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iqbal-lab-org / pling

Plasmid analysis using rearrangement distances
MIT License
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Issue getting pling running #65

Open JavierFFavieres opened 1 week ago

JavierFFavieres commented 1 week ago

Hi, I have tried running pling but found myself into an error I don't know how to solve.

Firstly, I have to specify that I installed the dependencies into a single conda environment. I'll add them here just in case:

packages in environment at /home/aru/miniforge3/envs/pling:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge aioeasywebdav 2.4.0 pyha770c72_0 conda-forge aiohttp 3.9.5 py311h459d7ec_0 conda-forge aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge amply 0.1.6 pyhd8ed1ab_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge argparse-dataclass 2.0.0 pyhd8ed1ab_0 conda-forge async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge attmap 0.13.2 pyhd8ed1ab_0 conda-forge attrs 23.2.0 pyh71513ae_0 conda-forge bcrypt 4.1.3 py311h5ecf98a_0 conda-forge boto3 1.34.136 pyhd8ed1ab_0 conda-forge botocore 1.34.136 pyge38_1234567_0 conda-forge brotli-python 1.1.0 py311hb755f60_1 conda-forge bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.28.1 hd590300_0 conda-forge ca-certificates 2024.6.2 hbcca054_0 conda-forge cachetools 5.3.3 pyhd8ed1ab_0 conda-forge certifi 2024.6.2 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py311hb3a22ac_0 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge coin-or-cbc 2.10.11 h56f689f_0 conda-forge coin-or-cgl 0.60.7 h516709c_0 conda-forge coin-or-clp 1.17.8 h1ee7a9c_0 conda-forge coin-or-osi 0.108.10 haf5fa05_0 conda-forge coin-or-utils 2.11.11 h8c65801_1 conda-forge coincbc 2.10.11 0_metapackage conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge conda-inject 1.3.2 pyhd8ed1ab_0 conda-forge configargparse 1.7 pyhd8ed1ab_0 conda-forge connection_pool 0.0.3 pyhd3deb0d_0 conda-forge cryptography 42.0.8 py311h4a61cc7_0 conda-forge datrie 0.8.2 py311h459d7ec_7 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge docutils 0.21.2 pyhd8ed1ab_0 conda-forge dpath 2.2.0 pyha770c72_0 conda-forge dropbox 12.0.2 pyhd8ed1ab_0 conda-forge eido 0.2.2 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge filechunkio 1.8 py_2 conda-forge frozenlist 1.4.1 py311h459d7ec_0 conda-forge ftputil 5.1.0 pyhd8ed1ab_0 conda-forge gitdb 4.0.11 pyhd8ed1ab_0 conda-forge gitpython 3.1.43 pyhd8ed1ab_0 conda-forge google-api-core 2.19.1 pyhd8ed1ab_0 conda-forge google-api-python-client 2.135.0 pyhd8ed1ab_0 conda-forge google-auth 2.30.0 pyhff2d567_0 conda-forge google-auth-httplib2 0.2.0 pyhd8ed1ab_0 conda-forge google-cloud-core 2.4.1 pyhd8ed1ab_0 conda-forge google-cloud-storage 2.17.0 pyhff2d567_0 conda-forge google-crc32c 1.1.2 py311h9b08b9c_5 conda-forge google-resumable-media 2.7.0 pyhd8ed1ab_0 conda-forge googleapis-common-protos 1.63.2 pyhd8ed1ab_0 conda-forge grpcio 1.62.2 py311ha6695c7_0 conda-forge httplib2 0.22.0 pyhd8ed1ab_0 conda-forge humanfriendly 10.0 pyhd8ed1ab_6 conda-forge idna 3.7 pyhd8ed1ab_0 conda-forge immutables 0.20 py311h459d7ec_1 conda-forge importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge jinja2 3.1.4 pyhd8ed1ab_0 conda-forge jmespath 1.0.1 pyhd8ed1ab_0 conda-forge jsonschema 4.22.0 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge jupyter_core 5.7.2 py311h38be061_0 conda-forge ld_impl_linux-64 2.40 hf3520f5_7 conda-forge libabseil 20240116.2 cxx17_h59595ed_0 conda-forge libblas 3.9.0 22_linux64_openblas conda-forge libcblas 3.9.0 22_linux64_openblas conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libexpat 2.6.2 h59595ed_0 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 14.1.0 h77fa898_0 conda-forge libgfortran-ng 14.1.0 h69a702a_0 conda-forge libgfortran5 14.1.0 hc5f4f2c_0 conda-forge libgomp 14.1.0 h77fa898_0 conda-forge libgrpc 1.62.2 h15f2491_0 conda-forge liblapack 3.9.0 22_linux64_openblas conda-forge liblapacke 3.9.0 22_linux64_openblas conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge libprotobuf 4.25.3 h08a7969_0 conda-forge libre2-11 2023.09.01 h5a48ba9_2 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsqlite 3.46.0 hde9e2c9_0 conda-forge libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libzlib 1.3.1 h4ab18f5_1 conda-forge logmuse 0.2.6 pyh8c360ce_0 conda-forge markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge markupsafe 2.1.5 py311h459d7ec_0 conda-forge mdurl 0.1.2 pyhd8ed1ab_0 conda-forge multidict 6.0.5 py311h459d7ec_0 conda-forge nbformat 5.10.4 pyhd8ed1ab_0 conda-forge ncurses 6.5 h59595ed_0 conda-forge numpy 2.0.0 py311h1461c94_0 conda-forge oauth2client 4.1.3 py_0 conda-forge openssl 3.3.1 h4ab18f5_1 conda-forge packaging 24.1 pyhd8ed1ab_0 conda-forge pandas 2.2.2 py311h14de704_1 conda-forge paramiko 3.4.0 pyhd8ed1ab_0 conda-forge peppy 0.40.2 pyhd8ed1ab_0 conda-forge pip 24.0 pyhd8ed1ab_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge plac 1.4.3 pyhd8ed1ab_0 conda-forge platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge pluggy 1.5.0 pyhd8ed1ab_0 conda-forge ply 3.11 pyhd8ed1ab_2 conda-forge prettytable 3.10.0 pyhd8ed1ab_0 conda-forge proto-plus 1.23.0 pyhd8ed1ab_0 conda-forge protobuf 4.25.3 py311h7b78aeb_0 conda-forge psutil 6.0.0 py311h331c9d8_0 conda-forge pulp 2.8.0 py311h38be061_0 conda-forge pyasn1 0.6.0 pyhd8ed1ab_0 conda-forge pyasn1-modules 0.4.0 pyhd8ed1ab_0 conda-forge pycparser 2.22 pyhd8ed1ab_0 conda-forge pygments 2.18.0 pyhd8ed1ab_0 conda-forge pynacl 1.5.0 py311h459d7ec_3 conda-forge pyopenssl 24.0.0 pyhd8ed1ab_0 conda-forge pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge pysftp 0.2.9 py_1 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytest 8.2.2 pyhd8ed1ab_0 conda-forge python 3.11.9 hb806964_0_cpython conda-forge python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge python-irodsclient 2.0.1 pyhd8ed1ab_0 conda-forge python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge python_abi 3.11 4_cp311 conda-forge pytz 2024.1 pyhd8ed1ab_0 conda-forge pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge pyyaml 6.0.1 py311h459d7ec_1 conda-forge re2 2023.09.01 h7f4b329_2 conda-forge readline 8.2 h8228510_1 conda-forge referencing 0.35.1 pyhd8ed1ab_0 conda-forge requests 2.32.3 pyhd8ed1ab_0 conda-forge reretry 0.11.8 pyhd8ed1ab_0 conda-forge rich 13.7.1 pyhd8ed1ab_0 conda-forge rpds-py 0.18.1 py311h5ecf98a_0 conda-forge rsa 4.9 pyhd8ed1ab_0 conda-forge s3transfer 0.10.2 pyhd8ed1ab_0 conda-forge setuptools 70.1.1 pyhd8ed1ab_0 conda-forge setuptools-scm 8.1.0 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge slack-sdk 3.30.0 pyha770c72_0 conda-forge slack_sdk 3.30.0 hd8ed1ab_0 conda-forge slacker 0.14.0 py_0 conda-forge smart_open 7.0.4 pyhd8ed1ab_0 conda-forge smmap 5.0.0 pyhd8ed1ab_0 conda-forge snakemake 8.14.0 hdfd78af_0 bioconda snakemake-interface-common 1.17.2 pyhdfd78af_0 bioconda snakemake-interface-executor-plugins 9.1.1 pyhdfd78af_0 bioconda snakemake-interface-report-plugins 1.0.0 pyhdfd78af_0 bioconda snakemake-interface-storage-plugins 3.2.2 pyhdfd78af_0 bioconda snakemake-minimal 8.14.0 pyhdfd78af_0 bioconda stone 3.3.2 pyhd8ed1ab_0 conda-forge stopit 1.1.2 py_0 conda-forge tabulate 0.9.0 pyhd8ed1ab_1 conda-forge throttler 1.2.2 pyhd8ed1ab_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge toposort 1.10 pyhd8ed1ab_0 conda-forge traitlets 5.14.3 pyhd8ed1ab_0 conda-forge typing-extensions 4.12.2 hd8ed1ab_0 conda-forge typing_extensions 4.12.2 pyha770c72_0 conda-forge tzdata 2024a h0c530f3_0 conda-forge ubiquerg 0.8.0 pyhd8ed1ab_0 conda-forge uritemplate 4.1.1 pyhd8ed1ab_0 conda-forge urllib3 1.26.19 pyhd8ed1ab_0 conda-forge veracitools 0.1.3 py_0 conda-forge wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge wheel 0.43.0 pyhd8ed1ab_1 conda-forge wrapt 1.16.0 py311h459d7ec_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge yarl 1.9.4 py311h459d7ec_0 conda-forge yte 1.5.4 pyha770c72_0 conda-forge zipp 3.19.2 pyhd8ed1ab_0 conda-forge

