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jeffhussmann / knock-knock

toolkit for analyzing genome editing experiments
GNU General Public License v3.0
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build-indices error #2

Closed HollyRuess closed 3 years ago

HollyRuess commented 3 years ago

I've install knock-knock in a conda environment with python=3.6. During the testing on example_data, I received an error during the build-indices step.

$ knock-knock build-indices project_folder hg38

"Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly"

jeffhussmann commented 3 years ago

Hi Holly -

As a temporary fix, it looks like downgrading to a version of Biopython <1.78 should prevent this error - https://biopython.org/wiki/Alphabet.

HollyRuess commented 3 years ago

Hi Jeff,

It appears that my bioconda is already 1.78. I already tried downgrading it to 1.70 but I run into multiple conflicts with conda-forge.

Here's a list and version of the packages in my environment.

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge argon2-cffi 20.1.0 py36h8f6f2f9_2 conda-forge async_generator 1.10 py_0 conda-forge attrs 20.3.0 pyhd3deb0d_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.1 py_0 conda-forge biopython 1.78 py36h8f6f2f9_1 conda-forge blast 2.7.1 h4422958_6 bioconda bleach 3.3.0 pyh44b312d_0 conda-forge bokeh 2.2.3 py36h5fab9bb_0 conda-forge boost 1.67.0 py36h3e44d54_0 conda-forge boost-cpp 1.67.0 h3a22d5f_0 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.17.1 h36c2ea0_0 conda-forge ca-certificates 2020.12.5 ha878542_0 conda-forge certifi 2020.12.5 py36h5fab9bb_1 conda-forge cffi 1.14.4 py36hc120d54_1 conda-forge cycler 0.10.0 py_2 conda-forge decorator 4.4.2 py_0 conda-forge defusedxml 0.6.0 py_0 conda-forge entrypoints 0.3 pyhd8ed1ab_1003 conda-forge freetype 2.10.4 h0708190_1 conda-forge gmp 6.1.2 hf484d3e_1000 conda-forge gnutls 3.5.19 h2a4e5f8_1 conda-forge hits 0.1 py36h4c5857e_1 bioconda htslib 1.11 hd3b49d5_1 bioconda icu 58.2 hf484d3e_1000 conda-forge importlib-metadata 3.4.0 py36h5fab9bb_0 conda-forge importlib_metadata 3.4.0 hd8ed1ab_0 conda-forge ipykernel 5.4.2 py36he448a4c_0 conda-forge ipython 7.16.1 py36he448a4c_2 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.6.3 pyhd3deb0d_0 conda-forge jedi 0.17.2 py36h5fab9bb_1 conda-forge jinja2 2.11.3 pyh44b312d_0 conda-forge jpeg 9d h36c2ea0_0 conda-forge jsonschema 3.2.0 py_2 conda-forge jupyter_client 6.1.11 pyhd8ed1ab_1 conda-forge jupyter_core 4.7.1 py36h5fab9bb_0 conda-forge jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge jupyterlab_widgets 1.0.0 pyhd8ed1ab_1 conda-forge kiwisolver 1.3.1 py36h605e78d_1 conda-forge knock-knock 0.2.1 py_0 bioconda krb5 1.17.2 h926e7f8_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 8_openblas conda-forge libcblas 3.9.0 8_openblas conda-forge libcurl 7.71.1 hcdd3856_8 conda-forge libdeflate 1.6 h516909a_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libffi 3.3 h58526e2_2 conda-forge libgcc-ng 9.3.0 h2828fa1_18 conda-forge libgfortran-ng 9.3.0 hff62375_18 conda-forge libgfortran5 9.3.0 hff62375_18 conda-forge libgomp 9.3.0 h2828fa1_18 conda-forge liblapack 3.9.0 8_openblas conda-forge libnghttp2 1.43.0 h812cca2_0 conda-forge libopenblas 0.3.12 pthreads_h4812303_1 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libssh2 1.9.0 hab1572f_5 conda-forge libstdcxx-ng 9.3.0 h6de172a_18 conda-forge libtiff 