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heche-psb / wgd

wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication
https://wgdv2.readthedocs.io/en/latest/
GNU General Public License v3.0
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wgd-1.1.1/wgd/codeml.py:131: SettingWithCopyWarning: #19

Closed abcbot123 closed 3 months ago

abcbot123 commented 6 months ago

Hi, I got this error, when I use this code python3 wgd-1.1.1/wgd_cli.py ksd wgd_dmd/newCDS.fa.mcl newCDS.fa How can I fix this,

/var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/codeml.py:131: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results_dict['Ks'][gene_2][gene_1] = ks_value /var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/codeml.py:133: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results_dict['Ka'][gene_2][gene_1] = ka_value /var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/codeml.py:135: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results_dict['Omega'][gene_2][gene_1] = w /var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/codeml.py:130: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results_dict['Ks'][gene_1][gene_2] = ks_value /var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/codeml.py:132: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results_dict['Ka'][gene_1][gene_2] = ka_value /var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/codeml.py:134: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results_dict['Omega'][gene_1][gene_2] = w 2024-01-05 16:26:57: INFO Performing analysis on gene family GF_000021 /var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/codeml.py:131: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results_dict['Ks'][gene_2][gene_1] = ks_value /var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/codeml.py:133: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results_dict['Ka'][gene_2][gene_1] = ka_value /var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/codeml.py:135: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results_dict['Omega'][gene_2][gene_1] = w /var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/codeml.py:130: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results_dict['Ks'][gene_1][gene_2] = ks_value /var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/codeml.py:132: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results_dict['Ka'][gene_1][gene_2] = ka_value /var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/codeml.py:134: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results_dict['Omega'][gene_1][gene_2] = w 2024-01-05 16:28:06: INFO Performing analysis on gene family GF_000022multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/usr/local/lib/python3.8/dist-packages/joblib/_parallel_backends.py", line 350, in call return self.func(*args, kwargs) File "/usr/local/lib/python3.8/dist-packages/joblib/parallel.py", line 131, in call return [func(*args, *kwargs) for func, args, kwargs in self.items] File "/usr/local/lib/python3.8/dist-packages/joblib/parallel.py", line 131, in return [func(args, kwargs) for func, args, kwargs in self.items] File "/var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/ks_distribution.py", line 307, in analyse_family out = _calculate_weighted_ks( File "/var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/ks_distribution.py", line 197, in _calculate_weighted_ks if pairwise_estimates['Ks'].iloc[i, j] > 5: TypeError: '>' not supported between instances of 'str' and 'int'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/usr/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/usr/local/lib/python3.8/dist-packages/joblib/_parallel_backends.py", line 359, in call raise TransportableException(text, e_type) joblib.my_exceptions.TransportableException: TransportableException

