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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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[BUG] biopython bug? #231

Closed camilagazolla closed 9 months ago

camilagazolla commented 1 year ago

Hello,

I am receiving the following warning messages. The error seems to be related to a biopython version 1.74 bug, according to https://github.com/arpcard/rgi/issues/62, however, I am using the 1.78 version.

WARNING 2023-06-01 15:19:42,402 : Exception : <class 'TypeError'> -> float() argument must be a string or a number, not 'NoneType' -> Model(2644)
WARNING 2023-06-01 15:19:42,402 : tetB(46) ---> hsp.bits: None <class 'NoneType'> ? <class 'str'>
WARNING 2023-06-01 15:19:42,404 : Exception : <class 'TypeError'> -> float() argument must be a string or a number, not 'NoneType' -> Model(5758)
WARNING 2023-06-01 15:19:42,404 : Helicobacter pylori pbp1 mutants conferring resistance to amoxicillin ---> hsp.bits: None <class 'NoneType'> ? <class 'float'>
WARNING 2023-06-01 15:19:42,406 : Exception : <class 'TypeError'> -> float() argument must be a string or a number, not 'NoneType' -> Model(5758)
WARNING 2023-06-01 15:19:42,406 : Helicobacter pylori pbp1 mutants conferring resistance to amoxicillin ---> hsp.bits: None <class 'NoneType'> ? <class 'float'>
WARNING 2023-06-01 15:19:42,403 : Exception : <class 'TypeError'> -> float() argument must be a string or a number, not 'NoneType' -> Model(2424)
WARNING 2023-06-01 15:19:42,419 : YojI ---> hsp.bits: None <class 'NoneType'> ? <class 'str'>
WARNING 2023-06-01 15:19:42,419 : Exception : <class 'TypeError'> -> float() argument must be a string or a number, not 'NoneType' -> Model(2643)
WARNING 2023-06-01 15:19:42,419 : tetA(46) ---> hsp.bits: None <class 'NoneType'> ? <class 'str'>
WARNING 2023-06-01 15:19:42,420 : Exception : <class 'TypeError'> -> float() argument must be a string or a number, not 'NoneType' -> Model(2422)
WARNING 2023-06-01 15:19:42,420 : efrB ---> hsp.bits: None <class 'NoneType'> ? <class 'str'>
WARNING 2023-06-01 15:19:42,420 : Exception : <class 'TypeError'> -> float() argument must be a string or a number, not 'NoneType' -> Model(1997)
WARNING 2023-06-01 15:19:42,420 : tlrC ---> hsp.bits: None <class 'NoneType'> ? <class 'str'>

My rgi/dependencies versions are:

  Name                     Version       Build               Channel    
──────────────────────────────────────────────────────────────────────────
  _libgcc_mutex            0.1           conda_forge         conda-forge
  _openmp_mutex            4.5           2_kmp_llvm          conda-forge
  abseil-cpp               20211102.0    h93e1e8c_3          conda-forge
  arrow-cpp                11.0.0        py38h613000e_0                 
  aws-c-common             0.4.57        he6710b0_1                     
  aws-c-event-stream       0.1.6         h2531618_5                     
  aws-checksums            0.1.9         he6710b0_0                     
  aws-sdk-cpp              1.8.185       hce553d0_0                     
  bamtools                 2.5.1         hd03093a_10         bioconda   
  beautifulsoup4           4.9.3         pyha847dfd_0                   
  bedtools                 2.31.0        hf5e1c6e_2          bioconda   
  biopython                1.78          py38h497a2fe_2      conda-forge
  blas                     1.0           mkl                            
  blast                    2.9.0         pl526he19e7b1_7     bioconda   
  bokeh                    3.1.1         pyhd8ed1ab_0        conda-forge
  boost-cpp                1.82.0        he19a28c_1          conda-forge
  bowtie2                  2.5.1         py38he00c5e5_2      bioconda   
  brotli                   1.0.9         h166bdaf_8          conda-forge
  brotli-bin               1.0.9         h166bdaf_8          conda-forge
  brotlipy                 0.7.0         py38h0a891b7_1005   conda-forge
  bwa                      0.7.17        he4a0461_11         bioconda   
  bzip2                    1.0.8         h7f98852_4          conda-forge
  c-ares                   1.19.1        hd590300_0          conda-forge
  ca-certificates          2023.5.7      hbcca054_0          conda-forge
  certifi                  2023.5.7      pyhd8ed1ab_0        conda-forge
  cffi                     1.15.0        py38h7f8727e_0                 
  chardet                  3.0.4         py38h924ce5b_1008   conda-forge
  click                    8.1.3         unix_pyhd8ed1ab_2   conda-forge
  cloudpickle              2.2.1         pyhd8ed1ab_0        conda-forge
  contourpy                1.0.7         py38hfbd4bf9_0      conda-forge
  cryptography             39.0.1        py38h9ce1e76_0                 
  curl                     7.87.0        h6312ad2_0          conda-forge
  cycler                   0.11.0        pyhd3eb1b0_0                   
  cytoolz                  0.12.0        py38h0a891b7_1      conda-forge
  dask                     2023.5.0      pyhd8ed1ab_0        conda-forge
  dask-core                2023.5.0      pyhd8ed1ab_0        conda-forge
  diamond                  0.8.36        h43eeafb_7          bioconda   
  distributed              2023.5.0      pyhd8ed1ab_0        conda-forge
  entrez-direct            16.2          he881be0_1          bioconda   
  filetype                 1.2.0         pyhd8ed1ab_0        conda-forge
  fonttools                4.39.4        py38h01eb140_0      conda-forge
  freetype                 2.12.1        hca18f0e_1          conda-forge
  fsspec                   2023.5.0      pyh1a96a4e_0        conda-forge
  gflags                   2.2.2         he1b5a44_1004       conda-forge
  giflib                   5.2.1         h0b41bf4_3          conda-forge
  glog                     0.5.0         h2531618_0                     
  grpc-cpp                 1.46.3        hc275302_1          conda-forge
  htslib                   1.9           h244ad75_9          bioconda   
  icu                      72.1          hcb278e6_0          conda-forge
  idna                     2.10          pyhd3eb1b0_0                   
  importlib-metadata       6.6.0         pyha770c72_0        conda-forge
  importlib_metadata       6.6.0         hd8ed1ab_0          conda-forge
  importlib_resources      5.12.0        pyhd8ed1ab_0        conda-forge
  jbig                     2.1           h7f98852_2003       conda-forge
  jinja2                   3.1.2         pyhd8ed1ab_1        conda-forge
  jpeg                     9e            h0b41bf4_3          conda-forge
  keyutils                 1.6.1         h166bdaf_0          conda-forge
  kiwisolver               1.4.4         py38h43d8883_1      conda-forge
  kma                      1.4.9         he4a0461_2          bioconda   
  krb5                     1.20.1        hf9c8cef_0          conda-forge
  lcms2                    2.12          h3be6417_0                     
  ld_impl_linux-64         2.40          h41732ed_0          conda-forge
  lerc                     2.2.1         h2531618_0                     
  libabseil                20211102.0    cxx17_h48a1fff_3    conda-forge
  libbrotlicommon          1.0.9         h166bdaf_8          conda-forge
  libbrotlidec             1.0.9         h166bdaf_8          conda-forge
  libbrotlienc             1.0.9         h166bdaf_8          conda-forge
  libcurl                  7.87.0        h6312ad2_0          conda-forge
  libdeflate               1.7           h27cfd23_5                     
  libedit                  3.1.20191231  h46ee950_2          conda-forge
  libev                    4.33          h7f8727e_1                     
  libevent                 2.1.10        h9b69904_4          conda-forge
  libffi                   3.2.1         hf484d3e_1007                  
  libgcc-ng                12.2.0        h65d4601_19         conda-forge
  libhwloc                 2.9.1         hf312287_1          conda-forge
  libiconv                 1.17          h166bdaf_0          conda-forge
  libidn2                  2.3.4         h5eee18b_0                     
  libnghttp2               1.51.0        hdcd2b5c_0          conda-forge
  libpng                   1.6.39        h5eee18b_0                     
  libprotobuf              3.20.3        h3eb15da_0          conda-forge
  libssh2                  1.10.0        haa6b8db_3          conda-forge
  libstdcxx-ng             12.2.0        h46fd767_19         conda-forge
  libthrift                0.15.0        he6d91bd_1          conda-forge
  libtiff                  4.3.0         hf544144_1          conda-forge
  libunistring             0.9.10        h7f98852_0          conda-forge
  libwebp                  1.2.4         h11a3e52_1                     
  libwebp-base             1.2.4         h5eee18b_1                     
