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linsalrob / PhiSpy

Prediction of prophages from bacterial genomes
MIT License
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output files not created #66

Open oirazoki opened 8 months ago

oirazoki commented 8 months ago

Hi!

I'm encountering a problem when running phispy (conda environment) with the provided test files. The analysis runs with no problems and I can see that it identifies prophages but then the output files are not created and I get the following error: 

 File "/Users/oihira/anaconda3/envs/prophaging/lib/python3.10/site-packages/PhiSpyModules/writers.py", line 325, in write_all_outputs
    self.record.get_entry(self.pp[i]['contig']).append_feature(SeqFeature(

TypeError: SeqFeature.__init__() got an unexpected keyword argument 'strand'.

Any idea why?

Thanks a lot! /Oihane

#packages in environment at /Users/xxxx/anaconda3/envs/phispy:
# Name                    Version                   Build  Channel
bcbio-gff                 0.7.0              pyh7cba7a3_0    bioconda
biopython                 1.83            py310hb372a2b_0    conda-forge
bx-python                 0.10.0          py310h260c36f_0    bioconda
bzip2                     1.0.8                h10d778d_5    conda-forge
ca-certificates           2023.11.17           h8857fd0_0    conda-forge
hmmer                     3.4                  h7133b54_0    bioconda
joblib                    1.3.2              pyhd8ed1ab_0    conda-forge
libblas                   3.9.0           20_osx64_openblas    conda-forge
libcblas                  3.9.0           20_osx64_openblas    conda-forge
libcxx                    16.0.6               hd57cbcb_0    conda-forge
libexpat                  2.5.0                hf0c8a7f_1    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           13_2_0_h97931a8_1    conda-forge
libgfortran5              13.2.0               h2873a65_1    conda-forge
liblapack                 3.9.0           20_osx64_openblas    conda-forge
libopenblas               0.3.25          openmp_hfef2a42_0    conda-forge
libsqlite                 3.44.2               h92b6c6a_0    conda-forge
libzlib                   1.2.13               h8a1eda9_5    conda-forge
llvm-openmp               17.0.6               hb6ac08f_0    conda-forge
ncurses                   6.4                  h93d8f39_2    conda-forge
numpy                     1.26.3          py310h4bfa8fc_0    conda-forge
openssl                   3.2.0                hd75f5a5_1    conda-forge
phispy                    4.2.21          py310hbdf848b_2    bioconda
pip                       23.3.2             pyhd8ed1ab_0    conda-forge
python                    3.10.13         h00d2728_1_cpython    conda-forge
python_abi                3.10                    4_cp310    conda-forge
readline                  8.2                  h9e318b2_1    conda-forge
scikit-learn              1.3.2           py310h04b1a37_2    conda-forge
scipy                     1.11.4          py310h3f1db6d_0    conda-forge
setuptools                69.0.3             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
threadpoolctl             3.2.0              pyha21a80b_0    conda-forge
tk                        8.6.13               h1abcd95_1    conda-forge
tzdata                    2023d                h0c530f3_0    conda-forge
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
legoodsw commented 6 months ago

I have the same issue. I get the log file but no other outputs. Help appreiciated.

legoodsw commented 6 months ago

I uninstalled biopython 1.83 and reinstalled 1.80 and it seems to have solved the issue and now I have all the output files