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output.txt
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output.txt
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~ INFO font search path ['/home/abigail/miniconda2/envs/cgb/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/ttf', '/home/abigail/miniconda2/envs/cgb/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm', '/home/abigail/miniconda2/envs/cgb/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts']
~ INFO Could not open font file /usr/share/fonts/truetype/noto/NotoColorEmoji.ttf
~ INFO generated new fontManager
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Downloading NC_008578.1
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Downloading NC_003450.3
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Downloading NC_006087.1
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Regulation parameters: 16.61 4.41
~ INFO Background parameters: -16.52 6.19
~ INFO Prior(regulation; ace): 0.03
~ INFO Calculating regulation probabilities (ace)
~ INFO Predicting operons - NC_008578.1 (ace)
~ INFO 6 operons split in NC_008578.1
~ INFO Number of operons (ace): 1087
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (ace).
~ INFO Identifying putative regulons (ace)
~ INFO --------------------------------------------------------------------------------
~ INFO Processing cgl
~ INFO Phylogeny weights: ['0.21', '0.73', '0.00', '0.01', '0.01', '0.04']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.30', '0.67', '0.00', '0.00', '0.01', '0.02']
~ INFO Setting TF-binding model (cgl)
~ INFO Building PSSM model (cgl)
~ INFO Regulation parameters: 15.04 5.08
~ INFO Background parameters: -12.77 6.26
~ INFO Prior(regulation; cgl): 0.03
~ INFO Calculating regulation probabilities (cgl)
~ INFO Predicting operons - NC_003450.3 (cgl)
~ INFO 4 operons split in NC_003450.3
~ INFO Number of operons (cgl): 1656
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (cgl).
~ INFO Identifying putative regulons (cgl)
~ INFO --------------------------------------------------------------------------------
~ INFO Processing lxy
~ INFO Phylogeny weights: ['0.20', '0.19', '0.15', '0.15', '0.15', '0.16']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.34', '0.21', '0.09', '0.05', '0.21', '0.09']
~ INFO Setting TF-binding model (lxy)
~ INFO Building PSSM model (lxy)
~ INFO Regulation parameters: 16.63 4.37
~ INFO Background parameters: -15.72 6.27
~ INFO Prior(regulation; lxy): 0.03
~ INFO Calculating regulation probabilities (lxy)
~ INFO Predicting operons - NC_006087.1 (lxy)
~ INFO 5 operons split in NC_006087.1
~ INFO Number of operons (lxy): 1331
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (lxy).
~ INFO Identifying putative regulons (lxy)
~ INFO Creating orthologous groups
~ INFO Loading orthologs cache.
~ INFO Constructing orthologous groups.
~ INFO Collapsing orthologous groups.
~ INFO Assigning COGs to orthologous groups
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Regulation parameters: 16.61 4.41
~ INFO Background parameters: -16.48 6.24
~ INFO Prior(regulation; ace): 0.03
~ INFO Calculating regulation probabilities (ace)
~ INFO Predicting operons - NC_008578.1 (ace)
~ INFO 6 operons split in NC_008578.1
~ INFO Number of operons (ace): 1087
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (ace).
~ INFO Identifying putative regulons (ace)
~ INFO --------------------------------------------------------------------------------
~ INFO Processing cgl
~ INFO Phylogeny weights: ['0.21', '0.73', '0.00', '0.01', '0.01', '0.04']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.30', '0.67', '0.00', '0.00', '0.01', '0.02']
~ INFO Setting TF-binding model (cgl)
~ INFO Building PSSM model (cgl)
~ INFO Regulation parameters: 15.04 5.08
~ INFO Background parameters: -12.79 6.42
~ INFO Prior(regulation; cgl): 0.03
~ INFO Calculating regulation probabilities (cgl)
~ INFO Predicting operons - NC_003450.3 (cgl)
~ INFO 3 operons split in NC_003450.3
~ INFO Number of operons (cgl): 1655
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (cgl).