4.2.0 hdc55705_0 conda-forge libwebp-base 1.2.0 h7f98852_0 conda-forge lz4-c 1.9.3 h9c3ff4c_0 conda-forge markupsafe 1.1.1 py36h8f6f2f9_3 conda-forge matplotlib 3.3.2 0 conda-forge matplotlib-base 3.3.2 py36he12231b_1 conda-forge minimap2 2.16 h84994c4_1 bioconda mistune 0.8.4 py36h8f6f2f9_1003 conda-forge nbclient 0.5.1 py_0 conda-forge nbconvert 6.0.7 py36h5fab9bb_3 conda-forge nbformat 5.1.2 pyhd8ed1ab_1 conda-forge ncurses 6.2 h58526e2_4 conda-forge nest-asyncio 1.4.3 pyhd8ed1ab_0 conda-forge nettle 3.3 0 conda-forge notebook 6.2.0 py36h5fab9bb_0 conda-forge numpy 1.19.5 py36h2aa4a07_1 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openssl 1.1.1i h7f98852_0 conda-forge packaging 20.9 pyh44b312d_0 conda-forge pandas 1.1.5 py36h284efc9_0 conda-forge pandoc 2.11.4 h7f98852_0 conda-forge pandocfilters 1.4.2 py_1 conda-forge parallel 20201122 ha770c72_0 conda-forge parso 0.7.1 pyh9f0ad1d_0 conda-forge pcre 8.44 he1b5a44_0 conda-forge perl 5.26.2 h36c2ea0_1008 conda-forge perl-archive-tar 2.32 pl526_0 bioconda perl-carp 1.38 pl526_3 bioconda perl-compress-raw-bzip2 2.087 pl526he1b5a44_0 bioconda perl-compress-raw-zlib 2.087 pl526hc9558a2_0 bioconda perl-exporter 5.72 pl526_1 bioconda perl-exporter-tiny 1.002001 pl526_0 bioconda perl-extutils-makemaker 7.36 pl526_1 bioconda perl-io-compress 2.087 pl526he1b5a44_0 bioconda perl-io-zlib 1.10 pl526_2 bioconda perl-list-moreutils 0.428 pl526_1 bioconda perl-list-moreutils-xs 0.428 pl526_0 bioconda perl-pathtools 3.75 pl526h14c3975_1 bioconda perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda perl-xsloader 0.24 pl526_0 bioconda pexpect 4.8.0 pyh9f0ad1d_2 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 8.1.0 py36ha6010c0_2 conda-forge pip 21.0.1 pyhd8ed1ab_0 conda-forge prometheus_client 0.9.0 pyhd3deb0d_0 conda-forge prompt-toolkit 3.0.14 pyha770c72_0 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pycparser 2.20 pyh9f0ad1d_2 conda-forge pygments 2.7.4 pyhd8ed1ab_0 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyrsistent 0.17.3 py36h8f6f2f9_2 conda-forge pysam 0.16.0.1 py36h4c34d4e_1 bioconda python 3.6.12 hffdb5ce_0_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python_abi 3.6 1_cp36m conda-forge pytz 2021.1 pyhd8ed1ab_0 conda-forge pyyaml 5.4.1 py36h8f6f2f9_0 conda-forge pyzmq 22.0.1 py36h81c33ee_0 conda-forge readline 8.0 he28a2e2_2 conda-forge samtools 1.11 h6270b1f_0 bioconda scipy 1.5.3 py36h9e8f40b_0 conda-forge send2trash 1.5.0 py_0 conda-forge setuptools 49.6.0 py36h5fab9bb_3 conda-forge six 1.15.0 pyh9f0ad1d_0 conda-forge sqlite 3.34.0 h74cdb3f_0 conda-forge star 2.7.7a 0 bioconda terminado 0.9.2 py36h5fab9bb_0 conda-forge testpath 0.4.4 py_0 conda-forge tk 8.6.10 h21135ba_1 conda-forge tornado 6.1 py36h8f6f2f9_1 conda-forge tqdm 4.56.0 pyhd8ed1ab_0 conda-forge traitlets 4.3.3 py36h9f0ad1d_1 conda-forge typing_extensions 3.7.4.3 py_0 conda-forge wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge webencodings 0.5.1 py_1 conda-forge wheel 0.36.2 pyhd3deb0d_0 conda-forge widgetsnbextension 3.5.1 py36h5fab9bb_4 conda-forge xz 5.2.5 h516909a_1 conda-forge yaml 0.2.5 h516909a_0 conda-forge zeromq 4.3.4 h9c3ff4c_0 conda-forge zipp 3.4.0 py_0 conda-forge zlib 1.2.11 h516909a_1010 conda-forge zstd 1.4.8 ha95c52a_1 conda-forge

HollyRuess commented 3 years ago

Jeff,

I should have read your note better. I was able to downgrade to biopython=1.77 and it seems to be working.