TypeError Fri Jan 5 16:31:01 2024 PID: 4726 Python 3.8.10: /usr/bin/python3 ........................................................................... /usr/local/lib/python3.8/dist-packages/joblib/parallel.py in call(self=) 126 def init(self, iterator_slice): 127 self.items = list(iterator_slice) 128 self._size = len(self.items) 129 130 def call(self): --> 131 return [func(*args, **kwargs) for func, args, kwargs in self.items] self.items = [(, ('GF_000007', {'ptg000001l.2310': 'MSPLSTLLLIISLALISTFVAADPDSLQDICVADYTTGIKVNGYPCKE...AFNSQLPGTQSLATTLFGASPQVPDNVLTKAFKIGTKEVDKIKSRFVAK', 'ptg000001l.2311': 'MASIATLLLLSFALFSTSIFADPDSLQDICVADLTSGTKLNGFPCKAN...AFNSQLPGTQSLGTTLFAATPQVPDNVLSKAFKISTKEVEIIKYKFAAK', 'ptg000001l.2312': 'MASLATLVLISFALFSTSFATDPDSLQDICVADLSGVKLNGFPCKETA...SAFNSQLPGTQSIATTLFGASPEVPDNVLAKAFKIDTKTVDQIKSSFAA', 'ptg000001l.2313': 'MASFATILLLSFALFSTSFATDADSLQDICVADLASGVKLNGYPCKET...AFNSQLPGTQSIATTLFGASPQVPSNVLSKAFKISQAEVDIIKFKFLVK', 'ptg000003l.1107': 'MIFPIFIFSLLLSSSYALTQDFCVGDLSLPDAPCGFPCKKVAKVNEND...VSFSSHNPGLQILDFALFANDLPSELVEKTTFLDDVQVKKLKKVLGGTG', 'ptg000003l.1379': 'MGSFYNLLASFFLLAFAFSPLANASCNGPLQDFCVAIDEPNNASYVNG...GFNHEFPGISRHGNSLFDAKPSINYKILMRGLKLDKATEELAEGIPSGA', 'ptg000003l.1695': 'MEKRNNSNPAANATCDPGPMQDFCVGINRTYKGAFVNGEFCKNPKEVT...QNPGLLLIPNSVFQTYPPINTSILARTYKIPVKLAMRIQRSFQAEPYKG', 'ptg000003l.1887': 'MESKALACLLIFAAIYNAFAYDPDSLQDLCVANTSSSIKVNGFVCKAE...NGQLPGTQSIALTLFTATPEVPDNVLTKAFQIGTKEVDKIKSKLAPKKT', 'ptg000003l.2099': 'MASTFLKYTILSIIVAILTSRMIQASDPNILSDFLPQNTTSPDASFFT...SCFGSANAGTVSVPTTVFGTGIDAGILAKAFKTDLSTIQKIKAGLAAKA', 'ptg000003l.2462': 'MYSFSRPLALDPSYPLTFQLLFHHPPVNVFLLTPSSSSSSSSSKFSNY...NSQLPGTQSIGLSLFAATPEVPDNVLSRAFQMGTKQIDKLKTKFAPKKT', ...}, {'ptg000001l.100': 'ATGGTGTCTAGCATCGATGAAAACGAAGTTTACGCTGACTTCGCTAGA...CGTAGATTCACATTCTTGCAAGATGTATATTTTGAAGCCAATTTCTTGA', 'ptg000001l.1000': 'ATGATTGGTCCCTCTTTACAAGCTCTTGTGAAGCAACAACATGGTGTC...ATTAAGAAAAGCGCCAGCTCATAGTTTAGTCGAAGTCAGAACTTCGTGA', 'ptg000001l.1001': 'ATGCGGCTTCAGTTGTCGCCTAGTATGAGAAGCATAACGATATCGAGC...GTCGAAGCACAAAAGAGGAAGGCCGGGGCAGCTCTTCTCTAAAGGCTAG', 'ptg000001l.1002': 'ATGGCAGGCGTTCAAGACCAGTTAGAGATTAAGTTTAGGTTGACTGAC...TCCTTTGGAAAAAGGTACAAACTTTTATCTGATCATTCACATTGAATAA', 'ptg000001l.1003': 'ATGGCGACATCATCGTTTAGTGGCCTGAATTCTCCTCTATACCATTCT...AGGTGCCTTGGATGAAAAAAACAAGGGGGCCTTTTCAGGGGCCGTGTAA', 'ptg000001l.1004': 'ATGGCTGCAAATACTTTTATGTCGTATGCTGTGGATAATAAATCTGAT...TGGATTAAACTTTGATGCAGAAGAAGAAGGCTCTAATCAAAATACATGA', 'ptg000001l.1005': 'ATGGCTGAGGACGGTATTGGTTTGCCAGCGGCTTCAGAAAAAAATAAG...AACAGTTATCTCCCTCCAAGAAAAAAGGCATCCTTCCGTGAACACTTGA', 'ptg000001l.1006': 'ATGGTGGCAACCATTGCTGTGTCTTGTTCGGAATTCATAAATTTTCAA...AGTTTCGGTTGGAGCCGTGAAAAAGACGGTCTCAAGCAAGAAACGGTAG', 'ptg000001l.1007': 'ATGTGGAATTTTGCATCTAATTGCATAGCTGGAAATATTGGATCAAAA...TTTTGCATATCCTAGTTTGGATTGGCTTGTCCGAGAAATCGTCCCTTAG', 'ptg000001l.1008': 'ATGTTTCCTATTTTACTCTTCCTCCTCACAGTTACTATTTCCACCACC...AAGGCTGCAAGTTGGGGCCTCGGATGATGAAAGTTCATCTTCATCCTAG', ...}, '/var/lib/condor/execute/slot1/dir_38140/ks_tmp.3c8e141cb9cee6', 'codeml', False, 1, 100, 'fasttree', 'mafft', '/var/lib/condor/execute/slot1/dir_38140/wgd_ksd'), {})] 132 133 def len(self): 134 return self._size 135

