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DerKevinRiehl / TransposonUltimate

TransposonUltimate - a holistic set of tools for transposon identification
GNU General Public License v3.0
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conda installation of rfsb raises error #14

Closed matthew-ackerman closed 9 months ago

matthew-ackerman commented 10 months ago

I did an install of transposon classifier rfsb in a clean conda environment, and on running transposon_classifier_RFSB it raised an error when loading the models--(models = pickle.load(file)#["model"]): ValieError: node array from the pickle has an incompatible dtype: ...

just wondering if anyone has any idea what might have gone wrong.

DerKevinRiehl commented 10 months ago

Hey Matthew, thanks for your interest in our work. Sounds to me that the pickle version you use is different from what the software expects to use. When you say clean conda environment, which python version did you specify?

Thanks for your answer, Best, Kevin

matthew-ackerman commented 10 months ago

I tried "conda create -n tu python=2.7" but when I do this I get the message "Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source." followed by a silent crash back to the prompt while it is "Collecting package metadata". There is a python 2.7 on the computer so I don't know what is going on. I asked some other people about it and could get any answers.

-Matt

On Sat, Jan 13, 2024 at 4:54 AM DerKevinRiehl @.***> wrote:

Hey Matthew, thanks for your interest in our work. Sounds to me that the pickle version you use is different from what the software expects to use. When you say clean conda environment, which python version did you specify?

Thanks for your answer, Best, Kevin

— Reply to this email directly, view it on GitHub https://github.com/DerKevinRiehl/TransposonUltimate/issues/14#issuecomment-1890416375, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACRUFUNK2LGBL5RGS76K6LYOJRVNAVCNFSM6AAAAABBVNQT5WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJQGQYTMMZXGU . You are receiving this because you authored the thread.Message ID: @.***>

DerKevinRiehl commented 10 months ago

Dear Matt, that sounds very weird to me.

Even having Python2.7 installed on the system doesnt mean that your conda (and the environments you create with it) use Python2.7, but rather 3.+.

This behaviour of infinite looping of conda is unfortunately a phenomenon of the recent years. Does the machine / cluster you are working on has proper access to the internet? Are you on a Windows or Linux Machine?

Maybe try the recommendations of this thread and let me know if this works. https://stackoverflow.com/questions/69187142/solving-environment-failed-with-current-repodata-json-will-retry-with-next-rep

It is a conda problem (not necessary your machines problem or the problem of TransposonUltimate :-( Still I am sure we can fix this together, please keep me updated. Best, Kevin

matthew-ackerman commented 9 months ago

So, I was able to follow your installation instructions more closely and I'm still experiencing problems. Once I had Transposon Classifier "RFSB" https://github.com/DerKevinRiehl/transposon_classifier_rfsb installed, the module I'm interested in using, I had to install a number of dependencies in python3--biopython, scikit-learn, and mathplotlib. I noticed in your wrapper script transposon_classifier_RFSB you explicitly invoke python3. But even after installing these libraries, the classifier crashes early on with the error "Traceback (most recent call last): File "/home/magmt/.conda/envs/TU_env/share/TransposonClassifierRFSB1.0.0/RFSB_TE_Classifier.py", line 201, in classifyTransposons(tempFileA, tempFileC, dbFile, modelFile, fastaFile, outputFile) File "/home/magmt/.conda/envs/TU_env/share/TransposonClassifierRFSB1.0.0/RFSB_ModelManager.py", line 255, in classifyTransposons models = pickle.load(file)#["model"] File "sklearn/tree/_tree.pyx", line 865, in sklearn.tree._tree.Tree.setstate File "sklearn/tree/_tree.pyx", line 1571, in sklearn.tree._tree._check_node_ndarray ValueError: node array from the pickle has an incompatible dtype:

Any idea what I'm doing wrong?

-Matt

On Tue, Jan 23, 2024 at 4:26 PM DerKevinRiehl @.***> wrote:

Dear Matt, that sounds very weird to me.

Even having Python2.7 installed on the system doesnt mean that your conda (and the environments you create with it) use Python2.7, but rather 3.+.

This behaviour of infinite looping of conda is unfortunately a phenomenon of the recent years. Does the machine / cluster you are working on has proper access to the internet? Are you on a Windows or Linux Machine?

Maybe try the recommendations of this thread and let me know if this works.

https://stackoverflow.com/questions/69187142/solving-environment-failed-with-current-repodata-json-will-retry-with-next-rep

It is a conda problem (not necessary your machines problem or the problem of TransposonUltimate :-( Still I am sure we can fix this together, please keep me updated. Best, Kevin

— Reply to this email directly, view it on GitHub https://github.com/DerKevinRiehl/TransposonUltimate/issues/14#issuecomment-1907024391, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACRUFVAQ2P4V24H7OX4W5LYQA2IDAVCNFSM6AAAAABBVNQT5WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBXGAZDIMZZGE . You are receiving this because you authored the thread.Message ID: @.***>

DerKevinRiehl commented 9 months ago

Dear matthew, I am sorry to hear you still have troubles.

Can you please show me your conda environment you are using? To do so, just open the terminal, activate the environment you are using and type

python --version
conda list

Or the python environment you are using? To do so, just open the terminal, and type