Holly

HollyRuess commented 3 years ago

Jeff,

I'm still trying to run the test data, however, I still get lots of errors and can't seem to get past them. Please let me know if you are using conda or pip for your installation. Plus, let me know the exact versions in the environments. I'm assuming that I will need to downgrade more packages (for instance matplotlib <3.3).

Here's what I tried and the errors: 1) $ knock-knock parallel example_data 2 /home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/experiment.py:2: MatplotlibDeprecationWarning: The 'warn' parameter of use() is deprecated since Matplotlib 3.1 and will be removed in 3.3. If any parameter follows 'warn', they should be pass as keyword, not positionally. matplotlib.use('Agg', warn=False) /home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/visualize.py:9: MatplotlibDeprecationWarning: The 'warn' parameter of use() is deprecated since Matplotlib 3.1 and will be removed in 3.3. If any parameter follows 'warn', they should be pass as keyword, not positionally. matplotlib.use('Agg', warn=False) /home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/svg.py:8: MatplotlibDeprecationWarning: The 'warn' parameter of use() is deprecated since Matplotlib 3.1 and will be removed in 3.3. If any parameter follows 'warn', they should be pass as keyword, not positionally. matplotlib.use('Agg', warn=False) Traceback (most recent call last): File "/home/.conda/envs/knock-knock/bin/knock-knock", line 285, in args.func(args) File "/home/.conda/envs/knock-knock/bin/knock-knock", line 59, in parallel exps = experiment.get_all_experiments(args.project_directory, args.conditions) File "/home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/experiment.py", line 1942, in get_all_experiments exp = exp_class(base_dir, group, name, description=description, progress=progress) File "/home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/experiment.py", line 1221, in init auto_length = int((self.target_info.amplicon_length 2.5 // 1000 + 1)) 1000 File "/home/.conda/envs/knock-knock/lib/python3.6/site-packages/hits/utilities.py", line 171, in memoized_f setattr(self, attr_name, f(self)) File "/home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/experiment.py", line 150, in target_info supplemental_headers=self.supplemental_headers, File "/home/.conda/envs/knock-knock/lib/python3.6/site-packages/hits/utilities.py", line 171, in memoized_f setattr(self, attr_name, f(self)) File "/home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/experiment.py", line 140, in supplemental_headers return {name: sam.header_from_STAR_index(d['STAR']) for name, d in self.supplemental_indices.items()} File "/home/.conda/envs/knock-knock/lib/python3.6/site-packages/hits/utilities.py", line 171, in memoized_f setattr(self, attr_name, f(self)) File "/home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/experiment.py", line 136, in supplemental_indices return {name: locations[name] for name in self.supplemental_index_names} File "/home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/experiment.py", line 136, in return {name: locations[name] for name in self.supplemental_index_names} KeyError: 'e_coli'

2) $ knock-knock process example_data illumina B_ULT /home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/experiment.py:2: MatplotlibDeprecationWarning: The 'warn' parameter of use() is deprecated since Matplotlib 3.1 and will be removed in 3.3. If any parameter follows 'warn', they should be pass as keyword, not positionally. matplotlib.use('Agg', warn=False) /home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/visualize.py:9: MatplotlibDeprecationWarning: The 'warn' parameter of use() is deprecated since Matplotlib 3.1 and will be removed in 3.3. If any parameter follows 'warn', they should be pass as keyword, not positionally. matplotlib.use('Agg', warn=False) /home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/svg.py:8: MatplotlibDeprecationWarning: The 'warn' parameter of use() is deprecated since Matplotlib 3.1 and will be removed in 3.3. If any parameter follows 'warn', they should be pass as keyword, not positionally. matplotlib.use('Agg', warn=False) Traceback (most recent call last): File "/home/.conda/envs/knock-knock/bin/knock-knock", line 285, in args.func(args) File "/home/.conda/envs/knock-knock/bin/knock-knock", line 111, in process exp.process(stage) File "/home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/experiment.py", line 1665, in process self.generate_alignments(read_type) File "/home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/experiment.py", line 319, in generate_alignments blast.blast(self.target_info.fns['ref_fasta'], File "/home/.conda/envs/knock-knock/lib/python3.6/site-packages/hits/utilities.py", line 171, in memoized_f setattr(self, attr_name, f(self)) File "/home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/experiment.py", line 151, in target_info infer_homology_arms=self.infer_homology_arms, File "/home/.conda/envs/knock-knock/lib/python3.6/site-packages/knock_knock/target_info.py", line 45, in init manifest = yaml.safe_load(manifest_fn.open()) File "/home/.conda/envs/knock-knock/lib/python3.6/pathlib.py", line 1183, in open opener=self._opener) File "/home/.conda/envs/knock-knock/lib/python3.6/pathlib.py", line 1037, in _opener return self._accessor.open(self, flags, mode) File "/home/.conda/envs/knock-knock/lib/python3.6/pathlib.py", line 387, in wrapped return strfunc(str(pathobj), *args) FileNotFoundError: [Errno 2] No such file or directory: 'test_data/targets/BCAP31_GFP11_U_ILL/manifest.yaml'

