Cannot get pharokka databases installed

[Jlee795]

• pharokka version: 1.5
• Python version: 3.7.3
• Operating System: linux cluster

Description

Trying to install the latest version of pharokka 1.5 and conda installs weren't working. Tried using micromamba and that still hasn't worked. went through a git clone and someone sent a yml file, still can't get the databases installed (see commands and errors below).

What I Did

pip install -e .

Obtaining file:///home/crk_w19039039/pharokka Collecting setuptools>=67.7.2 (from Pharokka==1.5.1) Using cached https://files.pythonhosted.org/packages/c7/42/be1c7bbdd83e1bfb160c94b9cafd8e25efc7400346cf7ccdbdb452c467fa/setuptools-68.0.0-py3-none-any.whl Collecting loguru>=0.5.4 (from Pharokka==1.5.1) Cache entry deserialization failed, entry ignored Using cached https://files.pythonhosted.org/packages/03/0a/4f6fed21aa246c6b49b561ca55facacc2a44b87d65b8b92362a8e99ba202/loguru-0.7.2-py3-none-any.whl Collecting pyyaml>=6.0 (from Pharokka==1.5.1) Cache entry deserialization failed, entry ignored Downloading https://files.pythonhosted.org/packages/cd/e5/af35f7ea75cf72f2cd079c95ee16797de7cd71f29ea7c68ae5ce7be1eda0/PyYAML-6.0.1.tar.gz (125kB) 100% |████████████████████████████████| 133kB 4.7MB/s Cache entry deserialization failed, entry ignored Installing build dependencies ... done Collecting pandas>=1.4.2 (from Pharokka==1.5.1) Could not find a version that satisfies the requirement pandas>=1.4.2 (from Pharokka==1.5.1) (from versions: 0.1, 0.2, 0.3.0, 0.4.0, 0.4.1, 0.4.2, 0.4.3, 0.5.0, 0.6.0, 0.6.1, 0.7.0, 0.7.1, 0.7.2, 0.7.3, 0.8.0, 0.8.1, 0.9.0, 0.9.1, 0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.13.0, 0.13.1, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.15.2, 0.16.0, 0.16.1, 0.16.2, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 0.19.2, 0.20.0, 0.20.1, 0.20.2, 0.20.3, 0.21.0, 0.21.1, 0.22.0, 0.23.0, 0.23.1, 0.23.2, 0.23.3, 0.23.4, 0.24.0, 0.24.1, 0.24.2, 0.25.0, 0.25.1, 0.25.2, 0.25.3, 1.0.0, 1.0.1, 1.0.2, 1.0.3, 1.0.4, 1.0.5, 1.1.0, 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.1.5, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.2.4, 1.2.5, 1.3.0, 1.3.1, 1.3.2, 1.3.3, 1.3.4, 1.3.5) No matching distribution found for pandas>=1.4.2 (from Pharokka==1.5.1)

did this command:

install_databases.py -d Traceback (most recent call last): File "/home/crk_w19039039/pharokka/bin/install_databases.py", line 7, in from databases import instantiate_install File "/home/crk_w19039039/pharokka/bin/databases.py", line 30, in from alive_progress import alive_bar ModuleNotFoundError: No module named 'alive_progress'

so did this: pip install alive-progress

Collecting alive-progress Cache entry deserialization failed, entry ignored Using cached https://files.pythonhosted.org/packages/d5/81/91e164705bdf4e2774cea59f566a41ab25f3c87affd716516fc8b03a4039/alive_progress-3.1.5-py3-none-any.whl Collecting about-time==4.2.1 (from alive-progress) Cache entry deserialization failed, entry ignored Using cached https://files.pythonhosted.org/packages/fb/cd/7ee00d6aa023b1d0551da0da5fee3bc23c3eeea632fbfc5126d1fec52b7e/about_time-4.2.1-py3-none-any.whl Collecting grapheme==0.6.0 (from alive-progress) Cache entry deserialization failed, entry ignored Using cached https://files.pythonhosted.org/packages/ce/e7/bbaab0d2a33e07c8278910c1d0d8d4f3781293dfbc70b5c38197159046bf/grapheme-0.6.0.tar.gz Building wheels for collected packages: grapheme Running setup.py bdist_wheel for grapheme ... done Stored in directory: /home/crk_w19039039/.cache/pip/wheels/1e/f7/2c/341b06952dda321b8550d9ebd573dff4c0640fa710d9f23ecd Successfully built grapheme twisted 18.7.0 requires PyHamcrest>=1.9.0, which is not installed. conda 4.12.0 requires ruamel_yaml_conda>=0.11.14, which is not installed. Installing collected packages: about-time, grapheme, alive-progress Could not install packages due to an EnvironmentError: [Errno 13] Permission denied: '/cm/shared/crick-apps/anaconda3/5.3.1/lib/python3.7/site-packages/about_time' Consider using the --user option or check the permissions.

