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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

Problem with gimme after updating the anaconda environment. #78

Closed jonasungerback closed 4 years ago

jonasungerback commented 5 years ago

Hello,

I have run into some gimme issues after updating of the anaconda environment. The first related to from scipy.misc import factorial where factorial has now been moved to scipy.special. This is however an easy fix where I can easily downgrade scipy or change the code in rank.py line 12. However, after trying both, I get the following error (both on Mac and in Ubuntu and for both gimme motifs and gimme maelstrom) that I cannot resolve:

`Traceback (most recent call last): File "/opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/genomepy/functions.py", line 287, in init super(Genome, self).init(name) File "/opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/pyfaidx/init.py", line 996, in init build_index=build_index) File "/opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/pyfaidx/init.py", line 333, in init if filename.lower().endswith('.bgz') or filename.lower().endswith( AttributeError: 'NoneType' object has no attribute 'lower'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/opt/anaconda3/envs/gimmemotifs/bin/gimme", line 513, in args.func(args) File "/opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/gimmemotifs/commands/motifs.py", line 69, in motifs gimme_motifs(args.inputfile, args.name, params) File "/opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/gimmemotifs/denovo.py", line 543, in gimme_motifs input_type, background = check_denovo_input(inputfile, params) File "/opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/gimmemotifs/validation.py", line 55, in check_denovo_input Genome(genome) File "/opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/genomepy/functions.py", line 290, in init if os.path.isdir(name) and len(glob.glob(os.path.join(name, "*.fa"))) == 1 and genome_dir is not None: File "/opt/anaconda3/envs/gimmemotifs/lib/python3.6/genericpath.py", line 42, in isdir st = os.stat(s) TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType`

I can also mention that I fail to roll back one step in my anaconda revisions due to missing packages from the earlier revision so I am a little stuck. Is this something you can help out with?

Thanks in advance!

Best, Jonas

simonvh commented 5 years ago

Hi Jonas,

I'm trying to recreate the error, can you give me the output of conda info and conda list?

jonasungerback commented 5 years ago

Here it is from both MacOS and Ubuntu 16.04 since I get the same error both times:

MacOS: conda info

 active environment : gimme
active env location : /anaconda3/envs/gimme
        shell level : 2
   user config file : /Users/Jonas/.condarc

populated config files : /Users/Jonas/.condarc conda version : 4.6.2 conda-build version : 3.17.6 python version : 3.7.1.final.0 base environment : /anaconda3 (writable) channel URLs : https://conda.anaconda.org/conda-forge/osx-64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/bioconda/osx-64 https://conda.anaconda.org/bioconda/noarch https://repo.anaconda.com/pkgs/main/osx-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/osx-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/osx-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /anaconda3/pkgs /Users/Jonas/.conda/pkgs envs directories : /anaconda3/envs /Users/Jonas/.conda/envs platform : osx-64 user-agent : conda/4.6.2 requests/2.21.0 CPython/3.7.1 Darwin/18.6.0 OSX/10.14.5 UID:GID : 501:20 netrc file : None offline mode : False

conda list

packages in environment at /anaconda3/envs/gimme:

#

Name Version Build Channel

_py-xgboost-mutex 2.0 cpu_0 conda-forge appdirs 1.4.3 py_1 conda-forge arrow-cpp 0.13.0 py36h29c365f_3 conda-forge asn1crypto 0.24.0 py36_1003 conda-forge atomicwrites 1.3.0 py_0 conda-forge attrs 19.1.0 py_0 conda-forge bcftools 1.9 h3a161e8_4 bioconda bedtools 2.28.0 h7fd0a75_0 bioconda blas 2.7 openblas conda-forge boltons 19.1.0 py_0 conda-forge boost-cpp 1.68.0 h6f8c590_1000 conda-forge brotli 1.0.7 h0a44026_1000 conda-forge bucketcache 0.12.1 py36_1 conda-forge bzip2 1.0.6 h1de35cc_1002 conda-forge ca-certificates 2019.5.15 0 anaconda certifi 2019.3.9 py36_0 anaconda cffi 1.12.3 py36hccf1714_0 conda-forge chardet 3.0.4 py36_1003 conda-forge click 7.0 py_0 conda-forge cryptography 2.7 py36h212c5bf_0 conda-forge curl 7.64.1 h22ea746_0 conda-forge cycler 0.10.0 py_1 conda-forge decorator 4.4.0 py_0 conda-forge diskcache 3.1.1 py_0 conda-forge expat 2.2.5 h0a44026_1002 conda-forge feather-format 0.4.0 py_1003 conda-forge freetype 2.10.0 h24853df_0 conda-forge future 0.17.1 py36_1000 conda-forge gadem 1.3.1 h470a237_1 bioconda genomepy 0.5.5 py36_0 bioconda gflags 2.2.2 h0a44026_1001 conda-forge ghostscript 9.22 h0a44026_1001 conda-forge gimmemotifs 0.13.1 py36ha65daf6_1 bioconda glog 0.4.0 h6de7cb9_0 conda-forge homer 4.9.1 pl526h470a237_6 bioconda htslib 1.9 h3a161e8_7 bioconda icu 58.2 h0a44026_1000 conda-forge idna 2.8 py36_1000 conda-forge importlib_metadata 0.17 py36_1 conda-forge intel-openmp 2019.4 233 jinja2 2.10.1 py_0 conda-forge joblib 0.13.2 py_0 conda-forge jpeg 9c h1de35cc_1001 conda-forge kiwisolver 1.1.0 py36h770b8ee_0 conda-forge krb5 1.16.3 hcfa6398_1001 conda-forge libblas 3.8.0 7_openblas conda-forge libcblas 3.8.0 7_openblas conda-forge libcurl 7.64.1 h16faf7d_0 conda-forge libcxx 8.0.0 2 conda-forge libcxxabi 8.0.0 2 conda-forge libdeflate 1.0 h1de35cc_1 bioconda libedit 3.1.20170329 hcfe32e1_1001 conda-forge libffi 3.2.1 h6de7cb9_1006 conda-forge libgcc 4.8.5 hdbeacc1_10 conda-forge libgfortran 3.0.1 0 conda-forge libiconv 1.15 h01d97ff_1005 conda-forge liblapack 3.8.0 7_openblas conda-forge liblapacke 3.8.0 7_openblas conda-forge libopenblas 0.3.6 hdc02c5d_0 anaconda libpng 1.6.37 h2573ce8_0 conda-forge libprotobuf 3.7.1 hfbae3c0_0 conda-forge libssh2 1.8.2 hcdc9a53_2 conda-forge libtiff 4.0.10 h344961e_1002 conda-forge libuuid 2.32.1 h1de35cc_1000 conda-forge libxgboost 0.82 h6de7cb9_0 conda-forge libxml2 2.9.9 hd80cff7_0 conda-forge libxslt 1.1.32 h33a18ac_1002 conda-forge llvm-meta 8.0.0 0 conda-forge llvm-openmp 8.0.0 h770b8ee_0 conda-forge logbook 1.4.3 py36h01d97ff_0 conda-forge lz4-c 1.8.3 h6de7cb9_1001 conda-forge markupsafe 1.1.1 py36h1de35cc_0 conda-forge matplotlib 3.1.0 py36_1 conda-forge matplotlib-base 3.1.0 py36h3a684a6_1 conda-forge meme 4.12.0 py36pl526hd869df4_2 bioconda mkl 2019.4 233 mkl_fft 1.0.13 py36h01d97ff_1 conda-forge mkl_random 1.0.4 py36h051e8ed_0 conda-forge more-itertools 4.3.0 py36_1000 conda-forge mpi 1.0 openmpi conda-forge mysql-connector-c 6.1.11 h42c63d9_1003 conda-forge ncurses 6.1 h0a44026_1002 conda-forge norns 0.1.4 py_0 bioconda nose 1.3.7 py36_1002 conda-forge numpy 1.16.4 