Holly

HollyRuess commented 3 years ago

I've managed to get the software installed and was able to run through the Illumina data. I had to downgrade a few packages and changes to mappingtools.py (replace LoadAndKeep with NoSharedMemory)

Here's the list of packages and versions in my conda environment (in case anyone else needs to troubleshoot the install)

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge argon2-cffi 20.1.0 py36h8f6f2f9_2 conda-forge async_generator 1.10 py_0 conda-forge attrs 20.3.0 pyhd3deb0d_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.1 py_0 conda-forge biopython 1.77 py36h8c4c3a4_1 conda-forge blast 2.7.1 h4422958_6 bioconda bleach 3.3.0 pyh44b312d_0 conda-forge bokeh 2.2.3 py36h5fab9bb_0 conda-forge boost 1.67.0 py36h3e44d54_0 conda-forge boost-cpp 1.67.0 h3a22d5f_0 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.17.1 h36c2ea0_0 conda-forge ca-certificates 2020.12.5 ha878542_0 conda-forge certifi 2020.12.5 py36h5fab9bb_1 conda-forge cffi 1.14.4 py36hc120d54_1 conda-forge cycler 0.10.0 py_2 conda-forge decorator 4.4.2 py_0 conda-forge defusedxml 0.6.0 py_0 conda-forge entrypoints 0.3 pyhd8ed1ab_1003 conda-forge freetype 2.10.4 h0708190_1 conda-forge gmp 6.1.2 hf484d3e_1000 conda-forge gnutls 3.5.19 h2a4e5f8_1 conda-forge hits 0.1 py36h4c5857e_1 bioconda htslib 1.11 hd3b49d5_1 bioconda icu 58.2 hf484d3e_1000 conda-forge importlib-metadata 3.4.0 py36h5fab9bb_0 conda-forge importlib_metadata 3.4.0 hd8ed1ab_0 conda-forge ipykernel 5.4.2 py36he448a4c_0 conda-forge ipython 7.16.1 py36he448a4c_2 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.6.3 pyhd3deb0d_0 conda-forge jedi 0.17.2 py36h5fab9bb_1 conda-forge jinja2 2.11.3 pyh44b312d_0 conda-forge jpeg 9d h36c2ea0_0 conda-forge jsonschema 3.2.0 py_2 conda-forge jupyter_client 6.1.11 pyhd8ed1ab_1 conda-forge jupyter_core 4.7.1 py36h5fab9bb_0 conda-forge jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge jupyterlab_widgets 1.0.0 pyhd8ed1ab_1 conda-forge kiwisolver 1.3.1 py36h605e78d_1 conda-forge knock-knock 0.2.1 py_0 bioconda krb5 1.17.2 h926e7f8_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 8_openblas conda-forge libcblas 3.9.0 8_openblas conda-forge libcurl 7.71.1 hcdd3856_8 conda-forge libdeflate 1.6 h516909a_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libffi 3.3 h58526e2_2 conda-forge libgcc-ng 9.3.0 h2828fa1_18 conda-forge libgfortran-ng 9.3.0 hff62375_18 conda-forge libgfortran5 9.3.0 hff62375_18 conda-forge libgomp 9.3.0 h2828fa1_18 conda-forge liblapack 3.9.0 8_openblas conda-forge libnghttp2 1.43.0 h812cca2_0 conda-forge libopenblas 0.3.12 pthreads_h4812303_1 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libssh2 1.9.0 hab1572f_5 conda-forge libstdcxx-ng 9.3.0 h6de172a_18 conda-forge libtiff 4.2.0 hdc55705_0 conda-forge libwebp-base 1.2.0 h7f98852_0 conda-forge lz4-c 1.9.3 h9c3ff4c_0 conda-forge markupsafe 1.1.1 py36h8f6f2f9_3 conda-forge matplotlib 3.2.2 1 conda-forge matplotlib-base 3.2.2 py36hef1b27d_0