went back to trying to install databases:

install_databases.py -d

Traceback (most recent call last): File "/home/crk_w19039039/pharokka/bin/install_databases.py", line 7, in from databases import instantiate_install File "/home/crk_w19039039/pharokka/bin/databases.py", line 30, in from alive_progress import alive_bar ModuleNotFoundError: No module named 'alive_progress'

don't know what to do with this

Paste the command(s) you ran and the output.
If there was a crash, please include the traceback here.

[gbouras13]

Hi @Jlee795 ,

This looks like a system issue for you. I'm not sure I can really help too much, it doesn't seem to be a problem with pharokka.

If you can't install things with pip e.g. pip install alive-progress fails, then there is a much deeper issue than conda or pharokka.

Based on the error messages

Permission denied: '/cm/shared/crick-apps/anaconda3/5.3.1/lib/python3.7/site-packages/about_time'
Consider using the --user option or check the permissions.

You might be lacking some permissions on your cluster. I'd contact the systems administrator for some advice.

George

[Jlee795]

Hi gbouras13, someone suggested it might be an issue with perl modules and then suggested me to do the following command:

export PERL5LIB=

I did this and I don't get the error I got above now but I get this one

Traceback (most recent call last): File "/home/crk_w19039039/pharokka/bin/pharokka.py", line 9, in from custom_db import run_custom_pyhmmer File "/home/crk_w19039039/pharokka/bin/custom_db.py", line 4, in import pyhmmer ModuleNotFoundError: No module named 'pyhmmer'

Tried installing it with the following output:

conda install pyhmmer Collecting package metadata (repodata.json): done Solving environment: done

All requested packages already installed.

so looks like pyhmmer installed, then I tried the pip -e . command again which seemed to work and the databases seemed to go in ok to but when I tried to execute a test on some data I got the same traceback error again:

Traceback (most recent call last): File "/home/crk_w19039039/pharokka/bin/pharokka.py", line 9, in from custom_db import run_custom_pyhmmer File "/home/crk_w19039039/pharokka/bin/custom_db.py", line 4, in import pyhmmer ModuleNotFoundError: No module named 'pyhmmer'

and pyhmmer is definitely in the environment (below is a list of environment dependencies):