python --version
pip list

Best, Kevin Riehl

matthew-ackerman commented 9 months ago

python --version: Python 2.7.15

conda list:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge alsa-lib 1.2.3.2 h166bdaf_0 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.functools_lru_cache 1.6.1 py_0 conda-forge backports_abc 0.5 py_1 conda-forge biopython 1.68 py27_0 bioconda blas 2.14 openblas conda-forge blast 2.15.0 pl5321h6f7f691_1 bioconda bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.11.0 h470a237_1 bioconda ca-certificates 2024.2.2 hbcca054_0 conda-forge cairo 1.16.0 hcf35c78_1003 conda-forge certifi 2019.11.28 py27h8c360ce_1 conda-forge curl 7.71.1 he644dc0_8 conda-forge cycler 0.10.0 py_2 conda-forge dbus 1.13.6 hfdff14a_1 conda-forge docutils 0.16 py27h8c360ce_1 conda-forge entrez-direct 16.2 he881be0_1 bioconda expat 2.5.0 hcb278e6_1 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge functools32 3.2.3.2 py_3 conda-forge futures 3.3.0 py27h8c360ce_1 conda-forge genometools-genometools 1.6.2 py27h6ad192e_0 bioconda gettext 0.21.1 h27087fc_0 conda-forge giflib 5.2.1 h0b41bf4_3 conda-forge glib 2.66.3 h58526e2_0 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge gst-plugins-base 1.14.5 h0935bb2_2 conda-forge gstreamer 1.14.5 h36ae1b5_2 conda-forge harfbuzz 2.4.0 h9f30f68_3 conda-forge icu 64.2 he1b5a44_1 conda-forge jpeg 9e h0b41bf4_3 conda-forge kiwisolver 1.1.0 py27h9e3301b_1 conda-forge krb5 1.17.2 h926e7f8_0 conda-forge lcms2 2.12 hddcbb42_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge libblas 3.8.0 14_openblas conda-forge libcblas 3.8.0 14_openblas conda-forge libcurl 7.71.1 hcdd3856_8 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.2.1 he1b5a44_1007 conda-forge libgcc-ng 13.2.0 h807b86a_5 conda-forge libgfortran-ng 7.5.0 h14aa051_20 conda-forge libgfortran4 7.5.0 h14aa051_20 conda-forge libglib 2.66.3 hbe7bbb4_0 conda-forge libgomp 13.2.0 h807b86a_5 conda-forge libiconv 1.17 hd590300_2 conda-forge libidn2 2.3.7 hd590300_0 conda-forge liblapack 3.8.0 14_openblas conda-forge liblapacke 3.8.0 14_openblas conda-forge libnghttp2 1.41.0 hab1572f_1 conda-forge libopenblas 0.3.7 h5ec1e0e_6 conda-forge libpng 1.6.42 h2797004_0 conda-forge libsqlite 3.44.2 h2797004_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge libtiff 4.2.0 hf544144_3 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libwebp-base 1.3.2 hd590300_0 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxml2 2.9.10 hee79883_0 conda-forge libzlib 1.2.13 hd590300_5 conda-forge matplotlib 2.2.5 ha770c72_3 conda-forge matplotlib-base 2.2.5 py27h250f245_1 conda-forge mmtf-python 1.0.2 py27_0 bioconda msgpack-python 1.0.0 py27h9e3301b_1 conda-forge ncbi-vdb 3.0.10 hdbdd923_0 bioconda ncurses 6.4 h59595ed_2 conda-forge numpy 1.16.5 py27h95a1406_0 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openblas 0.3.7 he1df0ab_6 conda-forge openjdk 11.0.8 hacce0ff_0 conda-forge openssl 1.1.1w hd590300_0 conda-forge ossuuid 1.6.2 hf484d3e_1000 conda-forge pandas 0.24.2 py27hf484d3e_0 conda-forge pango 1.42.4 h7062337_4 conda-forge pcre 8.45 h9c3ff4c_0 conda-forge perl 5.26.2 h36c2ea0_1008 conda-forge perl-app-cpanminus 1.7044 pl526_1 bioconda perl-archive-tar 2.32 pl526_0 bioconda perl-business-isbn 3.004 pl526_0 bioconda perl-business-isbn-data 20140910.003 pl526_0 bioconda perl-carp 1.38 pl526_3 bioconda perl-common-sense 3.74 pl526_2 bioconda perl-compress-raw-bzip2 2.087 pl526he1b5a44_0 bioconda perl-compress-raw-zlib 2.087 pl526hc9558a2_0 bioconda perl-constant 1.33 pl526_1 bioconda perl-data-dumper 2.173 pl526_0 bioconda perl-encode 2.88 pl526_1 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-file-path 2.16 pl526_0 bioconda perl-file-temp 0.2304 pl526_2 bioconda perl-io-compress 2.087 pl526he1b5a44_0 bioconda perl-io-zlib 1.10 pl526_2 bioconda perl-json 4.02 pl526_0 bioconda perl-json-xs 2.34 pl526h6bb024c_3 bioconda perl-list-moreutils 0.428 pl526_1 bioconda perl-list-moreutils-xs 0.428 pl526_0 bioconda perl-mime-base64 3.15 pl526_1 bioconda perl-parent 0.236 pl526_1 bioconda perl-pathtools 3.75 pl526h14c3975_1 bioconda perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda perl-types-serialiser 1.0 pl526_2 bioconda perl-uri 1.76 pl526_0 bioconda perl-xml-libxml 2.0132 pl526h7ec2d77_1 bioconda perl-xml-namespacesupport 1.12 pl526_0 bioconda perl-xml-sax 1.02 pl526_0 bioconda perl-xml-sax-base 1.09 pl526_0 bioconda perl-xsloader 0.24 pl526_0 bioconda pillow 6.2.1 py27hd70f55b_1 conda-forge pip 20.1.1 pyh9f0ad1d_0 conda-forge pixman 0.38.0 h516909a_1003 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyqt 5.9.2 py27hcca6a23_4 conda-forge python 2.7.15 h5a48372_1011_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python_abi 2.7 1_cp27mu conda-forge pytz 2020.1 pyh9f0ad1d_0 conda-forge qt 5.9.7 h0c104cb_3 conda-forge readline 8.2 h8228510_1 conda-forge reportlab 3.5.42 py27heca39a3_0 conda-forge scikit-learn 0.20.3 py27ha8026db_1 conda-forge scipy 1.2.1 py27h921218d_2 conda-forge setuptools 44.0.0 py27_0 conda-forge singledispatch 3.6.1 pyh44b312d_0 conda-forge sip 4.19.8 py27hf484d3e_1000 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sqlite 3.44.2 h2c6b66d_0 conda-forge statistics 1.0.3.5 py_1002 conda-forge subprocess32 3.5.4 py27h516909a_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge tornado 5.1.1 py27h14c3975_1000 conda-forge transposon_annotation_tools_helitronscanner 1.0.0 1 derkevinriehl transposon_annotation_tools_mitefinderii 1.0.0 0 derkevinriehl transposon_annotation_tools_mitetracker 1.0.1 1 derkevinriehl transposon_annotation_tools_proteinncbicdd1000 1.0.0 1 derkevinriehl transposon_annotation_tools_sinefinder 1.0.1 0 derkevinriehl transposon_classifier_rfsb 1.0.0 0 derkevinriehl vsearch 2.27.0 h6a68c12_0 bioconda wget 1.20.3 ha56f1ee_1 conda-forge wheel 0.37.1 pyhd8ed1ab_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 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.7 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge xorg-libxi 1.7.10 h7f98852_0 conda-forge xorg-libxrender 0.9.11 hd590300_0 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 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstd 1.5.5 hfc55251_0 conda-forge

pip list:

DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support Package Version

backports-abc 0.5 backports.functools-lru-cache 1.6.1 biopython 1.68 certifi 2019.11.28 cycler 0.10.0 docutils 0.16 functools32 3.2.3.post2 futures 3.3.0 GenomeTools 1.6.2 kiwisolver 1.1.0 matplotlib 2.2.5 mmtf-python 1.0.2 msgpack 1.0.0 numpy 1.16.5 olefile 0.46 pandas 0.24.2 Pillow 6.2.1 pip 20.1.1 pyparsing 2.4.7 python-dateutil 2.8.1 pytz 2020.1 reportlab 3.5.42 scikit-learn 0.20.3 scipy 1.2.1 setuptools 44.0.0.post20200102 singledispatch 0.0.0 six 1.16.0 statistics 1.0.3.5 subprocess32 3.5.4 tornado 5.1.1 wheel 0.37.1

On Sun, Feb 11, 2024 at 3:30 AM DerKevinRiehl @.***> wrote:

Dear matthew, I am sorry to hear you still have troubles.

