conda-forge mysql-connector-c 6.1.11 h6eb9d5d_1007 conda-forge mysql-libs 8.0.23 h935591d_2 conda-forge ncurses 6.2 h58526e2_4 conda-forge norns 0.1.5 pyh864c0ab_1 bioconda nose 1.3.7 py_1006 conda-forge nspr 4.30 h9c3ff4c_0 conda-forge nss 3.65 hb5efdd6_0 conda-forge numba 0.53.1 py39h4292f66_0 conda-forge numpy 1.20.3 py39hdbf815f_0 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openjdk 11.0.9.1 h5cc2fde_1 conda-forge openjpeg 2.4.0 hb52868f_1 conda-forge openmpi 4.1.1 hbfc84c5_0 conda-forge openssl 1.1.1k h7f98852_0 conda-forge orc 1.6.7 h89a63ab_2 conda-forge palettable 3.3.0 py_0 conda-forge pandas 1.2.4 py39hde0f152_0 conda-forge parquet-cpp 1.5.1 2 conda-forge pathlib 1.0.1 py39hf3d152e_4 conda-forge patsy 0.5.1 py_0 conda-forge pcre 8.44 he1b5a44_0 conda-forge perl 5.26.2 h36c2ea0_1008 conda-forge perl-algorithm-cluster 1.58 pl526h14c3975_0 bioconda perl-app-cpanminus 1.7044 pl526_1 bioconda perl-base 2.23 pl526_1 bioconda perl-carp 1.38 pl526_3 bioconda perl-cgi 4.44 pl526h14c3975_1 bioconda perl-common-sense 3.74 pl526_2 bioconda perl-constant 1.33 pl526_1 bioconda perl-dbi 1.642 pl526_0 bioconda perl-encode 2.88 pl526_1 bioconda perl-exporter 5.72 pl526_1 bioconda perl-extutils-makemaker 7.36 pl526_1 bioconda perl-file-path 2.16 pl526_0 bioconda perl-file-temp 0.2304 pl526_2 bioconda perl-file-which 1.23 pl526_0 bioconda perl-html-parser 3.72 pl526h6bb024c_5 bioconda perl-html-tagset 3.20 pl526_3 bioconda perl-html-template 2.97 pl526_1 bioconda perl-html-tree 5.07 pl526_1 bioconda perl-json 4.02 pl526_0 bioconda perl-json-xs 2.34 pl526h6bb024c_3 bioconda perl-log-log4perl 1.49 pl526_0 bioconda perl-math-cdf 0.1 pl526h14c3975_5 bioconda perl-parent 0.236 pl526_1 bioconda perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda perl-types-serialiser 1.0 pl526_2 bioconda perl-xml-namespacesupport 1.12 pl526_0 bioconda perl-xml-parser 2.44_01 pl526ha1d75be_1002 conda-forge perl-xml-sax 1.02 pl526_0 bioconda perl-xml-sax-base 1.09 pl526_0 bioconda perl-xml-sax-expat 0.51 pl526_3 bioconda perl-xml-simple 2.25 pl526_1 bioconda perl-xsloader 0.24 pl526_0 bioconda perl-yaml 1.29 pl526_0 bioconda pillow 8.2.0 py39hf95b381_1 conda-forge pip 21.1.2 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge prosampler 1.0 hc9558a2_0 bioconda pthread-stubs 0.4 h36c2ea0_1001 conda-forge py-xgboost 1.4.0 py39hf3d152e_0 conda-forge pyarrow 4.0.0 py39h3ebc44c_3_cpu conda-forge pybedtools 0.8.2 py39h39abbe0_1 bioconda pybigwig 0.3.18 py39h015b436_1 bioconda pycparser 2.20 pyh9f0ad1d_2 conda-forge pyfaidx 0.5.9.5 pyh3252c3a_0 bioconda pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyqt 5.12.3 py39hf3d152e_7 conda-forge pyqt-impl 5.12.3 py39h0fcd23e_7 conda-forge pyqt5-sip 4.19.18 py39he80948d_7 conda-forge pyqtchart 5.12 py39h0fcd23e_7 conda-forge pyqtwebengine 5.12.1 py39h0fcd23e_7 conda-forge pysam 0.16.0.1 py39h051187c_3 bioconda pysocks 1.7.1 py39hf3d152e_3 conda-forge python 3.9.4 hffdb5ce_0_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python-xxhash 2.0.2 py39h3811e60_0 conda-forge python_abi 3.9 1_cp39 conda-forge pytz 2021.1 pyhd8ed1ab_0 conda-forge pyyaml 5.4.1 py39h3811e60_0 conda-forge qnorm 0.7.0 pyh44b312d_0 conda-forge qt 5.12.9 hda022c4_4 conda-forge re2 2021.04.01 h9c3ff4c_0 conda-forge readline 8.1 h46c0cb4_0 conda-forge represent 1.6.0 py39h07f9747_2 conda-forge requests 2.25.1 pyhd3deb0d_0 conda-forge s2n 1.0.8 h9b69904_0 conda-forge scikit-learn 0.24.2 py39h4dfa638_0 conda-forge scipy 1.6.3 py39hee8e79c_0 conda-forge seaborn 0.11.1 hd8ed1ab_1 conda-forge seaborn-base 0.11.1 pyhd8ed1ab_1 conda-forge setuptools 49.6.0 py39hf3d152e_3 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.1.8 he1b5a44_3 conda-forge sqlite 3.35.5 h74cdb3f_0 conda-forge statsmodels 0.12.2 py39hce5d2b2_0 conda-forge threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge tk 8.6.10 h21135ba_1 conda-forge tornado 6.1 py39h3811e60_1 conda-forge tqdm 4.61.0 pyhd8ed1ab_0 conda-forge trawler 2.0 hdfd78af_4 bioconda tzdata 2021a he74cb21_0 conda-forge ucsc-bedtogenepred 377 h0b8a92a_2 bioconda ucsc-bigbedtobed 377 h0b8a92a_2 bioconda ucsc-genepredtobed 377 h0b8a92a_4 bioconda ucsc-genepredtogtf 377 h0b8a92a_4 bioconda ucsc-gff3togenepred 377 h0b8a92a_2 bioconda ucsc-gtftogenepred 377 h0b8a92a_4 bioconda ucx 1.9.0 h13c9de0_1 conda-forge unzip 6.0 h7f98852_2 conda-forge urllib3 1.26.4 pyhd8ed1ab_0 conda-forge weeder 2.0 h7d875b9_5 bioconda wget 1.20.1 h22169c7_0 conda-forge wheel 0.36.2 pyhd3deb0d_0 conda-forge xdg 5.0.2 pyhd8ed1ab_0 conda-forge xgboost 1.4.0 py39hf3d152e_0 conda-forge xmltodict 0.12.0 py_0 conda-forge xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-inputproto 2.3.2 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.7.1 h7f98852_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h7f98852_1 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge xorg-libxi 1.7.10 h7f98852_0 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-libxtst 1.2.3 h7f98852_1002 conda-forge xorg-recordproto 1.14.2 h7f98852_1002 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xxhash 0.8.0 h7f98852_3 conda-forge xxmotif 1.6 h2d50403_2 bioconda xz 5.2.5 h516909a_1 conda-forge yaml 0.2.5 h516909a_0 conda-forge zlib 1.2.11 h516909a_1010 conda-forge zstd 1.4.9 ha95c52a_0 conda-forge