........................................................................... /usr/local/lib/python3.8/dist-packages/joblib/parallel.py in (.0=)TypeError: '>' not supported between instances of 'str' and 'int'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "wgd-1.1.1/wgd_cli.py", line 1447, in cli() File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 829, in call return self.main(args, kwargs) File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, ctx.params) File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 610, in invoke return callback(args, **kwargs) File "wgd-1.1.1/wgdcli.py", line 625, in ksd ksd( File "wgd-1.1.1/wgdcli.py", line 763, in ksd results = ks_analysis_paranome( File "/var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/ks_distribution.py", line 641, in ks_analysis_paranome Parallel(n_jobs=n_threads)(delayed(analysis_function)( File "/usr/local/lib/python3.8/dist-packages/joblib/parallel.py", line 789, in call self.retrieve() File "/usr/local/lib/python3.8/dist-packages/joblib/parallel.py", line 740, in retrieve raise exception joblib.my_exceptions.JoblibTypeError: JoblibTypeError/var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/ks_distribution.py in analyse_family(family_id='GF_000007', family={'ptg000001l.2310': 'MSPLSTLLLIISLALISTFVAADPDSLQDICVADYTTGIKVNGYPCKE...AFNSQLPGTQSLATTLFGASPQVPDNVLTKAFKIGTKEVDKIKSRFVAK', 'ptg000001l.2311': 'MASIATLLLLSFALFSTSIFADPDSLQDICVADLTSGTKLNGFPCKAN...AFNSQLPGTQSLGTTLFAATPQVPDNVLSKAFKISTKEVEIIKYKFAAK', 'ptg000001l.2312': 'MASLATLVLISFALFSTSFATDPDSLQDICVADLSGVKLNGFPCKETA...SAFNSQLPGTQSIATTLFGASPEVPDNVLAKAFKIDTKTVDQIKSSFAA', 'ptg000001l.2313': 'MASFATILLLSFALFSTSFATDADSLQDICVADLASGVKLNGYPCKET...AFNSQLPGTQSIATTLFGASPQVPSNVLSKAFKISQAEVDIIKFKFLVK', 'ptg000003l.1107': 'MIFPIFIFSLLLSSSYALTQDFCVGDLSLPDAPCGFPCKKVAKVNEND...VSFSSHNPGLQILDFALFANDLPSELVEKTTFLDDVQVKKLKKVLGGTG', 'ptg000003l.1379': 'MGSFYNLLASFFLLAFAFSPLANASCNGPLQDFCVAIDEPNNASYVNG...GFNHEFPGISRHGNSLFDAKPSINYKILMRGLKLDKATEELAEGIPSGA', 'ptg000003l.1695': 'MEKRNNSNPAANATCDPGPMQDFCVGINRTYKGAFVNGEFCKNPKEVT...QNPGLLLIPNSVFQTYPPINTSILARTYKIPVKLAMRIQRSFQAEPYKG', 'ptg000003l.1887': 'MESKALACLLIFAAIYNAFAYDPDSLQDLCVANTSSSIKVNGFVCKAE...NGQLPGTQSIALTLFTATPEVPDNVLTKAFQIGTKEVDKIKSKLAPKKT', 'ptg000003l.2099': 'MASTFLKYTILSIIVAILTSRMIQASDPNILSDFLPQNTTSPDASFFT...SCFGSANAGTVSVPTTVFGTGIDAGILAKAFKTDLSTIQKIKAGLAAKA', 'ptg000003l.2462': 'MYSFSRPLALDPSYPLTFQLLFHHPPVNVFLLTPSSSSSSSSSKFSNY...NSQLPGTQSIGLSLFAATPEVPDNVLSRAFQMGTKQIDKLKTKFAPKKT', ...