~ INFO Identifying putative regulons (cgl)
~ INFO --------------------------------------------------------------------------------
~ INFO Processing lxy
~ INFO Phylogeny weights: ['0.20', '0.19', '0.15', '0.15', '0.15', '0.16']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.34', '0.21', '0.09', '0.05', '0.21', '0.09']
~ INFO Setting TF-binding model (lxy)
~ INFO Building PSSM model (lxy)
~ INFO Regulation parameters: 16.63 4.37
~ INFO Background parameters: -15.69 6.29
~ INFO Prior(regulation; lxy): 0.03
~ INFO Calculating regulation probabilities (lxy)
~ INFO Predicting operons - NC_006087.1 (lxy)
~ INFO 5 operons split in NC_006087.1
~ INFO Number of operons (lxy): 1331
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (lxy).
~ INFO Identifying putative regulons (lxy)
~ INFO Creating orthologous groups
~ INFO Loading orthologs cache.
~ INFO Constructing orthologous groups.
~ INFO Collapsing orthologous groups.
~ INFO Writing out orthologous groups
~ INFO Error for gene CGL_RS04645. Missing protein ID
~ INFO Missing protein ID in cgl genome. Revise your input file
~ INFO Generating plots
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Regulation parameters: 16.61 4.41
~ INFO Background parameters: -16.58 6.24
~ INFO Prior(regulation; ace): 0.03
~ INFO Calculating regulation probabilities (ace)
~ INFO Predicting operons - NC_008578.1 (ace)
~ INFO 6 operons split in NC_008578.1
~ INFO Number of operons (ace): 1087
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (ace).
~ INFO Identifying putative regulons (ace)
~ INFO --------------------------------------------------------------------------------
~ INFO Processing cgl
~ INFO Phylogeny weights: ['0.21', '0.73', '0.00', '0.01', '0.01', '0.04']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.30', '0.67', '0.00', '0.00', '0.01', '0.02']
~ INFO Setting TF-binding model (cgl)
~ INFO Building PSSM model (cgl)
~ INFO Regulation parameters: 15.04 5.08
~ INFO Background parameters: -12.73 6.38
~ INFO Prior(regulation; cgl): 0.03
~ INFO Calculating regulation probabilities (cgl)
~ INFO Predicting operons - NC_003450.3 (cgl)
~ INFO 4 operons split in NC_003450.3
~ INFO Number of operons (cgl): 1656
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (cgl).
~ INFO Identifying putative regulons (cgl)
~ INFO --------------------------------------------------------------------------------
~ INFO Processing lxy
~ INFO Phylogeny weights: ['0.20', '0.19', '0.15', '0.15', '0.15', '0.16']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.34', '0.21', '0.09', '0.05', '0.21', '0.09']
~ INFO Setting TF-binding model (lxy)
~ INFO Building PSSM model (lxy)
~ INFO Regulation parameters: 16.63 4.37
~ INFO Background parameters: -15.73 6.24
~ INFO Prior(regulation; lxy): 0.03
~ INFO Calculating regulation probabilities (lxy)
~ INFO Predicting operons - NC_006087.1 (lxy)
~ INFO 5 operons split in NC_006087.1
~ INFO Number of operons (lxy): 1331
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (lxy).
~ INFO Identifying putative regulons (lxy)
~ INFO Creating orthologous groups
~ INFO Loading orthologs cache.
~ INFO Constructing orthologous groups.
~ INFO Collapsing orthologous groups.
~ INFO Writing out orthologous groups
~ INFO Error for gene CGL_RS04645. Missing protein ID
~ INFO Missing protein ID in cgl genome. Revise your input file
~ INFO Generating plots
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Regulation parameters: 16.61 4.41
~ INFO Background parameters: -16.40 6.23
~ INFO Prior(regulation; ace): 0.03
~ INFO Calculating regulation probabilities (ace)
~ INFO Predicting operons - NC_008578.1 (ace)
~ INFO 6 operons split in NC_008578.1
~ INFO Number of operons (ace): 1087
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (ace).
~ INFO Identifying putative regulons (ace)
~ INFO --------------------------------------------------------------------------------
~ INFO Processing cgl
~ INFO Phylogeny weights: ['0.21', '0.73', '0.00', '0.01', '0.01', '0.04']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.30', '0.67', '0.00', '0.00', '0.01', '0.02']
~ INFO Setting TF-binding model (cgl)
~ INFO Building PSSM model (cgl)
~ INFO Regulation parameters: 15.04 5.08
~ INFO Background parameters: -12.85 6.39
~ INFO Prior(regulation; cgl): 0.03
~ INFO Calculating regulation probabilities (cgl)
~ INFO Predicting operons - NC_003450.3 (cgl)
~ INFO 4 operons split in NC_003450.3
~ INFO Number of operons (cgl): 1656
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (cgl).