minimap2 2.16 h84994c4_1 bioconda mistune 0.8.4 py36h8f6f2f9_1003 conda-forge nbconvert 5.6.1 py36h9f0ad1d_1 conda-forge nbformat 4.4.0 py_1 conda-forge ncurses 6.2 h58526e2_4 conda-forge nest-asyncio 1.4.3 pyhd8ed1ab_0 conda-forge nettle 3.3 0 conda-forge notebook 6.2.0 py36h5fab9bb_0 conda-forge numpy 1.19.5 py36h2aa4a07_1 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openssl 1.1.1i h7f98852_0 conda-forge packaging 20.9 pyh44b312d_0 conda-forge pandas 1.1.5 py36h284efc9_0 conda-forge pandoc 2.11.4 h7f98852_0 conda-forge pandocfilters 1.4.2 py_1 conda-forge parallel 20201122 ha770c72_0 conda-forge parso 0.7.1 pyh9f0ad1d_0 conda-forge pcre 8.44 he1b5a44_0 conda-forge perl 5.26.2 h36c2ea0_1008 conda-forge perl-archive-tar 2.32 pl526_0 bioconda perl-carp 1.38 pl526_3 bioconda perl-compress-raw-bzip2 2.087 pl526he1b5a44_0 bioconda perl-compress-raw-zlib 2.087 pl526hc9558a2_0 bioconda perl-exporter 5.72 pl526_1 bioconda perl-exporter-tiny 1.002001 pl526_0 bioconda perl-extutils-makemaker 7.36 pl526_1 bioconda perl-io-compress 2.087 pl526he1b5a44_0 bioconda perl-io-zlib 1.10 pl526_2 bioconda perl-list-moreutils 0.428 pl526_1 bioconda perl-list-moreutils-xs 0.428 pl526_0 bioconda perl-pathtools 3.75 pl526h14c3975_1 bioconda perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda perl-xsloader 0.24 pl526_0 bioconda pexpect 4.8.0 pyh9f0ad1d_2 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 8.1.0 py36ha6010c0_2 conda-forge pip 21.0.1 pyhd8ed1ab_0 conda-forge prometheus_client 0.9.0 pyhd3deb0d_0 conda-forge prompt-toolkit 3.0.14 pyha770c72_0 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pycparser 2.20 pyh9f0ad1d_2 conda-forge pygments 2.7.4 pyhd8ed1ab_0 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyrsistent 0.17.3 py36h8f6f2f9_2 conda-forge pysam 0.16.0.1 py36h4c34d4e_1 bioconda python 3.6.12 hffdb5ce_0_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python_abi 3.6 1_cp36m conda-forge pytz 2021.1 pyhd8ed1ab_0 conda-forge pyyaml 5.4.1 py36h8f6f2f9_0 conda-forge pyzmq 22.0.1 py36h81c33ee_0 conda-forge readline 8.0 he28a2e2_2 conda-forge samtools 1.11 h6270b1f_0 bioconda scipy 1.5.3 py36h9e8f40b_0 conda-forge send2trash 1.5.0 py_0 conda-forge setuptools 49.6.0 py36h5fab9bb_3 conda-forge six 1.15.0 pyh9f0ad1d_0 conda-forge sqlite 3.34.0 h74cdb3f_0 conda-forge star 2.7.7a 0 bioconda terminado 0.9.2 py36h5fab9bb_0 conda-forge testpath 0.4.4 py_0 conda-forge tk 8.6.10 h21135ba_1 conda-forge tornado 6.1 py36h8f6f2f9_1 conda-forge tqdm 4.56.0 pyhd8ed1ab_0 conda-forge traitlets 4.3.3 py36h9f0ad1d_1 conda-forge typing_extensions 3.7.4.3 py_0 conda-forge wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge webencodings 0.5.1 py_1 conda-forge wheel 0.36.2 pyhd3deb0d_0 conda-forge widgetsnbextension 3.5.1 py36h5fab9bb_4 conda-forge xz 5.2.5 h516909a_1 conda-forge yaml 0.2.5 h516909a_0 conda-forge zeromq 4.3.4 h9c3ff4c_0 conda-forge zipp 3.4.0 py_0 conda-forge zlib 1.2.11 h516909a_1010 conda-forge zstd 1.4.8 ha95c52a_1 conda-forge