py36h6b0580a_0 conda-forge numpy-base 1.14.3 py36ha9ae307_0 anaconda olefile 0.46 py_0 conda-forge openblas 0.3.5 h436c29b_1001 conda-forge openjdk 11.0.1 h01d97ff_1016 conda-forge openmpi 4.0.1 ha90c164_1 conda-forge openssl 1.1.1 h1de35cc_0 anaconda packaging 19.0 py_0 conda-forge pandas 0.24.2 py36h86efe34_0 conda-forge parquet-cpp 1.5.1 2 conda-forge pathlib 1.0.1 py_1 conda-forge patsy 0.5.1 py_0 conda-forge perl 5.26.2 haec8ef5_1006 conda-forge perl-algorithm-cluster 1.58 pl526h1de35cc_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 pl526h1de35cc_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 pl526h04f5b5a_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 pl526h04f5b5a_3 bioconda perl-log-log4perl 1.49 pl526_0 bioconda perl-math-cdf 0.1 pl526h1de35cc_5 bioconda perl-parent 0.236 pl526_1 bioconda perl-scalar-list-utils 1.50 pl526h1de35cc_0 bioconda perl-types-serialiser 1.0 pl526_2 bioconda perl-xml-namespacesupport 1.12 pl526_0 bioconda perl-xml-parser 2.44_01 pl526h776b7f1_1001 conda-forge perl-xml-sax 1.00 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 6.0.0 py36h7095ceb_0 conda-forge pip 19.1.1 py36_0 conda-forge pluggy 0.12.0 py_0 conda-forge py 1.8.0 py_0 conda-forge py-xgboost 0.82 py36h6de7cb9_0 conda-forge pyarrow 0.13.0 py36hb37e6aa_0 conda-forge pybedtools 0.8.0 py36h5c9b4e4_1 bioconda pycparser 2.19 py36_1 conda-forge pyfaidx 0.5.5.2 py_1 bioconda pyopenssl 19.0.0 py36_0 conda-forge pyparsing 2.4.0 py_0 conda-forge pysam 0.15.2 py36h1719d13_3 bioconda pysocks 1.7.0 py36_0 conda-forge pytest 4.6.2 py36_0 conda-forge python 3.6.7 h8dc6b48_1004 conda-forge python-dateutil 2.8.0 py_0 conda-forge python-xxhash 1.3.0 py36h1de35cc_0 conda-forge pytz 2019.1 py_0 conda-forge pyyaml 5.1.1 py36h01d97ff_0 conda-forge re2 2019.06.01 h6de7cb9_0 conda-forge readline 7.0 hcfe32e1_1001 conda-forge represent 1.6.0 py36h01d97ff_0 conda-forge requests 2.22.0 py36_0 conda-forge samtools 1.9 h7c4ea83_11 bioconda scikit-learn 0.21.2 py36h2a6a0b8_0 conda-forge scipy 1.2.1 py36h1a1e112_0 anaconda seaborn 0.9.0 py_1 conda-forge setuptools 41.0.1 py36_0 conda-forge six 1.12.0 py36_1000 conda-forge sklearn-contrib-lightning 0.5.0 py36_0 conda-forge snappy 1.1.7 h0a44026_1002 conda-forge sqlite 3.28.0 h9721f7c_0 conda-forge statsmodels 0.9.0 py36h1d22016_0 anaconda thrift-cpp 0.12.0 hdedcb34_1002 conda-forge tk 8.6.9 h2573ce8_1002 conda-forge tornado 6.0.2 py36h01d97ff_0 conda-forge tqdm 4.32.1 py_0 conda-forge trawler 2.0 pl526_2 bioconda ucsc-bedtogenepred 377 he2eb843_0 bioconda ucsc-bigbedtobed 366 h1341992_0 bioconda ucsc-genepredtobed 377 he2eb843_2 bioconda ucsc-genepredtogtf 377 he2eb843_2 bioconda ucsc-gtftogenepred 377 he2eb843_2 bioconda urllib3 1.24.3 py36_0 conda-forge wcwidth 0.1.7 py_1 conda-forge weeder 2.0 h04f5b5a_3 bioconda wheel 0.33.4 py36_0 conda-forge xdg 3.0.2 0 conda-forge xgboost 0.82 py36h6de7cb9_0 conda-forge xmltodict 0.12.0 py_0 conda-forge xxmotif 1.6 0 bioconda xz 5.2.4 h1de35cc_1001 conda-forge yaml 0.1.7 h1de35cc_1001 conda-forge zipp 0.5.1 py_0 conda-forge zlib 1.2.11 h1de35cc_1004 conda-forge zstd 1.3.3 1 conda-forge