~ INFO Identifying putative regulons (cgl)
~ INFO --------------------------------------------------------------------------------
~ INFO Processing lxy
~ INFO Phylogeny weights: ['0.20', '0.19', '0.15', '0.15', '0.15', '0.16']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.34', '0.21', '0.09', '0.05', '0.21', '0.09']
~ INFO Setting TF-binding model (lxy)
~ INFO Building PSSM model (lxy)
~ INFO Regulation parameters: 16.63 4.37
~ INFO Background parameters: -15.80 6.34
~ INFO Prior(regulation; lxy): 0.03
~ INFO Calculating regulation probabilities (lxy)
~ INFO Predicting operons - NC_006087.1 (lxy)
~ INFO 5 operons split in NC_006087.1
~ INFO Number of operons (lxy): 1331
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (lxy).
~ INFO Identifying putative regulons (lxy)
~ INFO Creating orthologous groups
~ INFO Loading orthologs cache.
~ INFO Constructing orthologous groups.
~ INFO Collapsing orthologous groups.
~ INFO Writing out orthologous groups
~ INFO Error for gene CGL_RS04645. Missing protein ID
~ INFO Missing protein ID in cgl genome. Revise your input file
~ INFO Generating plots
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Regulation parameters: 16.61 4.41
~ INFO Background parameters: -16.57 6.23
~ INFO Prior(regulation; ace): 0.03
~ INFO Calculating regulation probabilities (ace)
~ INFO Predicting operons - NC_008578.1 (ace)
~ INFO 6 operons split in NC_008578.1
~ INFO Number of operons (ace): 1087
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (ace).
~ INFO Identifying putative regulons (ace)
~ INFO --------------------------------------------------------------------------------
~ INFO Processing cgl
~ INFO Phylogeny weights: ['0.21', '0.73', '0.00', '0.01', '0.01', '0.04']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.30', '0.67', '0.00', '0.00', '0.01', '0.02']
~ INFO Setting TF-binding model (cgl)
~ INFO Building PSSM model (cgl)
~ INFO Regulation parameters: 15.04 5.08
~ INFO Background parameters: -12.76 6.35
~ INFO Prior(regulation; cgl): 0.03
~ INFO Calculating regulation probabilities (cgl)
~ INFO Predicting operons - NC_003450.3 (cgl)
~ INFO 4 operons split in NC_003450.3
~ INFO Number of operons (cgl): 1656
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (cgl).
~ INFO Identifying putative regulons (cgl)
~ INFO --------------------------------------------------------------------------------
~ INFO Processing lxy
~ INFO Phylogeny weights: ['0.20', '0.19', '0.15', '0.15', '0.15', '0.16']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.34', '0.21', '0.09', '0.05', '0.21', '0.09']
~ INFO Setting TF-binding model (lxy)
~ INFO Building PSSM model (lxy)
~ INFO Regulation parameters: 16.63 4.37
~ INFO Background parameters: -15.62 6.32
~ INFO Prior(regulation; lxy): 0.03
~ INFO Calculating regulation probabilities (lxy)
~ INFO Predicting operons - NC_006087.1 (lxy)
~ INFO 5 operons split in NC_006087.1
~ INFO Number of operons (lxy): 1331
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (lxy).
~ INFO Identifying putative regulons (lxy)
~ INFO Creating orthologous groups
~ INFO Loading orthologs cache.
~ INFO Constructing orthologous groups.
~ INFO Collapsing orthologous groups.
~ INFO Writing out orthologous groups
~ INFO Error for gene CGL_RS04645. Missing protein ID
~ INFO Missing protein ID in cgl genome. Revise your input file
~ INFO Generating plots
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Regulation parameters: 16.61 4.41
~ INFO Background parameters: -16.44 6.25
~ INFO Prior(regulation; ace): 0.03
~ INFO Calculating regulation probabilities (ace)
~ INFO Predicting operons - NC_008578.1 (ace)
~ INFO 6 operons split in NC_008578.1
~ INFO Number of operons (ace): 1087
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (ace).