}, nucleotide={'ptg000001l.100': 'ATGGTGTCTAGCATCGATGAAAACGAAGTTTACGCTGACTTCGCTAGA...CGTAGATTCACATTCTTGCAAGATGTATATTTTGAAGCCAATTTCTTGA', 'ptg000001l.1000': 'ATGATTGGTCCCTCTTTACAAGCTCTTGTGAAGCAACAACATGGTGTC...ATTAAGAAAAGCGCCAGCTCATAGTTTAGTCGAAGTCAGAACTTCGTGA', 'ptg000001l.1001': 'ATGCGGCTTCAGTTGTCGCCTAGTATGAGAAGCATAACGATATCGAGC...GTCGAAGCACAAAAGAGGAAGGCCGGGGCAGCTCTTCTCTAAAGGCTAG', 'ptg000001l.1002': 'ATGGCAGGCGTTCAAGACCAGTTAGAGATTAAGTTTAGGTTGACTGAC...TCCTTTGGAAAAAGGTACAAACTTTTATCTGATCATTCACATTGAATAA', 'ptg000001l.1003': 'ATGGCGACATCATCGTTTAGTGGCCTGAATTCTCCTCTATACCATTCT...AGGTGCCTTGGATGAAAAAAACAAGGGGGCCTTTTCAGGGGCCGTGTAA', 'ptg000001l.1004': 'ATGGCTGCAAATACTTTTATGTCGTATGCTGTGGATAATAAATCTGAT...TGGATTAAACTTTGATGCAGAAGAAGAAGGCTCTAATCAAAATACATGA', 'ptg000001l.1005': 'ATGGCTGAGGACGGTATTGGTTTGCCAGCGGCTTCAGAAAAAAATAAG...AACAGTTATCTCCCTCCAAGAAAAAAGGCATCCTTCCGTGAACACTTGA', 'ptg000001l.1006': 'ATGGTGGCAACCATTGCTGTGTCTTGTTCGGAATTCATAAATTTTCAA...AGTTTCGGTTGGAGCCGTGAAAAAGACGGTCTCAAGCAAGAAACGGTAG', 'ptg000001l.1007': 'ATGTGGAATTTTGCATCTAATTGCATAGCTGGAAATATTGGATCAAAA...TTTTGCATATCCTAGTTTGGATTGGCTTGTCCGAGAAATCGTCCCTTAG', 'ptg000001l.1008': 'ATGTTTCCTATTTTACTCTTCCTCCTCACAGTTACTATTTCCACCACC...AAGGCTGCAAGTTGGGGCCTCGGATGATGAAAGTTCATCTTCATCCTAG', ...}, tmp='/var/lib/condor/execute/slot1/dir_38140/ks_tmp.3c8e141cb9cee6', codeml=, preserve=False, times=1, min_length=100, method='fasttree', aligner='mafft', output_dir='/var/lib/condor/execute/slot1/dir_38140/wgd_ksd') 302 results_dict, msa=msa_path_protein, method="alc") 303 else: 304 clustering, pairwise_distances, tree_path = _weighting( 305 results_dict, msa=msa_path_protein, method=method) 306 if clustering is not None: --> 307 out = _calculate_weighted_ks( out = undefined clustering = array([[2.00000000e+01, 1.80000000e+01, 5.845136...1.23000000e+02, 1.64341494e+00, 6.30000000e+01]]) results_dict = {'Ka': ptg000001l.2310 ptg000001l.2311 ... 0.0698 0.0