Can you please show me your conda environment you are using? To do so, just open the terminal, activate the environment you are using and type

python --version conda list

Or the python environment you are using? To do so, just open the terminal, and type

python --version pip list

Best, Kevin Riehl

— Reply to this email directly, view it on GitHub https://github.com/DerKevinRiehl/TransposonUltimate/issues/14#issuecomment-1937490896, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACRUFWNCRWJXRV45JYXN2LYTCFTTAVCNFSM6AAAAABBVNQT5WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZXGQ4TAOBZGY . You are receiving this because you authored the thread.Message ID: @.***>

DerKevinRiehl commented 9 months ago

Dear Matthew, can you setup an environment with python=3.6? https://github.com/DerKevinRiehl/transposon_annotation_reasonaTE/blob/main/environment_yml/transposon_annotation_reasonaTE.yml

You need an environment similar to this one in order to use reasonaTE probably. Try to create a clean new python environment with python 3.6 and try again:

conda create --name testenv python==3.6
conda install -c derkevinriehl -c bioconda transposon_classifier_rfsb

Please let me know if this helped solving your issues. Best, Kevin

matthew-ackerman commented 9 months ago

I get a bunch of 'UnsatisfiableError: The following specifications were found to be incompatible with each other:', in xz, _libgcc_mutex, openssl, transposon_classifier_rfsb (its complaining about the version of python),

transposon_classifier_rfsb -> python -> ca-certificates setuptools -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates python_abi -> python=2.7 -> ca-certificates wheel -> python[version='!=3.0,!=3.1,!=3.2,!=3.3,!=3.4'] -> ca-certificates openssl -> ca-certificates pip -> python -> ca-certificates ca-certificates python==3.6 -> openssl=1.0 -> ca-certificates

and a bunch of other stuff. Is it possible I've messed up my base conda environment somehow and this is carrying over to my fresh environment? I attached the total error output if it is helpful. I'm really pretty green when it comes to conda and it always seems to give me nothing but trouble.

-Matt

On Wed, Feb 14, 2024 at 9:11 AM DerKevinRiehl @.***> wrote:

Dear Matthew, can you setup an environment with python=3.6?

https://github.com/DerKevinRiehl/transposon_annotation_reasonaTE/blob/main/environment_yml/transposon_annotation_reasonaTE.yml

You need an environment similar to this one in order to use reasonaTE probably. Try to create a clean new python environment with python 3.6 and try again:

conda create --name testenv python==3.6 conda install -c derkevinriehl -c bioconda transposon_classifier_rfsb

Please let me know if this helped solving your issues. Best, Kevin

— Reply to this email directly, view it on GitHub https://github.com/DerKevinRiehl/TransposonUltimate/issues/14#issuecomment-1944030289, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACRUFXUVTKYDZLU6KVBAZDYTTHYVAVCNFSM6AAAAABBVNQT5WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBUGAZTAMRYHE . You are receiving this because you authored the thread.Message ID: @.***>

conda install -c derkevinriehl -c bioconda transposon_classifier_rfsb Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: | Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package xz conflicts for: transposon_classifier_rfsb -> python -> xz[version='5.0.|5.2.|>=5.2.3,<6.0.0a0|>=5.2.4,<6.0.0a0|>=5.2.5,<6.0.0a0|>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.6,<6.0.0a0|>=5.4.5,<6.0a0|>=5.4.2,<6.0a0|>=5.2.10,<6.0a0|>=5.2.8,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0'] setuptools -> python[version='>=3.7'] -> xz[version='5.0.|5.2.|>=5.2.10,<6.0a0|>=5.2.3,<6.0.0a0|>=5.2.4,<6.0.0a0|>=5.2.5,<6.0.0a0|>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.6,<6.0.0a0|>=5.4.5,<6.0a0|>=5.4.2,<6.0a0|>=5.2.8,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0'] python_abi -> python=3.11 -> xz[version='5.0.|5.2.|>=5.2.10,<6.0a0|>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0|>=5.4.5,<6.0a0|>=5.4.2,<6.0a0|>=5.2.8,<6.0a0|>=5.2.6,<6.0.0a0|>=5.2.5,<6.0.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0.0a0|>=5.2.3,<6.0a0'] python==3.6 -> xz=5.2 wheel -> python[version='>=3.7'] -> xz[version='5.0.|5.2.|>=5.2.10,<6.0a0|>=5.2.3,<6.0.0a0|>=5.2.4,<6.0.0a0|>=5.2.5,<6.0.0a0|>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.6,<6.0.0a0|>=5.4.5,<6.0a0|>=5.4.2,<6.0a0|>=5.2.8,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0'] pip -> python[version='>=3.7'] -> xz[version='5.0.|5.2.|>=5.2.10,<6.0a0|>=5.2.3,<6.0.0a0|>=5.2.4,<6.0.0a0|>=5.2.5,<6.0.0a0|>=5.2.6,<5.3.0a0|>=5.2.6,<6.0a0|>=5.2.6,<6.0.0a0|>=5.4.5,<6.0a0|>=5.4.2,<6.0a0|>=5.2.8,<6.0a0|>=5.2.5,<6.0a0|>=5.2.4,<6.0a0|>=5.2.3,<6.0a0'] xz

Package _libgcc_mutex conflicts for: libgomp -> _libgcc_mutex==0.1[build='conda_forge|main'] openssl -> libgcc-ng[version='>=12'] -> _libgcc_mutex[version='|0.1',build='conda_forge|main|main'] libzlib -> libgcc-ng[version='>=12'] -> _libgcc_mutex[version='|0.1',build='conda_forge|main|main'] tk -> libgcc-ng[version='>=12'] -> _libgcc_mutex[version='|0.1',build='conda_forge|main|main'] libgcc-ng -> _libgcc_mutex[version='|0.1|0.1',build='conda_forge|main|main'] xz -> libgcc-ng[version='>=12'] -> _libgcc_mutex[version='|0.1|0.1',build='conda_forge|main|main'] readline -> libgcc-ng[version='>=12'] -> _libgcc_mutex[version='|0.1',build='conda_forge|main|main'] _openmp_mutex -> _libgcc_mutex==0.1[build='conda_forge|main'] sqlite -> libgcc-ng[version='>=12'] -> _libgcc_mutex[version='|0.1',build='conda_forge|main|main'] ncurses -> libgcc-ng[version='>=12'] -> _libgcc_mutex[version='|0.1',build='conda_forge|main|main'] _libgcc_mutex zlib -> libgcc-ng[version='>=12'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main|main']