Ubuntu

conda info

 active environment : gimmemotifs
active env location : /opt/anaconda3/envs/gimmemotifs
        shell level : 1
   user config file : /home/jonas/.condarc

populated config files : conda version : 4.6.14 conda-build version : 3.17.8 python version : 3.6.8.final.0 base environment : /opt/anaconda3 (read only) channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /opt/anaconda3/pkgs /home/jonas/.conda/pkgs envs directories : /home/jonas/.conda/envs /opt/anaconda3/envs platform : linux-64 user-agent : conda/4.6.14 requests/2.21.0 CPython/3.6.8 Linux/4.13.0-43-generic ubuntu/16.04.6 glibc/2.23 UID:GID : 1001:1100 netrc file : None offline mode : False

(gimmemotifs)

conda list

packages in environment at /opt/anaconda3/envs/gimmemotifs:

#

Name Version Build Channel

_py-xgboost-mutex 2.0 cpu_0 conda-forge appdirs 1.4.3 py_1 conda-forge arrow-cpp 0.12.1 py36h0e61e49_0 conda-forge asn1crypto 0.24.0 py36_1003 conda-forge atk 2.25.90 hb9dd440_1002 conda-forge atomicwrites 1.3.0 py_0 conda-forge attrs 19.1.0 py_0 conda-forge bcftools 1.9 ha228f0b_4 bioconda bedtools 2.28.0 hdf88d34_0 bioconda blas 2.7 openblas conda-forge boltons 19.1.0 py_0 conda-forge boost-cpp 1.68.0 h11c811c_1000 conda-forge bucketcache 0.12.1 py36_1 conda-forge bzip2 1.0.6 h14c3975_1002 conda-forge ca-certificates 2019.5.15 0 anaconda cairo 1.16.0 ha4e643d_1000 conda-forge certifi 2019.3.9 py36_0 anaconda cffi 1.12.3 py36h8022711_0 conda-forge chardet 3.0.4 py36_1003 conda-forge click 7.0 py_0 conda-forge cryptography 2.7 py36h72c5cf5_0 conda-forge cryptography-vectors 2.7 py_0 conda-forge curl 7.64.1 hf8cf82a_0 conda-forge cycler 0.10.0 py_1 conda-forge dbus 1.13.6 he372182_0 conda-forge decorator 4.4.0 py_0 conda-forge diskcache 3.1.1 py_0 conda-forge expat 2.2.5 hf484d3e_1002 conda-forge feather-format 0.4.0 py_1003 conda-forge fontconfig 2.13.1 he4413a7_1000 conda-forge freetype 2.10.0 he983fc9_0 conda-forge future 0.17.1 py36_1000 conda-forge gadem 1.3.1 h470a237_1 bioconda gdk-pixbuf 2.36.12 h49783d7_1002 conda-forge genomepy 0.5.5 py36_0 bioconda gettext 0.19.8.1 hc5be6a0_1002 conda-forge ghostscript 9.22 hf484d3e_1001 conda-forge gimmemotifs 0.13.1 py36hdd2ebf5_1 bioconda glib 2.58.3 hf63aee3_1001 conda-forge gobject-introspection 1.58.2 py36h2da5eee_1000 conda-forge graphite2 1.3.13 hf484d3e_1000 conda-forge gst-plugins-base 1.14.5 h0935bb2_0 conda-forge gstreamer 1.14.5 h36ae1b5_0 conda-forge gtk2 2.24.31 hb68c50a_1001 conda-forge harfbuzz 2.4.0 h37c48d4_0 conda-forge homer 4.9.1 pl526h2d50403_6 bioconda htslib 1.9 ha228f0b_7 bioconda icu 58.2 hf484d3e_1000 conda-forge idna 2.8 py36_1000 conda-forge importlib_metadata 0.17 py36_1 conda-forge intel-openmp 2019.4 243 jinja2 2.10.1 py_0 conda-forge joblib 0.13.2 py_0 conda-forge jpeg 9c h14c3975_1001 conda-forge kiwisolver 1.1.0 py36hc9558a2_0 conda-forge krb5 1.16.3 h05b26f9_1001 conda-forge libblas 3.8.0 7_openblas conda-forge libboost 1.67.0 h46d08c1_4 libcblas 3.8.0 7_openblas conda-forge libcurl 7.64.1 hda55be3_0 conda-forge libdeflate 1.0 h14c3975_1 bioconda libedit 3.1.20170329 hf8c457e_1001 conda-forge libevent 2.1.8 h9d9f1b6_0 conda-forge libffi 3.2.1 he1b5a44_1006 conda-forge libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 8.2.0 hdf63c60_1 libgfortran 3.0.0 1 conda-forge libgfortran-ng 7.3.0 hdf63c60_0 libiconv 1.15 h516909a_1005 conda-forge liblapack 3.8.0 7_openblas conda-forge liblapacke 3.8.0 7_openblas conda-forge libopenblas 0.3.6 h5a2b251_0 anaconda libpng 1.6.37 hed695b0_0 conda-forge libprotobuf 3.6.1 hdbcaa40_1001 conda-forge libssh2 1.8.2 h22169c7_2 conda-forge libstdcxx-ng 8.2.0 hdf63c60_1 libtiff 4.0.10 h57b8799_1003 conda-forge libuuid 2.32.1 h14c3975_1000 conda-forge libxcb 1.13 h14c3975_1002 conda-forge libxgboost 0.82 he1b5a44_0 conda-forge libxml2 2.9.9 h13577e0_0 conda-forge libxslt 1.1.32 h4785a14_1002 conda-forge logbook 1.4.3 py36h516909a_0 conda-forge lz4-c 1.8.3 he1b5a44_1001 conda-forge markupsafe 1.1.1 py36h14c3975_0 conda-forge matplotlib 3.1.0 py36_1 conda-forge matplotlib-base 3.1.0 py36hfd891ef_1 