[63 rows x 63 columns], 'Ks': ptg000001l.2310 ptg000001l.2311 ... 0.7065 0.0

[63 rows x 63 columns], 'Omega': ptg000001l.2310 ptg000001l.2311 ... 0.0988 0.0

[63 rows x 63 columns]} pairwise_distances = {0: {0: 0.0, 1: 0.158656603, 2: 0.19943205, 3: 0.22707782199999998, 4: 1.17499233, 5: 1.3474487700000002, 6: 1.342737019, 7: 0.370011188, 8: 1.2996123169999998, 9: 0.39746069300000003, ...}, 1: {0: 0.158656603, 1: 0.0, 2: 0.144857715, 3: 0.172503487, 4: 1.168688817, 5: 1.3411452570000002, 6: 1.336433506, 7: 0.363707675, 8: 1.2933088039999998, 9: 0.39115718000000005, ...}, 2: {0: 0.19943205, 1: 0.144857715, 2: 0.0, 3: 0.148519106, 4: 1.209464264, 5: 1.381920704, 6: 1.377208953, 7: 0.40448312200000003, 8: 1.334084251, 9: 0.431932627, ...}, 3: {0: 0.22707782199999998, 1: 0.172503487, 2: 0.148519106, 3: 0.0, 4: 1.237110036, 5: 1.4095664760000002, 6: 1.404854725, 7: 0.432128894, 8: 1.3617300229999998, 9: 0.459578399, ...}, 4: {0: 1.17499233, 1: 1.168688817, 2: 1.2094642640000002, 3: 1.2371100359999998, 4: 0.0, 5: 1.7149128360000003, 6: 1.7102010850000002, 7: 1.179148544, 8: 1.667076383, 9: 1.2065980490000001, ...}, 5: {0: 1.34744877, 1: 1.3411452570000002, 2: 1.3819207039999999, 3: 1.409566476, 4: 1.714912836, 5: 0.0, 6: 1.066055209, 7: 1.351604984, 8: 1.6259631669999999, 9: 1.3790544889999998, ...}, 6: {0: 1.342737019, 1: 1.3364335059999999, 2: 1.377208953, 3: 1.404854725, 4: 1.710201085, 5: 1.066055209, 6: 0.0, 7: 1.346893233, 8: 1.6212514159999998, 9: 1.374342738, ...}, 7: {0: 0.370011188, 1: 0.363707675, 2: 0.40448312200000003, 3: 0.432128894, 4: 1.179148544, 5: 1.3516049840000002, 6: 1.346893233, 7: 0.0, 8: 1.3037685309999998, 9: 0.266968891, ...}, 8: {0: 1.2996123170000002, 1: 1.2933088040000003, 2: 1.3340842510000002, 3: 1.3617300230000002, 4: 1.6670763830000002, 5: 1.6259631670000003, 6: 1.6212514160000002, 7: 1.3037685310000002, 8: 0.0, 9: 1.331218036, ...}, 9: {0: 0.3974606930000001, 1: 0.39115718, 2: 0.431932627, 3: 0.4595783990000001, 4: 1.2065980490000001, 5: 1.3790544890000003, 6: 1.3743427380000002, 7: 0.26696889100000004, 8: 1.3312180359999999, 9: 0.0, ...}, ...} family_id = 'GF_000007' 308 clustering, results_dict, pairwise_distances, family_id 309 ) 310 out = add_alignmentstats(out, stats) 311 logging.debug(out)

........................................................................... /var/lib/condor/execute/slot1/dir_38140/wgd-1.1.1/wgd/ks_distribution.py in _calculate_weighted_ks(clustering=array([[2.00000000e+01, 1.80000000e+01, 5.845136...1.23000000e+02, 1.64341494e+00, 6.30000000e+01]]), pairwise_estimates={'Ka': ptg000001l.2310 ptg000001l.2311 ... 0.0698 0.0