Package openssl conflicts for: pip -> python[version='>=3.7'] -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=1.1.1q,<1.1.2a|>=1.1.1s,<1.1.2a|>=3.1.0,<4.0a0|>=3.1.1,<4.0a0|>=3.1.2,<4.0a0|>=3.1.3,<4.0a0|>=3.2.0,<4.0a0|>=3.0.7,<4.0a0|>=3.0.5,<4.0a0|>=3.1.4,<4.0a0|>=3.0.3,<4.0a0|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0|>=3.0.12,<4.0a0|>=3.0.11,<4.0a0|>=3.0.10,<4.0a0|>=1.1.1v,<1.1.2a|>=1.1.1u,<1.1.2a|>=3.0.9,<4.0a0|>=3.0.8,<4.0a0|>=1.1.1t,<1.1.2a|>=1.1.1m,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a'] python==3.6 -> openssl=1.0 openssl transposon_classifier_rfsb -> python -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=1.1.1q,<1.1.2a|>=1.1.1s,<1.1.2a|>=3.1.0,<4.0a0|>=3.1.1,<4.0a0|>=3.1.2,<4.0a0|>=3.1.3,<4.0a0|>=3.2.0,<4.0a0|>=3.0.7,<4.0a0|>=3.0.5,<4.0a0|>=3.1.4,<4.0a0|>=3.0.3,<4.0a0|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0|>=3.0.12,<4.0a0|>=3.0.11,<4.0a0|>=3.0.10,<4.0a0|>=1.1.1v,<1.1.2a|>=1.1.1u,<1.1.2a|>=3.0.9,<4.0a0|>=3.0.8,<4.0a0|>=1.1.1t,<1.1.2a|>=1.1.1m,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a'] python_abi -> python=3.11 -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=1.1.1q,<1.1.2a|>=1.1.1s,<1.1.2a|>=3.1.0,<4.0a0|>=3.1.1,<4.0a0|>=3.1.2,<4.0a0|>=3.1.3,<4.0a0|>=3.2.0,<4.0a0|>=3.0.7,<4.0a0|>=3.0.5,<4.0a0|>=3.0.12,<4.0a0|>=3.0.10,<4.0a0|>=1.1.1v,<1.1.2a|>=1.1.1u,<1.1.2a|>=3.0.9,<4.0a0|>=3.0.8,<4.0a0|>=1.1.1t,<1.1.2a|>=3.1.4,<4.0a0|>=3.0.3,<4.0a0|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0|>=1.1.1m,<1.1.2a|>=3.2.1,<4.0a0|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a'] wheel -> python[version='>=3.7'] -> openssl[version='1.0.|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=1.1.1q,<1.1.2a|>=1.1.1s,<1.1.2a|>=3.1.0,<4.0a0|>=3.1.1,<4.0a0|>=3.1.2,<4.0a0|>=3.1.3,<4.0a0|>=3.2.0,<4.0a0|>=3.0.7,<4.0a0|>=3.0.5,<4.0a0|>=3.1.4,<4.0a0|>=3.0.3,<4.0a0|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0|>=3.0.12,<4.0a0|>=3.0.11,<4.0a0|>=3.0.10,<4.0a0|>=1.1.1v,<1.1.2a|>=1.1.1u,<1.1.2a|>=3.0.9,<4.0a0|>=3.0.8,<4.0a0|>=1.1.1t,<1.1.2a|>=1.1.1m,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a'] setuptools -> python[version='>=3.7'] -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=1.1.1q,<1.1.2a|>=1.1.1s,<1.1.2a|>=3.1.0,<4.0a0|>=3.1.1,<4.0a0|>=3.1.2,<4.0a0|>=3.1.3,<4.0a0|>=3.2.0,<4.0a0|>=3.0.7,<4.0a0|>=3.0.5,<4.0a0|>=3.1.4,<4.0a0|>=3.0.3,<4.0a0|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0|>=3.0.12,<4.0a0|>=3.0.11,<4.0a0|>=3.0.10,<4.0a0|>=1.1.1v,<1.1.2a|>=1.1.1u,<1.1.2a|>=3.0.9,<4.0a0|>=3.0.8,<4.0a0|>=1.1.1t,<1.1.2a|>=1.1.1m,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=3.2.1,<4.0a0|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a']

Package ca-certificates conflicts for: transposon_classifier_rfsb -> python -> ca-certificates setuptools -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates python_abi -> python=2.7 -> ca-certificates wheel -> python[version='!=3.0,!=3.1,!=3.2,!=3.3,!=3.4'] -> ca-certificates openssl -> ca-certificates pip -> python -> ca-certificates ca-certificates python==3.6 -> openssl=1.0 -> ca-certificates

Package libstdcxx-ng conflicts for: sqlite -> libstdcxx-ng[version='>=4.9|>=7.3.0'] _openmp_mutex -> llvm-openmp[version='>=9.0.1'] -> libstdcxx-ng[version='>=7.3.0'] python_abi -> python=3.9 -> libstdcxx-ng[version='>=11.2.0|>=7.5.0|>=9.3.0|>=7.3.0|>=9.4.0|>=4.9|>=7.2.0'] sqlite -> ncurses[version='>=6.2,<7.0.0a0'] -> libstdcxx-ng[version='>=7.2.0|>=7.5.0'] setuptools -> python[version='>=3.7'] -> libstdcxx-ng[version='>=11.2.0|>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0'] ncurses -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=7.2.0'] readline -> ncurses[version='>=6.2,<7.0.0a0'] -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=7.2.0'] transposon_classifier_rfsb -> biopython -> libstdcxx-ng[version='>=10.3.0|>=12|>=7.2.0|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0'] wheel -> python[version='>=3.7'] -> libstdcxx-ng[version='>=11.2.0|>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0'] pip -> python[version='>=3.7'] -> libstdcxx-ng[version='>=11.2.0|>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0']

Package libgomp conflicts for: libgcc-ng -> _openmp_mutex[version='>=4.5'] -> libgomp[version='>=7.3.0|>=7.5.0'] _openmp_mutex -> libgomp[version='>=7.3.0|>=7.5.0'] libgomp