~ INFO Identifying putative regulons (ace)
~ INFO --------------------------------------------------------------------------------
~ INFO Processing cgl
~ INFO Phylogeny weights: ['0.21', '0.73', '0.00', '0.01', '0.01', '0.04']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.30', '0.67', '0.00', '0.00', '0.01', '0.02']
~ INFO Setting TF-binding model (cgl)
~ INFO Building PSSM model (cgl)
~ INFO Regulation parameters: 15.04 5.08
~ INFO Background parameters: -12.74 6.37
~ INFO Prior(regulation; cgl): 0.03
~ INFO Calculating regulation probabilities (cgl)
~ INFO Predicting operons - NC_003450.3 (cgl)
~ INFO 4 operons split in NC_003450.3
~ INFO Number of operons (cgl): 1656
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (cgl).
~ INFO Identifying putative regulons (cgl)
~ INFO --------------------------------------------------------------------------------
~ INFO Processing lxy
~ INFO Phylogeny weights: ['0.20', '0.19', '0.15', '0.15', '0.15', '0.16']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.34', '0.21', '0.09', '0.05', '0.21', '0.09']
~ INFO Setting TF-binding model (lxy)
~ INFO Building PSSM model (lxy)
~ INFO Regulation parameters: 16.63 4.37
~ INFO Background parameters: -15.83 6.31
~ INFO Prior(regulation; lxy): 0.03
~ INFO Calculating regulation probabilities (lxy)
~ INFO Predicting operons - NC_006087.1 (lxy)
~ INFO 5 operons split in NC_006087.1
~ INFO Number of operons (lxy): 1331
~ INFO Regulation probability threshold: 0.97
~ INFO Inferring regulated operons in (lxy).
~ INFO Identifying putative regulons (lxy)
~ INFO Creating orthologous groups
~ INFO Loading orthologs cache.
~ INFO Constructing orthologous groups.
~ INFO Collapsing orthologous groups.
~ INFO Writing out orthologous groups
~ INFO Error for gene CGL_RS04645. Missing protein ID
~ INFO Missing protein ID in cgl genome. Revise your input file
~ INFO Generating plots
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)
~ INFO Building PSSM model (ace)
~ INFO Regulation parameters: 16.61 4.41
~ INFO Background parameters: -16.48 6.23
~ INFO Prior(regulation; ace): 0.03
~ INFO Calculating regulation probabilities (ace)
~ INFO Checking input file
~ INFO Setting output directory: output
~ INFO Using [email protected] as Entrez email address
~ INFO Using da8f5e3fb2bdbcbf9cf0f2baeb81170f2509 as Entrez API key
~ INFO Using 1.500000 as additional delay for NCBI API
~ INFO Started: create proteins
~ INFO Initializing NP_217236.2.
~ INFO Initializing WP_003857389.1.
~ INFO Initializing NP_464827.1.
~ INFO Initializing WP_001208760.1.
~ INFO Initializing NP_389668.1.
~ INFO Initializing WP_003433043.1.
~ INFO Finished: create proteins
~ INFO Started: create genomes
~ INFO Creating genome: ace [u'NC_008578.1']
~ INFO Creating genome: cgl [u'NC_003450.3']
~ INFO Creating genome: lxy [u'NC_006087.1']
~ INFO Finished: create genomes
~ INFO Identifying TF instance for (ace)
~ INFO WP_202943454.1
~ INFO Identifying TF instance for (cgl)
~ INFO WP_003857389.1
~ INFO Identifying TF instance for (lxy)
~ INFO WP_011186375.1
~ INFO --------------------------------------------------------------------------------
~ INFO Processing ace
~ INFO Phylogeny weights: ['0.22', '0.20', '0.14', '0.14', '0.14', '0.15']
~ INFO Site count weights: ['0.30', '0.20', '0.10', '0.06', '0.24', '0.10']
~ INFO Final weights: ['0.37', '0.22', '0.08', '0.05', '0.20', '0.08']
~ INFO Setting TF-binding model (ace)