conda-forge meme 4.12.0 py36pl526h96dd833_2 bioconda mkl 2019.4 243 mkl_fft 1.0.13 py36h516909a_1 conda-forge mkl_random 1.0.4 py36hf2d7682_0 conda-forge more-itertools 4.3.0 py36_1000 conda-forge mpi 1.0 openmpi conda-forge mysql-connector-c 6.1.11 hd2bbab6_1003 conda-forge ncurses 6.1 hf484d3e_1002 conda-forge nomkl 3.0 0 norns 0.1.4 py_0 bioconda nose 1.3.7 py36_1002 conda-forge numpy 1.16.4 py36h95a1406_0 conda-forge numpy-base 1.16.4 py36h2f8d375_0 anaconda olefile 0.46 py_0 conda-forge openblas 0.3.5 h9ac9557_1001 conda-forge openblas-devel 0.3.6 0 anaconda openjdk 11.0.1 h516909a_1016 conda-forge openmpi 4.0.1 hc99cbb1_1 conda-forge openssl 1.1.1 h7b6447c_0 anaconda packaging 19.0 py_0 conda-forge pandas 0.24.2 py36hb3f55d8_0 conda-forge pango 1.40.14 h4ea9474_1004 conda-forge parquet-cpp 1.5.1 4 conda-forge pathlib 1.0.1 py_1 conda-forge patsy 0.5.1 py_0 conda-forge pcre 8.41 hf484d3e_1003 conda-forge perl 5.26.2 h516909a_1006 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-data-dumper 2.173 pl526_0 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 1.50 pl526h14c3975_0 bioconda perl-types-serialiser 1.0 pl526_2 bioconda perl-xml-namespacesupport 1.12 pl526_0 bioconda perl-xml-parser 2.44_01 pl526h3a4f0e9_1 conda-forge perl-xml-sax 1.00 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 6.0.0 py36he7afcd5_0 conda-forge pip 19.1.1 py36_0 conda-forge pixman 0.34.0 h14c3975_1003 conda-forge pluggy 0.12.0 py_0 conda-forge pthread-stubs 0.4 h14c3975_1001 conda-forge py 1.8.0 py_0 conda-forge py-xgboost 0.82 py36he1b5a44_0 conda-forge pyarrow 0.12.1 py36hbbcf98d_0 conda-forge pybedtools 0.8.0 py36he860b03_1 bioconda pycparser 2.19 py36_1 conda-forge pyfaidx 0.5.5.2 py_1 bioconda pyopenssl 19.0.0 py36_0 conda-forge pyparsing 2.4.0 py_0 conda-forge pyqt 5.9.2 py36hcca6a23_0 conda-forge pysam 0.15.2 py36h4b7d16d_3 bioconda pysocks 1.7.0 py36_0 conda-forge pytest 4.6.2 py36_0 conda-forge python 3.6.7 h381d211_1004 conda-forge python-dateutil 2.8.0 py_0 conda-forge python-xxhash 1.3.0 py36h14c3975_0 conda-forge pytz 2019.1 py_0 conda-forge pyyaml 5.1.1 py36h516909a_0 conda-forge qt 5.9.7 h52cfd70_2 conda-forge readline 7.0 hf8c457e_1001 conda-forge represent 1.6.0 py36h516909a_0 conda-forge requests 2.22.0 py36_0 conda-forge samtools 1.9 h8571acd_11 bioconda scikit-learn 0.21.2 py36h627018c_0 conda-forge scipy 1.2.1 py36he2b7bc3_0 anaconda seaborn 0.9.0 py_1 conda-forge setuptools 41.0.1 py36_0 conda-forge sip 4.19.8 py36hf484d3e_1000 conda-forge six 1.12.0 py36_1000 conda-forge sklearn-contrib-lightning 0.5.0 py36_0 conda-forge snappy 1.1.7 hf484d3e_1002 conda-forge sqlite 3.28.0 h8b20d00_0 conda-forge statsmodels 0.9.0 py36h3010b51_1000 conda-forge thrift-cpp 0.12.0 h0a07b25_1002 conda-forge tk 8.6.9 hed695b0_1002 conda-forge tornado 6.0.2 py36h516909a_0 conda-forge tqdm 4.32.1 py_0 conda-forge trawler 2.0 pl526_2 bioconda ucsc-bedtogenepred 377 h35c10e6_0 bioconda ucsc-bigbedtobed 357 1 bioconda ucsc-genepredtobed 377 h35c10e6_2 bioconda ucsc-genepredtogtf 377 h35c10e6_2 bioconda ucsc-gtftogenepred 377 h35c10e6_2 bioconda urllib3 1.24.3 py36_0 conda-forge wcwidth 0.1.7 py_1 conda-forge weeder 2.0 h6bb024c_3 bioconda wheel 0.33.4 py36_0 conda-forge xdg 3.0.2 0 conda-forge xgboost 0.82 py36he1b5a44_0 conda-forge xmltodict 0.12.0 py_0 conda-forge xorg-kbproto 1.0.7 h14c3975_1002 conda-forge xorg-libice 1.0.9 h516909a_1004 conda-forge xorg-libsm 1.2.3 h84519dc_1000 conda-forge xorg-libx11 1.6.7 h14c3975_1000 conda-forge xorg-libxau 1.0.9 h14c3975_0 conda-forge xorg-libxdmcp 1.1.3 h516909a_0 conda-forge xorg-libxext 1.3.4 h516909a_0 conda-forge xorg-libxrender 0.9.10 h516909a_1002 conda-forge xorg-libxt 1.1.5 h14c3975_1002 conda-forge xorg-renderproto 0.11.1 h14c3975_1002 conda-forge xorg-xextproto 7.3.0 h14c3975_1002 conda-forge xorg-xproto 7.0.31 h14c3975_1007 conda-forge xxmotif 1.6 h2d50403_2 bioconda xz 5.2.4 h14c3975_1001 conda-forge yaml 0.1.7 h14c3975_1001 conda-forge zipp 0.5.1 py_0 conda-forge zlib 1.2.11 h14c3975_1004 conda-forge zstd 1.4.0 h3b9ef0a_0 conda-forge