Package libzlib conflicts for: pip -> python[version='>=3.7'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0'] sqlite -> zlib[version='>=1.2.12,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13|1.3',build='h36c2ea0_1013|h166bdaf_1014|h166bdaf_4|h166bdaf_4|hd590300_5|h166bdaf_3|h166bdaf_2|h166bdaf_1|h166bdaf_0|h36c2ea0_1012|hd590300_0'] tk -> zlib[version='>=1.2.11,<1.3.0a0'] -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h36c2ea0_1013|h166bdaf_1014|h166bdaf_4|h166bdaf_4|hd590300_5|h166bdaf_3|h166bdaf_2|h166bdaf_1|h166bdaf_0|h36c2ea0_1012'] libzlib python_abi -> python=3.11 -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0'] setuptools -> python[version='>=3.7'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0'] zlib -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13|1.2.13|1.3',build='h36c2ea0_1012|h36c2ea0_1013|h166bdaf_0|h166bdaf_2|h166bdaf_4|h166bdaf_4|hd590300_5|hd590300_0|h166bdaf_3|h166bdaf_1|h166bdaf_1014'] tk -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.13,<1.3.0a0'] wheel -> python[version='>=3.7'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0'] sqlite -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0'] _openmp_mutex -> llvm-openmp[version='>=9.0.1'] -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.13,<1.3.0a0'] transposon_classifier_rfsb -> blast -> libzlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0'] python==3.6 -> zlib=1.2 -> libzlib[version='1.2.11|1.2.11|1.2.11|1.2.12|1.2.12|1.2.12|1.2.12|1.2.12|1.2.13',build='h36c2ea0_1013|h166bdaf_1014|h166bdaf_4|h166bdaf_4|hd590300_5|h166bdaf_3|h166bdaf_2|h166bdaf_1|h166bdaf_0|h36c2ea0_1012']

Package libsqlite conflicts for: pip -> python[version='>=3.7'] -> libsqlite[version='>=3.39.2,<4.0a0|>=3.39.4,<4.0a0|>=3.40.0,<4.0a0|>=3.42.0,<4.0a0|>=3.43.0,<4.0a0|>=3.44.2,<4.0a0|>=3.43.2,<4.0a0|>=3.41.2,<4.0a0'] wheel -> python[version='>=3.7'] -> libsqlite[version='>=3.39.2,<4.0a0|>=3.39.4,<4.0a0|>=3.40.0,<4.0a0|>=3.42.0,<4.0a0|>=3.43.0,<4.0a0|>=3.44.2,<4.0a0|>=3.43.2,<4.0a0|>=3.41.2,<4.0a0'] sqlite -> libsqlite[version='3.39.2|3.39.3|3.39.4|3.40.0|3.40.0|3.41.2|3.42.0|3.43.0|3.43.2|3.44.0|3.44.1|3.44.2|3.45.1',build='h753d276_0|h753d276_0|h753d276_0|h2797004_0|h2797004_1|h753d276_1|h753d276_1'] setuptools -> python[version='>=3.7'] -> libsqlite[version='>=3.39.2,<4.0a0|>=3.39.4,<4.0a0|>=3.40.0,<4.0a0|>=3.42.0,<4.0a0|>=3.43.0,<4.0a0|>=3.44.2,<4.0a0|>=3.43.2,<4.0a0|>=3.41.2,<4.0a0'] python_abi -> python=3.11 -> libsqlite[version='>=3.39.2,<4.0a0|>=3.39.4,<4.0a0|>=3.40.0,<4.0a0|>=3.42.0,<4.0a0|>=3.43.0,<4.0a0|>=3.44.2,<4.0a0|>=3.43.2,<4.0a0|>=3.41.2,<4.0a0'] transposon_classifier_rfsb -> blast -> libsqlite[version='>=3.39.2,<4.0a0|>=3.39.4,<4.0a0|>=3.40.0,<4.0a0|>=3.42.0,<4.0a0|>=3.43.0,<4.0a0|>=3.44.0,<4.0a0|>=3.44.2,<4.0a0|>=3.43.2,<4.0a0|>=3.41.2,<4.0a0']

Package libgcc-ng conflicts for: tk -> libzlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=10.3.0|>=11.2.0'] openssl -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0'] sqlite -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0'] pip -> python[version='>=3.7'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0'] libgcc-ng tk -> libgcc-ng[version='>=12|>=9.4.0|>=7.5.0|>=7.3.0|>=4.9|>=7.2.0'] xz -> libgcc-ng[version='>=11.2.0|>=12|>=7.5.0|>=7.3.0|>=4.9|>=7.2.0'] python_abi -> python=3.11 -> libgcc-ng[version='>=10.3.0|>=11.2.0|>=12|>=9.4.0|>=7.5.0|>=9.3.0|>=7.3.0|>=4.9|>=7.2.0'] python==3.6 -> openssl=1.0 -> libgcc-ng[version='>=10.3.0|>=11.2.0|>=12|>=4.9|>=7.3.0|>=7.2.0|>=7.5.0'] libzlib -> libgcc-ng[version='>=10.3.0|>=12|>=7.5.0'] _openmp_mutex -> llvm-openmp[version='>=9.0.1'] -> libgcc-ng[version='>=7.3.0'] zlib -> libgcc-ng[version='>=10.3.0|>=12|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0'] setuptools -> python[version='>=3.7'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0'] wheel -> python[version='>=3.7'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0'] transposon_classifier_rfsb -> biopython -> libgcc-ng[version='>=10.3.0|>=11.2.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=7.2.0'] readline -> libgcc-ng[version='>=11.2.0|>=12|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=7.2.0'] readline -> ncurses[version='>=6.3,<7.0a0'] -> libgcc-ng[version='>=10.3.0|>=9.4.0'] ncurses -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0']

Package ncurses conflicts for: transposon_classifier_rfsb -> python -> ncurses[version='5.9.|5.9|>=6.1,<7.0.0a0|>=6.2,<6.3.0a0|>=6.3,<7.0a0|>=6.4,<7.0a0|>=6.2,<7.0.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.'] sqlite -> readline[version='>=8.0,<9.0a0'] -> ncurses[version='6.0.|>=6.0,<7.0a0|>=6.1,<7.0a0'] sqlite -> ncurses[version='5.9|5.9.|>=6.1,<7.0.0a0|>=6.2,<7.0.0a0|>=6.3,<7.0a0|>=6.4,<7.0a0|>=6.2,<7.0a0'] python==3.6 -> ncurses=5.9 wheel -> python[version='>=3.7'] -> ncurses[version='5.9.|5.9|>=6.1,<7.0.0a0|>=6.2,<6.3.0a0|>=6.3,<7.0a0|>=6.4,<7.0a0|>=6.2,<7.0.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.'] pip -> python[version='>=3.7'] -> ncurses[version='5.9.|5.9|>=6.1,<7.0.0a0|>=6.2,<6.3.0a0|>=6.3,<7.0a0|>=6.4,<7.0a0|>=6.2,<7.0.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.'] readline -> ncurses[version='5.9.|>=6.1,<7.0.0a0|>=6.2,<7.0.0a0|>=6.3,<7.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.'] ncurses python_abi -> python=3.11 -> ncurses[version='5.9.|5.9|>=6.1,<7.0.0a0|>=6.2,<6.3.0a0|>=6.3,<7.0a0|>=6.4,<7.0a0|>=6.2,<7.0.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.'] setuptools -> python[version='>=3.7'] -> ncurses[version='5.9.|5.9|>=6.1,<7.0.0a0|>=6.2,<6.3.0a0|>=6.3,<7.0a0|>=6.4,<7.0a0|>=6.2,<7.0.0a0|>=6.2,<7.0a0|>=6.1,<7.0a0|>=6.0,<7.0a0|6.0.']