  libxml2                  2.10.4        hfdac1af_0          conda-forge
  libxslt                  1.1.37        h873f0b0_0          conda-forge
  libzlib                  1.2.13        h166bdaf_4          conda-forge
  llvm-openmp              16.0.4        h4dfa4b3_0          conda-forge
  locket                   1.0.0         pyhd8ed1ab_0        conda-forge
  lxml                     4.6.5         py38hf1fe3a4_0      conda-forge
  lz4                      4.3.2         py38hd012fdc_0      conda-forge
  lz4-c                    1.9.4         hcb278e6_0          conda-forge
  markupsafe               2.1.2         py38h1de0b5d_0      conda-forge
  matplotlib-base          3.7.1         py38h417a72b_1                 
  mkl                      2023.1.0      h84fe81f_48680      conda-forge
  mkl-service              2.4.0         py38h5eee18b_1                 
  mkl_fft                  1.3.6         py38h417a72b_1                 
  mkl_random               1.2.2         py38h417a72b_1                 
  msgpack-python           1.0.5         py38hfbd4bf9_0      conda-forge
  munkres                  1.1.4         py_0                           
  ncurses                  6.1           hf484d3e_1002       conda-forge
  numpy                    1.24.3        py38hf6e8229_1                 
  numpy-base               1.24.3        py38h060ed82_1                 
  oligoarrayaux            3.8           hc9558a2_0          bioconda   
  openssl                  1.1.1u        hd590300_0          conda-forge
  orc                      1.7.4         hb3bc3d3_1                     
  packaging                23.1          pyhd8ed1ab_0        conda-forge
  pandas                   2.0.2         py38h01efb38_0      conda-forge
  partd                    1.4.0         pyhd8ed1ab_0        conda-forge
  pcre                     8.45          h295c915_0                     
  perl                     5.26.2        h36c2ea0_1008       conda-forge
  perl-archive-tar         2.32          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-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-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-pathtools           3.75          pl526h14c3975_1     bioconda   
  perl-scalar-list-utils   1.52          pl526h516909a_0     bioconda   
  perl-types-serialiser    1.0           pl526_2             bioconda   
  perl-xsloader            0.24          pl526_0             bioconda   
  pillow                   9.4.0         py38h6a678d5_0                 
  pip                      23.1.2        pyhd8ed1ab_0        conda-forge
  prodigal                 2.6.3         h031d066_6          bioconda   
  psutil                   5.9.5         py38h1de0b5d_0      conda-forge
  pyahocorasick            2.0.0         py38h1de0b5d_0      conda-forge
  pyarrow                  11.0.0        py38h992f0b0_0                 
  pycparser                2.21          pyhd3eb1b0_0                   
  pyfaidx                  0.7.2.1       pyh7cba7a3_1        bioconda   
  pyopenssl                23.2.0        pyhd8ed1ab_1        conda-forge
  pyparsing                3.0.9         pyhd8ed1ab_0        conda-forge
  pyrodigal                2.1.0         py38he5da3d1_3      bioconda   
  pysam                    0.16.0.1      py38hf7546f9_3      bioconda   
  pysocks                  1.7.1         pyha2e5f31_6        conda-forge
  python                   3.8.6         h852b56e_0_cpython  conda-forge
  python-dateutil          2.8.2         pyhd3eb1b0_0                   
  python-tzdata            2023.3        pyhd8ed1ab_0        conda-forge
  python_abi               3.8           3_cp38              conda-forge
  pytz                     2023.3        pyhd8ed1ab_0        conda-forge
  pyvcf3                   1.0.3         pyhdfd78af_0        bioconda   
  pyyaml                   6.0           py38h0a891b7_5      conda-forge
  re2                      2022.04.01    h295c915_0                     
  readline                 8.0           h46ee950_1          conda-forge
  requests                 2.24.0        py_0                           
  rgi                      6.0.2         pyha8f3691_0        bioconda   
  samtools                 1.9           h10a08f8_12         bioconda   
  seaborn                  0.12.2        py38h06a4308_0                 
  setuptools               67.8.0        py38h06a4308_0                 
  six                      1.16.0        pyhd3eb1b0_1                   
  snappy                   1.1.10        h9fff704_0          conda-forge
  sortedcontainers         2.4.0         pyhd3eb1b0_0                   
  soupsieve                2.4           py38h06a4308_0                 
  sqlite                   3.40.1        h5082296_0                     
  tbb                      2021.9.0      hf52228f_0          conda-forge
  tblib                    1.7.0         pyhd3eb1b0_0                   
  tk                       8.6.12        h1ccaba5_0                     
  toolz                    0.12.0        pyhd8ed1ab_0        conda-forge
  tornado                  6.3.2         py38h01eb140_0      conda-forge
  unicodedata2             15.0.0        py38h5eee18b_0                 
  urllib3                  1.25.11       py_0                           
  utf8proc                 2.6.1         h27cfd23_0                     
  wget                     1.21.3        h0b77cf5_0                     
  wheel                    0.40.0        pyhd8ed1ab_0        conda-forge
  xyzservices              2023.5.0      pyhd8ed1ab_1        conda-forge
  xz                       5.2.10        h5eee18b_1                     
  yaml                     0.2.5         h7f98852_2          conda-forge
  zict                     3.0.0         pyhd8ed1ab_0        conda-forge
  zipp                     3.15.0        pyhd8ed1ab_0        conda-forge
  zlib                     1.2.13        h166bdaf_4          conda-forge
  zstd                     1.5.5         hc292b87_0

Thank you in advance for any help you can give me! :)

raphenya commented 11 months ago

@camilagazolla I will need an input file to test (if you can share it). The other option is to try if you get the same warnings with the new version (6.0.3). Cheers.

raphenya commented 9 months ago

@camilagazolla I will close this issue. Please open another issue if you have the same issue with version 6.0.3 or future releases. Cheers.