jonasungerback commented 5 years ago

Could also be worth mentioning that I installed per your recommendation:

conda create -n gimme python=3 gimmemotifs about 6 months ago or so and then just the other day ran a conda update --all in that environment.

simonvh commented 5 years ago

Hmm, What is the full gimme motifs command line, and what is the full path of the genome that you supply?

jonasungerback commented 5 years ago

Very basic. I have mainly used gimme motifs or gimme maelstrom up to this point with very basic:

gimme motifs BM_FL_HSC_LMPP.ATAC_peaks.merged.bed -g mm10 -n test or gimme maelstrom clust_grps_FLvsABM_LMPP_opening_closing_t_5_n_101_4_for_maelstrom.txt mm10 clust_grps_FLvsABM_LMPP_opening_closing_t_5_n_101_4_maelstrom_out

I have however not tried to install the genome after the update. Should I perhaps try that? Will not change the fact that factorial has moved to a different scipy-package but that is of course an easy fix.

jonasungerback commented 5 years ago

Those commands worked up until the anaconda environment update.

jonasungerback commented 5 years ago

Reinstallation of the genome with genomepy install mm10 UCSC --annotation seems to solve my issue. At least both motifs and maelstrom is running now.

simonvh commented 5 years ago

Yes, the factorial issue is one that I will fix!