[63 rows x 63 columns], 'Ks': ptg000001l.2310 ptg000001l.2311 ... 0.7065 0.0

[63 rows x 63 columns], 'Omega': ptg000001l.2310 ptg000001l.2311 ... 0.0988 0.0

[63 rows x 63 columns]}, pairwise_distances={0: {0: 0.0, 1: 0.158656603, 2: 0.19943205, 3: 0.22707782199999998, 4: 1.17499233, 5: 1.3474487700000002, 6: 1.342737019, 7: 0.370011188, 8: 1.2996123169999998, 9: 0.39746069300000003, ...}, 1: {0: 0.158656603, 1: 0.0, 2: 0.144857715, 3: 0.172503487, 4: 1.168688817, 5: 1.3411452570000002, 6: 1.336433506, 7: 0.363707675, 8: 1.2933088039999998, 9: 0.39115718000000005, ...}, 2: {0: 0.19943205, 1: 0.144857715, 2: 0.0, 3: 0.148519106, 4: 1.209464264, 5: 1.381920704, 6: 1.377208953, 7: 0.40448312200000003, 8: 1.334084251, 9: 0.431932627, ...}, 3: {0: 0.22707782199999998, 1: 0.172503487, 2: 0.148519106, 3: 0.0, 4: 1.237110036, 5: 1.4095664760000002, 6: 1.404854725, 7: 0.432128894, 8: 1.3617300229999998, 9: 0.459578399, ...}, 4: {0: 1.17499233, 1: 1.168688817, 2: 1.2094642640000002, 3: 1.2371100359999998, 4: 0.0, 5: 1.7149128360000003, 6: 1.7102010850000002, 7: 1.179148544, 8: 1.667076383, 9: 1.2065980490000001, ...}, 5: {0: 1.34744877, 1: 1.3411452570000002, 2: 1.3819207039999999, 3: 1.409566476, 4: 1.714912836, 5: 0.0, 6: 1.066055209, 7: 1.351604984, 8: 1.6259631669999999, 9: 1.3790544889999998, ...}, 6: {0: 1.342737019, 1: 1.3364335059999999, 2: 1.377208953, 3: 1.404854725, 4: 1.710201085, 5: 1.066055209, 6: 0.0, 7: 1.346893233, 8: 1.6212514159999998, 9: 1.374342738, ...}, 7: {0: 0.370011188, 1: 0.363707675, 2: 0.40448312200000003, 3: 0.432128894, 4: 1.179148544, 5: 1.3516049840000002, 6: 1.346893233, 7: 0.0, 8: 1.3037685309999998, 9: 0.266968891, ...}, 8: {0: 1.2996123170000002, 1: 1.2933088040000003, 2: 1.3340842510000002, 3: 1.3617300230000002, 4: 1.6670763830000002, 5: 1.6259631670000003, 6: 1.6212514160000002, 7: 1.3037685310000002, 8: 0.0, 9: 1.331218036, ...}, 9: {0: 0.3974606930000001, 1: 0.39115718, 2: 0.431932627, 3: 0.4595783990000001, 4: 1.2065980490000001, 5: 1.3790544890000003, 6: 1.3743427380000002, 7: 0.26696889100000004, 8: 1.3312180359999999, 9: 0.0, ...}, ...}, family_id='GF_000007') 192 pairwise_estimates['Ka'].iloc[i, j], 193 pairwise_estimates['Omega'].iloc[i, j], 194 distance, grouping_node 195 ] 196 --> 197 if pairwise_estimates['Ks'].iloc[i, j] > 5: pairwise_estimates.iloc = undefined i = 20 j = 18 198 out.add(grouping_node) 199 200 df = pd.DataFrame.from_dict(weights, orient='index') 201 df.columns = ['Paralog1', 'Paralog2', 'Family',

TypeError: '>' not supported between instances of 'str' and 'int'

heche-psb commented 5 months ago

Hi, a quick test to help debugging. Could you try to install wgd v1 using python 3.6.5 instead of python 3.8 and try again?