Package certifi conflicts for: wheel -> setuptools -> certifi[version='>=2016.09|>=2016.9.26'] pip -> setuptools -> certifi[version='>=2016.09|>=2016.9.26'] setuptools -> certifi[version='>=2016.09|>=2016.9.26']

Package packaging conflicts for: pip -> wheel -> packaging[version='>=20.2'] wheel -> packaging[version='>=20.2']

Package wheel conflicts for: pip -> wheel python==3.6 -> pip -> wheel wheel

Package zlib conflicts for: python_abi -> python=3.11 -> zlib[version='1.2.|1.2.11|>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0|1.2.8|1.2.11.'] python==3.6 -> zlib=1.2 zlib pip -> python[version='>=3.7'] -> zlib[version='1.2.|1.2.11|>=1.2.11,<1.3.0a0|>=1.2.13,<1.3.0a0|>=1.2.12,<1.3.0a0|1.2.8|1.2.11.'] tk -> zlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0'] sqlite -> zlib[version='>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0|>=1.2.13,<2.0a0'] _openmp_mutex -> llvm-openmp[version='>=9.0.1'] -> zlib[version='>=1.2.12,<1.3.0a0'] wheel -> python[version='>=3.7'] -> zlib[version='1.2.|1.2.11|>=1.2.11,<1.3.0a0|>=1.2.13,<1.3.0a0|>=1.2.12,<1.3.0a0|1.2.8|1.2.11.'] setuptools -> python[version='>=3.7'] -> zlib[version='1.2.|1.2.11|>=1.2.11,<1.3.0a0|>=1.2.13,<1.3.0a0|>=1.2.12,<1.3.0a0|1.2.8|1.2.11.'] transposon_classifier_rfsb -> blast -> zlib[version='1.2.|1.2.11|1.2.11.|>=1.2.11,<1.3.0a0|>=1.2.12,<1.3.0a0|>=1.2.13,<1.3.0a0|1.2.8.*|1.2.8']

Package sqlite conflicts for: setuptools -> python[version='>=3.7'] -> sqlite[version='3.13.|3.20.|>=3.24.0,<4.0a0|>=3.25.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.30.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|>=3.37.0,<4.0a0|>=3.37.1,<4.0a0|>=3.38.5,<4.0a0|>=3.41.2,<4.0a0|>=3.41.1,<4.0a0|>=3.40.1,<4.0a0|>=3.40.0,<4.0a0|>=3.39.3,<4.0a0|>=3.38.0,<4.0a0|>=3.37.2,<4.0a0|>=3.39.2,<4.0a0|>=3.38.3,<4.0a0|>=3.38.2,<4.0a0|>=3.35.4,<4.0a0|>=3.31.1,<4.0a0|>=3.30.0,<4.0a0|>=3.29.0,<4.0a0|>=3.27.2,<4.0a0|>=3.39.1,<4.0a0|>=3.23.1,<4.0a0|>=3.22.0,<4.0a0|>=3.20.1,<4.0a0|3.9.'] transposon_classifier_rfsb -> python -> sqlite[version='3.13.|3.20.|>=3.24.0,<4.0a0|>=3.25.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.30.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|>=3.37.0,<4.0a0|>=3.37.1,<4.0a0|>=3.38.5,<4.0a0|3.9.|>=3.41.2,<4.0a0|>=3.41.1,<4.0a0|>=3.40.1,<4.0a0|>=3.40.0,<4.0a0|>=3.39.3,<4.0a0|>=3.38.0,<4.0a0|>=3.37.2,<4.0a0|>=3.39.2,<4.0a0|>=3.38.3,<4.0a0|>=3.38.2,<4.0a0|>=3.35.4,<4.0a0|>=3.31.1,<4.0a0|>=3.30.0,<4.0a0|>=3.29.0,<4.0a0|>=3.27.2,<4.0a0|>=3.23.1,<4.0a0|>=3.22.0,<4.0a0|>=3.20.1,<4.0a0'] python==3.6 -> sqlite=3.13 pip -> python[version='>=3.7'] -> sqlite[version='3.13.|3.20.|>=3.24.0,<4.0a0|>=3.25.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.30.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|>=3.37.0,<4.0a0|>=3.37.1,<4.0a0|>=3.38.5,<4.0a0|>=3.41.2,<4.0a0|>=3.41.1,<4.0a0|>=3.40.1,<4.0a0|>=3.40.0,<4.0a0|>=3.39.3,<4.0a0|>=3.38.0,<4.0a0|>=3.37.2,<4.0a0|>=3.39.2,<4.0a0|>=3.38.3,<4.0a0|>=3.38.2,<4.0a0|>=3.35.4,<4.0a0|>=3.31.1,<4.0a0|>=3.30.0,<4.0a0|>=3.29.0,<4.0a0|>=3.27.2,<4.0a0|>=3.23.1,<4.0a0|>=3.22.0,<4.0a0|>=3.20.1,<4.0a0|3.9.'] sqlite wheel -> python[version='>=3.7'] -> sqlite[version='3.13.|3.20.|>=3.24.0,<4.0a0|>=3.25.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.30.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|>=3.37.0,<4.0a0|>=3.37.1,<4.0a0|>=3.38.5,<4.0a0|>=3.41.2,<4.0a0|>=3.41.1,<4.0a0|>=3.40.1,<4.0a0|>=3.40.0,<4.0a0|>=3.39.3,<4.0a0|>=3.38.0,<4.0a0|>=3.37.2,<4.0a0|>=3.39.2,<4.0a0|>=3.38.3,<4.0a0|>=3.38.2,<4.0a0|>=3.35.4,<4.0a0|>=3.31.1,<4.0a0|>=3.30.0,<4.0a0|>=3.29.0,<4.0a0|>=3.27.2,<4.0a0|3.9.|>=3.23.1,<4.0a0|>=3.22.0,<4.0a0|>=3.20.1,<4.0a0'] python_abi -> python=3.11 -> sqlite[version='3.13.|3.20.|>=3.24.0,<4.0a0|>=3.25.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.30.0,<4.0a0|>=3.30.1,<4.0a0|>=3.32.3,<4.0a0|>=3.33.0,<4.0a0|>=3.34.0,<4.0a0|>=3.35.5,<4.0a0|>=3.36.0,<4.0a0|>=3.37.0,<4.0a0|>=3.37.1,<4.0a0|>=3.38.5,<4.0a0|>=3.40.1,<4.0a0|>=3.41.1,<4.0a0|>=3.41.2,<4.0a0|>=3.40.0,<4.0a0|>=3.39.3,<4.0a0|>=3.38.0,<4.0a0|>=3.37.2,<4.0a0|>=3.39.2,<4.0a0|>=3.39.1,<4.0a0|>=3.38.2,<4.0a0|>=3.38.3,<4.0a0|>=3.35.4,<4.0a0|>=3.31.1,<4.0a0|>=3.29.0,<4.0a0|>=3.27.2,<4.0a0|>=3.23.1,<4.0a0|>=3.22.0,<4.0a0|>=3.20.1,<4.0a0|3.9.*']