packages in environment at /home/crk_w19039039/.conda/envs/pharokka:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge about-time 4.2.1 pyhd8ed1ab_0 conda-forge alive-progress 3.1.5 pyhd8ed1ab_0 conda-forge aragorn 1.2.41 h031d066_1 bioconda archspec 0.2.2 pyhd8ed1ab_0 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.tempfile 1.0 py_0 conda-forge backports.weakref 1.0.post1 pyhd8ed1ab_1003 conda-forge bcbio-gff 0.7.0 pyh7cba7a3_0 bioconda biopython 1.81 py310h2372a71_1 conda-forge black 23.10.1 py310hff52083_0 conda-forge blast 2.15.0 pl5321h6f7f691_1 bioconda brotli 1.1.0 hd590300_1 conda-forge brotli-bin 1.1.0 hd590300_1 conda-forge brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge bx-python 0.10.0 py310h551a815_0 bioconda bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.22.1 hd590300_0 conda-forge ca-certificates 2023.11.17 hbcca054_0 conda-forge capnproto 0.9.1 ha19adfc_4 conda-forge certifi 2023.11.17 pyhd8ed1ab_0 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge click 8.1.7 unix_pyh707e725_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge contourpy 1.2.0 py310hd41b1e2_0 conda-forge coverage 7.3.2 py310h2372a71_0 conda-forge curl 8.4.0 hca28451_0 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge dnaapler 0.4.0 pyhdfd78af_0 bioconda entrez-direct 16.2 he881be0_1 bioconda exceptiongroup 1.1.3 pyhd8ed1ab_0 conda-forge fastpath 1.9 py310h2372a71_3 conda-forge fonttools 4.44.3 py310h2372a71_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge gawk 5.3.0 ha916aea_0 conda-forge gettext 0.21.1 h27087fc_0 conda-forge gmp 6.3.0 h59595ed_0 conda-forge grapheme 0.6.0 pyhd8ed1ab_0 conda-forge gsl 2.7 he838d99_0 conda-forge icu 70.1 h27087fc_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge infernal 1.1.4 pl5321h031d066_4 bioconda iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge isort 5.12.0 pyhd8ed1ab_1 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 py310hd41b1e2_1 conda-forge krb5 1.21.2 h659d440_0 conda-forge lcms2 2.15 hb7c19ff_3 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libblas 3.9.0 19_linux64_openblas conda-forge libbrotlicommon 1.1.0 hd590300_1 conda-forge libbrotlidec 1.1.0 hd590300_1 conda-forge libbrotlienc 1.1.0 hd590300_1 conda-forge libcblas 3.9.0 19_linux64_openblas conda-forge libcurl 8.4.0 hca28451_0 conda-forge libdeflate 1.19 hd590300_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 13.2.0 h807b86a_3 conda-forge libgfortran-ng 13.2.0 h69a702a_3 conda-forge libgfortran5 13.2.0 ha4646dd_3 conda-forge libgomp 13.2.0 h807b86a_3 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libidn2 2.3.4 h166bdaf_0 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge liblapack 3.9.0 19_linux64_openblas conda-forge libnghttp2 1.58.0 h47da74e_0 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.24 pthreads_h413a1c8_0 conda-forge libpng 1.6.39 h753d276_0 conda-forge libsqlite 3.44.0 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge libtiff 4.6.0 ha9c0a0a_2 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 2.9.14 h22db469_4 conda-forge libzlib 1.2.13 hd590300_5 conda-forge loguru 0.7.2 py310hff52083_1 conda-forge mash 2.3 ha9a2dd8_3 bioconda matplotlib-base 3.8.1 py310h62c0568_0 conda-forge minced 0.4.2 hdfd78af_1 bioconda mmseqs2 13.45111 pl5321hf1761c0_2 bioconda mpfr 4.2.1 h9458935_0 conda-forge munkres 1.0.7 py_1 bioconda mypy_extensions 1.0.0 pyha770c72_0 conda-forge ncbi-vdb 3.0.8 hdbdd923_0 bioconda ncurses 6.4 h59595ed_2 conda-forge numpy 1.26.0 py310hb13e2d6_0 conda-forge openjdk 11.0.1 h516909a_1016 conda-forge openjpeg 2.5.0 h488ebb8_3 conda-forge openssl 3.1.4 hd590300_0 conda-forge ossuuid 1.6.2 hf484d3e_1000 conda-forge packaging 23.2 pyhd8ed1ab_0 conda-forge pandas 2.1.3 py310hcc13569_0 conda-forge pathspec 0.11.2 pyhd8ed1ab_0 conda-forge patsy 0.5.3 pyhd8ed1ab_0 conda-forge pcre 8.45 h9c3ff4c_0 conda-forge perl 5.32.1 4_hd590300_perl5 conda-forge perl-alien-build 2.48 pl5321hec16e2b_0 bioconda perl-alien-libxml2 0.17 pl5321hec16e2b_0 bioconda perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda perl-business-isbn 3.007 pl5321hdfd78af_0 bioconda perl-business-isbn-data 20210112.006 pl5321hdfd78af_0 bioconda perl-capture-tiny 0.48 pl5321hdfd78af_2 bioconda perl-carp 1.38 pl5321hdfd78af_4 bioconda perl-common-sense 3.75 pl5321hdfd78af_0 bioconda perl-compress-raw-bzip2 2.201 pl5321h87f3376_1 bioconda