simonvh commented 3 years ago

This is really strange. All you dependencies seem to be in order.

Can you try to install the development version of GimmeMotifs, to see if that helps (I'm really out of ideas here):

conda activate gimme
pip install git+https://github.com/vanheeringen-lab/gimmemotifs.git@develop
# run gimme command again
fneuh commented 3 years ago

Hi, sorry for not having written back in a while.. I tried it with the development version of gimmemotifs, but that also did not work.

I also installed gimmemotifs version v0.14.4 and tried running it with that, which also didn't help..

I will try to run this on another server and see if I get the same error there.

simonvh commented 3 years ago

@fneuh any update on this?

mdozmorov commented 2 years ago

This error may be due to some regions being long. Encountered the same error, troubleshooting involved starting with a few regions and increasing until the error occurred. Not sure what's the reasonable length threshold.

Traceback (most recent call last):
  File "/home/user/miniconda3/envs/gimme/bin/gimme", line 11, in <module>
    cli(sys.argv[1:])
  File "/home/user/miniconda3/envs/gimme/lib/python3.8/site-packages/gimmemotifs/cli.py", line 746, in cli
    args.func(args)
  File "/home/user/miniconda3/envs/gimme/lib/python3.8/site-packages/gimmemotifs/commands/pfmscan.py", line 19, in pfmscan
    scan_to_file(
  File "/home/user/miniconda3/envs/gimme/lib/python3.8/site-packages/gimmemotifs/scanner.py", line 401, in scan_to_file
    for line in command_scan(
  File "/home/user/miniconda3/envs/gimme/lib/python3.8/site-packages/gimmemotifs/scanner.py", line 317, in command_scan
    s.set_threshold(fpr=fpr, threshold=cutoff)
  File "/home/user/miniconda3/envs/gimme/lib/python3.8/site-packages/gimmemotifs/scanner.py", line 989, in set_threshold
    df = self._threshold_from_seqs(scan_motifs, seqs, fpr).set_index(
  File "/home/user/miniconda3/envs/gimme/lib/python3.8/site-packages/gimmemotifs/scanner.py", line 724, in _threshold_from_seqs
    for gc_bin, result in zip(
  File "/home/user/miniconda3/envs/gimme/lib/python3.8/site-packages/gimmemotifs/scanner.py", line 1199, in _scan_sequences_with_motif
    for ret in self._scan_jobs(scan_func, seqs):
  File "/home/user/miniconda3/envs/gimme/lib/python3.8/site-packages/gimmemotifs/scanner.py", line 1230, in _scan_jobs
    for i in range(math.ceil(len(scan_seqs) / chunksize)):
ZeroDivisionError: division by zero