Package tk conflicts for: setuptools -> python[version='>=3.7'] -> tk[version='8.5.|8.6.|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.12,<8.7.0a0|>=8.6.13,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0'] tk python==3.6 -> tk=8.5 python_abi -> python=3.11 -> tk[version='8.5.|8.6.|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.12,<8.7.0a0|>=8.6.13,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0'] transposon_classifier_rfsb -> matplotlib -> tk[version='8.5.|8.6.|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0|>=8.6.13,<8.7.0a0|>=8.6.12,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.10,<8.7.0a0|>=8.6.9,<8.7.0a0'] wheel -> python[version='>=3.7'] -> tk[version='8.5.|8.6.|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.12,<8.7.0a0|>=8.6.13,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0'] pip -> python[version='>=3.7'] -> tk[version='8.5.|8.6.|>=8.6.10,<8.7.0a0|>=8.6.11,<8.7.0a0|>=8.6.12,<8.7.0a0|>=8.6.13,<8.7.0a0|>=8.6.9,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.7,<8.7.0a0']

Package pip conflicts for: transposon_classifier_rfsb -> python -> pip setuptools -> python[version='>=3.7'] -> pip python_abi -> python=3.11 -> pip pip wheel -> python[version='>=3.7'] -> pip python==3.6 -> pip

Package pyparsing conflicts for: transposon_classifier_rfsb -> matplotlib -> pyparsing wheel -> packaging[version='>=20.2'] -> pyparsing[version='<3,>=2.0.2|>=2.0.2,!=3.0.5|>=2.0.2,<3|>=2.0.2']

Package _openmp_mutex conflicts for: openssl -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] libzlib -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] libgcc-ng -> _openmp_mutex[version='>=4.5'] zlib -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] xz -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] transposon_classifier_rfsb -> scikit-learn -> _openmp_mutex[version='>=4.5'] readline -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] _openmp_mutex ncurses -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] sqlite -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] tk -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5']

Package setuptools conflicts for: pip -> setuptools python==3.6 -> pip -> setuptools setuptools transposon_classifier_rfsb -> matplotlib -> setuptools wheel -> setuptools

Package python_abi conflicts for: wheel -> python[version='>=3.7'] -> python_abi[version='3.10.|3.10.|3.9|3.8|3.8.|3.7|3.6|3.9.|3.7.|3.8.|3.11.|3.6.',build='_cp36m|_cp311|_cp38|_cp37m|_cp39|_pypy37_pp73|_pypy38_pp73|_graalpy230_310_native|_pypy39_pp73|_graalpy223_38_native|_pypy36_pp73|_cp310'] setuptools -> python_abi[version='3.10.|3.7.|3.9.|3.9|3.8.|3.8|3.7|3.11.|3.6.|3.6',build='_cp36m|_pypy37_pp73|_cp38|_cp310|_cp37m|_cp39|_pypy39_pp73|_pypy38_pp73|_cp311|_pypy36_pp73'] pip -> python[version='>=3.7'] -> python_abi[version='3.10.|3.10.|3.9|3.8|3.8.|3.7|3.9.|3.7.|3.8.|3.11.|3.6.|3.6',build='_cp36m|_cp311|_cp38|_cp37m|_cp39|_pypy37_pp73|_pypy38_pp73|_graalpy230_310_native|_pypy39_pp73|_graalpy223_38_native|_cp310|_pypy36_pp73'] transposon_classifier_rfsb -> biopython -> python_abi[version='3.10.|3.10.|3.11.|3.12.|3.8.|3.9.|3.9|3.8|3.7.|3.7|3.6.|3.6|3.8.',build='_graalpy230_310_native|_cp36m|_cp37m|_pypy38_pp73|_cp39|_cp311|_cp38|_cp312|_cp310|_pypy39_pp73|_pypy37_pp73|_pypy36_pp73|_graalpy223_38_native'] python_abi setuptools -> python[version='>=3.7'] -> python_abi[version='2.7.|3.10.|3.8.',build='_graalpy230_310_native|_graalpy223_38_native|_cp27mu']

Package readline conflicts for: sqlite -> readline[version='6.2.|7.0|7.0.|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0'] setuptools -> python[version='>=3.7'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|7.|7.0.'] readline python==3.6 -> readline=6.2 transposon_classifier_rfsb -> python -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|7.0.|7.'] pip -> python[version='>=3.7'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|7.|7.0.'] wheel -> python[version='>=3.7'] -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|7.0.|7.'] python_abi -> python=3.11 -> readline[version='6.2.|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0|>=8.1.2,<9.0a0|>=8.2,<9.0a0|>=8.1,<9.0a0|7.|7.0.*']

Package _python_rc conflicts for: setuptools -> python[version='>=3.7'] -> _python_rc transposon_classifier_rfsb -> python -> _python_rc wheel -> python[version='>=3.7'] -> _python_rc pip -> python[version='>=3.7'] -> _python_rc

Package llvm-openmp conflicts for: _openmp_mutex -> llvm-openmp[version='>=9.0.1'] libgcc-ng -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1']

Package xorg-libx11 conflicts for: python_abi -> pypy3.9=7.3 -> xorg-libx11[version='>=1.8.4,<2.0a0|>=1.8.6,<2.0a0|>=1.8.7,<2.0a0'] setuptools -> pypy3.9[version='>=7.3.9'] -> xorg-libx11[version='>=1.8.4,<2.0a0|>=1.8.6,<2.0a0|>=1.8.7,<2.0a0']The following specifications were found to be incompatible with your system:

Your installed version is: 2.28

Note that strict channel priority may have removed packages required for satisfiability.

DerKevinRiehl commented 9 months ago

Hi Matthew, okay, maybe you can tell me what operating system you are using.