I then installed pling using 'git clone https://github.com/iqbal-lab-org/pling.git' as stated on the repo.

However when running I get this error:

python /home/aru/Documentos/Programs/pling/pling/run_pling.py input.txt output_dir/ align

Batching...

ModuleNotFoundError in file /home/aru/Documentos/Programs/pling/pling/batching/Snakefile, line 1: No module named 'pling' File "/home/aru/Documentos/Programs/pling/pling/batching/Snakefile", line 1, in

Command 'snakemake --snakefile /home/aru/Documentos/Programs/pling/pling/batching/Snakefile --configfile output_dir//tmp_files/config.yaml --cores 1 --use-conda --rerun-incomplete --nolock ' returned non-zero exit status 1. Traceback (most recent call last): File "/home/aru/Documentos/Programs/pling/pling/run_pling.py", line 182, in main() File "/home/aru/Documentos/Programs/pling/pling/run_pling.py", line 179, in main pling(args) File "/home/aru/Documentos/Programs/pling/pling/run_pling.py", line 130, in pling raise e File "/home/aru/Documentos/Programs/pling/pling/run_pling.py", line 125, in pling subprocess.run(f"snakemake --snakefile {get_pling_path()}/batching/Snakefile {snakemake_args}", shell=True, check=True, capture_output=True) File "/home/aru/miniforge3/envs/pling/lib/python3.11/subprocess.py", line 571, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command 'snakemake --snakefile /home/aru/Documentos/Programs/pling/pling/batching/Snakefile --configfile output_dir//tmp_files/config.yaml --cores 1 --use-conda --rerun-incomplete --nolock ' returned non-zero exit status 1.

I am not as well versed on code reading so I am unable to identify exactly what went wrong. Could you help me? Thanks, Javier

babayagaofficial commented 3 days ago

Hi Javier,

you need to add PYTHONPATH=/home/aru/Documentos/Programs/pling before the command you are running, i.e. run:

PYTHONPATH=/home/aru/Documentos/Programs/pling python /home/aru/Documentos/Programs/pling/pling/run_pling.py input.txt output_dir/ align

I am aware that this is a little clunky, but it'll hopefully be fixed in the next version!

JavierFFavieres commented 18 hours ago

Thank you so much, that worked perfectly!