I'm glad that the genome reinstall worked, not sure of the cause though :(

jonasungerback commented 5 years ago

Thanks for your quick help. Both motifs and maelstrom ran fine but it could be worth mentioning that maelstrom gave me these warnings which probably is a sign of future troubles:

/opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/joblib/init.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+. warnings.warn(msg, category=DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/six.py:31: DeprecationWarning: The module is deprecated in version 0.21 and will be removed in version 0.23 since we've dropped support for Python 2.7. Please rely on the official version of six (https://pypi.org/project/six/). "(https://pypi.org/project/six/).", DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/joblib/init.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+. warnings.warn(msg, category=DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/six.py:31: DeprecationWarning: The module is deprecated in version 0.21 and will be removed in version 0.23 since we've dropped support for Python 2.7. Please rely on the official version of six (https://pypi.org/project/six/). "(https://pypi.org/project/six/).", DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/joblib/init.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+. warnings.warn(msg, category=DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/six.py:31: DeprecationWarning: The module is deprecated in version 0.21 and will be removed in version 0.23 since we've dropped support for Python 2.7. Please rely on the official version of six (https://pypi.org/project/six/). "(https://pypi.org/project/six/).", DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/joblib/init.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+. warnings.warn(msg, category=DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/six.py:31: DeprecationWarning: The module is deprecated in version 0.21 and will be removed in version 0.23 since we've dropped support for Python 2.7. Please rely on the official version of six (https://pypi.org/project/six/). "(https://pypi.org/project/six/).", DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/joblib/init.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+. warnings.warn(msg, category=DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/six.py:31: DeprecationWarning: The module is deprecated in version 0.21 and will be removed in version 0.23 since we've dropped support for Python 2.7. Please rely on the official version of six (https://pypi.org/project/six/). "(https://pypi.org/project/six/).", DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/joblib/init.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+. warnings.warn(msg, category=DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/six.py:31: DeprecationWarning: The module is deprecated in version 0.21 and will be removed in version 0.23 since we've dropped support for Python 2.7. Please rely on the official version of six (https://pypi.org/project/six/). "(https://pypi.org/project/six/).", DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/joblib/init.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+. warnings.warn(msg, category=DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/six.py:31: DeprecationWarning: The module is deprecated in version 0.21 and will be removed in version 0.23 since we've dropped support for Python 2.7. Please rely on the official version of six (https://pypi.org/project/six/). "(https://pypi.org/project/six/).", DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/joblib/init.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+. warnings.warn(msg, category=DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/joblib/init.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+. warnings.warn(msg, category=DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/six.py:31: DeprecationWarning: The module is deprecated in version 0.21 and will be removed in version 0.23 since we've dropped support for Python 2.7. Please rely on the official version of six (https://pypi.org/project/six/). "(https://pypi.org/project/six/).", DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/six.py:31: DeprecationWarning: The module is deprecated in version 0.21 and will be removed in version 0.23 since we've dropped support for Python 2.7. Please rely on the official version of six (https://pypi.org/project/six/). "(https://pypi.org/project/six/).", DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/joblib/init.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+. warnings.warn(msg, category=DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/six.py:31: DeprecationWarning: The module is deprecated in version 0.21 and will be removed in version 0.23 since we've dropped support for Python 2.7. Please rely on the official version of six (https://pypi.org/project/six/). "(https://pypi.org/project/six/).", DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/joblib/init.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+. warnings.warn(msg, category=DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/six.py:31: DeprecationWarning: The module is deprecated in version 0.21 and will be removed in version 0.23 since we've dropped support for Python 2.7. Please rely on the official version of six (https://pypi.org/project/six/). "(https://pypi.org/project/six/).", DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/joblib/init.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+. warnings.warn(msg, category=DeprecationWarning) /opt/anaconda3/envs/gimmemotifs/lib/python3.6/site-packages/sklearn/externals/six.py:31: DeprecationWarning: The module is deprecated in version 0.21 and will be removed in version 0.23 since we've dropped support for Python 2.7. Please rely on the official version of six (https://pypi.org/project/six/).