I tried myself and I found that the conda package management system says it has conflicts but dont tell me which on my machine:

(base) C:\>conda activate rfsb

(rfsb) C:\> conda install derkevinriehl::transposon_classifier_rfsb
Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

(rfsb) C:\>

The big issue here is I packaged my software with a package manager so you dont have the troubles that you are currently experiencing with installation. It seems that conda servers changed and now many packages are not running installation anymore.

Here what I did to install without conda just directly from my GitHub: (Just make sure blast is installed on your system before these steps, and command rpstblastn must be available from your terminal**)

conda create --name rfsb python==3.6.13
conda activate rfsb

pip install biopython
pip install scikit-learn
pip install matplotlib

git clone https://github.com/DerKevinRiehl/transposon_classifier_rfsb.git

cd transposon_classifier_rfsb

Then in the same folder you try to run this command:

python RFSB_TE_Classifier.py --help

And then this command:

python RFSB_TE_Classifier.py -mode classify -fastaFile demoFiles/demo1_seq.fasta -outputPredictionFile demoFiles/demo1_results.txt

Honestly, I also dont have a Linux machine at the moment where I have the right to install blast to fully reproduce the error...

Hope this helps and solved the issue?

Best, Kevin

matthew-ackerman commented 9 months ago

This worked, thank you! If this ever gets put into a paper we'll be sure to cite you!

-Matt

On Thu, Feb 15, 2024 at 3:12 AM DerKevinRiehl @.***> wrote:

Hi Matthew, okay, maybe you can tell me what operating system you are using.

I tried myself and I found that the conda package management system says it has conflicts but dont tell me which on my machine:

(base) C:>conda activate rfsb

(rfsb) C:> conda install derkevinriehl::transposon_classifier_rfsb Collecting package metadata (current_repodata.json): done Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve. Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source. Collecting package metadata (repodata.json): done Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve. Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

(rfsb) C:>

The big issue here is I packaged my software with a package manager so you dont have the troubles that you are currently experiencing with installation. It seems that conda servers changed and now many packages are not running installation anymore.

Here what I did to install without conda just directly from my GitHub: (Just make sure blast is installed on your system before these steps, and command rpstblastn must be available from your terminal**)

conda create --name rfsb python==3.6.13 conda activate rfsb

pip install biopython pip install scikit-learn pip install matplotlib

git clone https://github.com/DerKevinRiehl/transposon_classifier_rfsb.git

cd transposon_classifier_rfsb

Then in the same folder you try to run this command:

python RFSB_TE_Classifier.py --help

And then this command:

python RFSB_TE_Classifier.py -mode classify -fastaFile demoFiles/demo1_seq.fasta -outputPredictionFile demoFiles/demo1_results.txt

Honestly, I also dont have a Linux machine at the moment where I have the right to install blast to fully reproduce the error...

Best, Kevin

— Reply to this email directly, view it on GitHub https://github.com/DerKevinRiehl/TransposonUltimate/issues/14#issuecomment-1945660742, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACRUFWPN5KZXULTTS4O6GLYTXGQHAVCNFSM6AAAAABBVNQT5WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBVGY3DANZUGI . You are receiving this because you authored the thread.Message ID: @.***>

DerKevinRiehl commented 9 months ago

Dear Matthew, so happy to hear. Wish you good luck and thanks for using TransposonUltimaTE. Cites are always welcome ;-).

Best, Kevin

matthew-ackerman commented 8 months ago

Sorry to bother you again, but I was trying to use the reasonaTE pipeline, because I wanted to use deTEct, and I ran into a few issues. When reasonaTE -mode parseAnnotations was running, all the annotations from reasonaTE -mode annotate -tool must had 23 fields, where the tool AnnotationParser.py checks the 24th field to see if it is equal to the string "Full Copy", and since this field is not present in must's annotations it caused the script to stop. I went ahead and just labeled all transcripts with only 23 fields as incomplete and the script continued, and then when running reasonaTE -mode pipeline it complained that I didn't have SeqKit, which was easy enough to download, but pipeline produces the error:

Transposon Sequences sorted...

Traceback (most recent call last): File "/home/matthew/.conda/envs/tu/share/TransposonAnnotator_reasonaTE/TransposonAnnotator.py", line 160, in

doTransposonClustering(os.path.join(arg1,arg2,"transposonCandB"),os.path.join(arg1,arg2,"transposonCandC"),os.path.join(arg1,arg2,"sequence.fasta")) File "/home/matthew/.conda/envs/tu/share/TransposonAnnotator_reasonaTE/TransposonClustering.py", line 186, in doTransposonClustering transpIDs.append(["transposon"+str(cluster[0]),key]) IndexError: list index out of range

before it finishing generating its files. Any idea why or what workaround I could use?

On Mon, Feb 26, 2024 at 3:58 PM DerKevinRiehl @.***> wrote:

Closed #14 https://github.com/DerKevinRiehl/TransposonUltimate/issues/14 as completed.

— Reply to this email directly, view it on GitHub https://github.com/DerKevinRiehl/TransposonUltimate/issues/14#event-11928157710, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACRUFSXYC5EXITJMXKFYRTYVUAQ7AVCNFSM6AAAAABBVNQT5WVHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJRHEZDQMJVG43TCMA . You are receiving this because you authored the thread.Message ID: @.*** com>

DerKevinRiehl commented 8 months ago

Dear Matthew, someone else contacted me with exact this same error recently. The issue is, that your must version is different from the one it should be, and therefore the output format is different from when I developed the software. You must make sure installed must has the right version.

Best, Kevin

matthew-ackerman commented 8 months ago

If I really buckled down and got everything working would you be interested in adding a docker installation of TransposonUltimate to your repository? I've had great luck with singularity/docker and it might be a nice alternative for people, like me, who can't follow complex installation instructions. I'd do everything, just wanted to know if you'd be willing to add the alternative install to your README.md.

-Matt

On Sat, Mar 16, 2024 at 6:46 AM DerKevinRiehl @.***> wrote:

Dear Matthew, someone else contacted me with exact this same error recently. The issue is, that your must version is different from the one it should be, and therefore the output format is different from when I developed the software. You must make sure installed must has the right version.

Best, Kevin

— Reply to this email directly, view it on GitHub https://github.com/DerKevinRiehl/TransposonUltimate/issues/14#issuecomment-2001960824, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACRUFXNHNUJPKQVVC2SKCDYYQWHRAVCNFSM6AAAAABBVNQT5WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBRHE3DAOBSGQ . You are receiving this because you authored the thread.Message ID: @.***>

DerKevinRiehl commented 8 months ago

Dear Matthew, indeed that could be interesting, however not everyone can run docker in their cluster environment, and there are other challenges such as loading large amounts of data into the docker system.

I guess, maybe when I have some more time, I could offer a Docker Version in future as an alternative to the manual installation process.

Thanks for your suggestion.

Best, Kevin