perl-compress-raw-zlib 2.105 pl5321h87f3376_0 bioconda perl-constant 1.33 pl5321hdfd78af_2 bioconda perl-data-dumper 2.183 pl5321hec16e2b_1 bioconda perl-encode 3.19 pl5321hec16e2b_1 bioconda perl-exporter 5.72 pl5321hdfd78af_2 bioconda perl-exporter-tiny 1.002002 pl5321hdfd78af_0 bioconda perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge perl-ffi-checklib 0.28 pl5321hdfd78af_0 bioconda perl-file-chdir 0.1010 pl5321hdfd78af_3 bioconda perl-file-path 2.18 pl5321hd8ed1ab_0 conda-forge perl-file-temp 0.2304 pl5321hd8ed1ab_0 conda-forge perl-file-which 1.24 pl5321hd8ed1ab_0 conda-forge perl-importer 0.026 pl5321hdfd78af_0 bioconda perl-io-compress 2.201 pl5321hdbdd923_2 bioconda perl-io-zlib 1.14 pl5321hdfd78af_0 bioconda perl-json 4.10 pl5321hdfd78af_0 bioconda perl-json-xs 2.34 pl5321h4ac6f70_6 bioconda perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda perl-list-moreutils-xs 0.430 pl5321h031d066_2 bioconda perl-mime-base64 3.16 pl5321hec16e2b_2 bioconda perl-parent 0.236 pl5321hdfd78af_2 bioconda perl-path-tiny 0.122 pl5321hdfd78af_0 bioconda perl-pathtools 3.75 pl5321hec16e2b_3 bioconda perl-scalar-list-utils 1.62 pl5321hec16e2b_1 bioconda perl-scope-guard 0.21 pl5321hdfd78af_3 bioconda perl-sub-info 0.002 pl5321hdfd78af_1 bioconda perl-term-table 0.016 pl5321hdfd78af_0 bioconda perl-test2-suite 0.000145 pl5321hdfd78af_0 bioconda perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda perl-uri 5.12 pl5321hdfd78af_0 bioconda perl-xml-libxml 2.0207 pl5321h661654b_0 bioconda perl-xml-namespacesupport 1.12 pl5321hdfd78af_1 bioconda perl-xml-sax 1.02 pl5321hdfd78af_1 bioconda perl-xml-sax-base 1.09 pl5321hdfd78af_1 bioconda phanotate 1.5.1 h0dbaff4_1 bioconda pharokka 1.5.1 dev_0 pillow 10.1.0 py310h01dd4db_0 conda-forge pip 23.3.1 pyhd8ed1ab_0 conda-forge platformdirs 4.0.0 pyhd8ed1ab_0 conda-forge pluggy 1.3.0 pyhd8ed1ab_0 conda-forge psutil 5.9.5 py310h2372a71_1 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pycirclize 1.0.0 pyhd8ed1ab_0 conda-forge pyhmmer 0.10.4 py310h4b81fae_0 bioconda pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge pyrodigal 3.1.1 py310h4b81fae_0 bioconda pyrodigal-gv 0.2.0 pyh7cba7a3_0 bioconda pysocks 1.7.1 pyha2e5f31_6 conda-forge pytest 7.4.3 pyhd8ed1ab_0 conda-forge pytest-cov 4.1.0 pyhd8ed1ab_0 conda-forge python 3.10.13 hd12c33a_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.10 4_cp310 conda-forge pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge pyyaml 6.0.1 py310h2372a71_1 conda-forge readline 8.2 h8228510_1 conda-forge requests 2.31.0 pyhd8ed1ab_0 conda-forge scipy 1.11.3 py310hb13e2d6_1 conda-forge seaborn 0.13.0 hd8ed1ab_0 conda-forge seaborn-base 0.13.0 pyhd8ed1ab_0 conda-forge setuptools 68.2.2 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge statsmodels 0.14.0 py310h1f7b6fc_2 conda-forge textwrap3 0.9.2 py_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge trnascan-se 2.0.12 pl5321h031d066_0 bioconda typing_extensions 4.8.0 pyha770c72_0 conda-forge tzdata 2023c h71feb2d_0 conda-forge unicodedata2 15.1.0 py310h2372a71_0 conda-forge urllib3 2.1.0 pyhd8ed1ab_0 conda-forge wget 1.20.3 ha35d2d1_1 conda-forge wheel 0.41.3 pyhd8ed1ab_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstd 1.5.5 hfc55251_0 conda-forge

[gbouras13]

maybe try to uninstall then reinstall.

conda uninstall pyhmmer 

conda install pyhmmer 

# or

pip install pyhmmer

[Jlee795]

Hmm, thank you. I have just tried that and it is still displaying the same traceback error message relating to pyhmmer. I am not sure what is doing

[gbouras13]

I think it's just one of those cases where the cluster is having some difficulties :(

If you have a laptop or desktop handy I'd give that a go (assuming you don't have thousands of contigs), Pharokka should handle it fine and probably easier to install!

[Jlee795]

I am on my laptop at the moment as where I work that is the only computer I have to hand (hotdesking issue). I will have lots to go through pharokka and my memory on my laptop isn't that great

[gbouras13]

Another option is this if you are struggling to install it https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpharokka%2Fpharokka%2F1.2.1%2Bgalaxy1&version=1.2.1%20galaxy1

It runs v1.3.2 but if you have lots of contigs, it might be a good option (in meta mode it won't be much different to v1.5.1)

[gbouras13]

Closing due to time since last post