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log_file.msg
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Warning: Invalid attributes in aerophilicity: facultative aerobe---microaerotolerant
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 104 of 10901 taxon IDs. The followings are left unrankd: 65497, 287094, 305698, 196083, 136160, 513651, 158080, 1606016, 1646339, 126790, 1017277, 332410, 114529, 2254, 1830421, 1400058, 683756, 88075, 61655, 92835, 76884, 300020, 165807, 134962, 48937, 263820, 1311788, 342610, 81037, 166934, 1398496, 307251, 237610, 219742, 154109, 1462563, 219741, 119541, 262776, 45461, 211759, 244407, 332057, 332056, 46170, 46170, 68202, 84593, 62153, 322609, 109214, 1398560, 228972, 355929, 866775, 1551, 1560, 289244, 86662, 168810, 495036, 1345697, 1166016, 741091, 195041, 85643, 140100, 62153, 675810, 228972, 65497, 861208, 340044, 335659, 546899, 656024, 440512, 147710, 931223, 420233, 332056, 68570, 68202, 81424, 563191, 665937, 469586, 469587, 665938, 469594, 52765, 52766, 699245, 97139, 327817, 644968, 228748, 477693, 652712, 699192, 796939, 796940, 36876, 93930
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 3 of 19738 taxon IDs. The followings are left unrankd: 1774956, 81037, 322609
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 6 of 1727 taxon IDs. The followings are left unrankd: 114529, 300020, 68570, 93930, 158080, 168810
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 6 of 833 taxon IDs. The followings are left unrankd: 114529, 300020, 68202, 68570, 237610, 137779
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 19 of 2443 taxon IDs. The followings are left unrankd: 866775, 289244, 289244, 86662, 195041, 861530, 656024, 1172, 931223, 68202, 327817, 652712, 195041, 469595, 1166016, 81424, 52765, 52766, 684949
Warning: Invalid attributes in biosafety level: biosafety level 1+---biosafety level 3**---biosafety level L1
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 2 of 26443 taxon IDs. The followings are left unrankd: 81037, 322609
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 50 of 4669 taxon IDs. The followings are left unrankd: 1476577, 471821, 263820, 1849491, 866775, 1547445, 1156433, 657310, 671223, 319236, 1104325, 1834200, 1226298, 1182571, 1986224, 319938, 1546149, 1662456, 1902251, 1662457, 1606016, 595593, 287094, 85643, 62928, 1662458, 656024, 1126211, 342610, 1418110, 90270, 697046, 1166016, 1870930, 237610, 1570328, 1653479, 741091, 62153, 861208, 338187, 86662, 338187, 1740162, 134962, 595500, 640511, 335659, 1418105, 68570
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 4 of 1042 taxon IDs. The followings are left unrankd: 68202, 68570, 158080, 237610
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 11 of 1874 taxon IDs. The followings are left unrankd: 196180, 52765, 52766, 158080, 168810, 114529, 300020, 137779, 68570, 68202, 93930
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 50 of 4665 taxon IDs. The followings are left unrankd: 1476577, 471821, 263820, 1849491, 1547445, 1156433, 866775, 671223, 319236, 1104325, 1986224, 1226298, 657310, 1834200, 1182571, 1902251, 1662456, 1546149, 1606016, 1126211, 319938, 62928, 595593, 1662457, 85643, 287094, 1662458, 697046, 1418110, 1166016, 342610, 1870930, 1653479, 656024, 237610, 1570328, 861208, 86662, 741091, 90270, 62153, 338187, 338187, 335659, 1740162, 134962, 1418105, 640511, 595500, 68570
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 58 of 8200 taxon IDs. The followings are left unrankd: 1830421, 1763447, 1427149, 1400058, 1398560, 1331730, 683756, 355929, 289244, 228972, 119541, 84593, 61655, 1183401, 866775, 741091, 342610, 338187, 85643, 420233, 366648, 332056, 300020, 262776, 237610, 196180, 168810, 158080, 137779, 114529, 93930, 90270, 68570, 68202, 52766, 52765, 327817, 332410, 86662, 656024, 168810, 861208, 861530, 931223, 1345697, 1050843, 796940, 665945, 665937, 195041, 469594, 68202, 690871, 68570, 495036, 52765, 196180, 65497
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 3 of 12684 taxon IDs. The followings are left unrankd: 1774956, 81037, 322609
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 32 of 7978 taxon IDs. The followings are left unrankd: 2832, 35130, 265526, 67004, 300020, 338187, 184592, 5749, 2832, 48937, 29398, 2832, 68570, 137779, 1172, 1172, 262776, 1172, 35624, 866775, 330, 330, 330, 330, 330, 114529, 1050843, 263820, 52766, 52765, 93930, 1295133
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 5 of 17559 taxon IDs. The followings are left unrankd: 158080, 759821, 81037, 1774956, 322609
Warning: Invalid attributes in hemolysis: CAMP test
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 56 of 3088 taxon IDs. The followings are left unrankd: 36876, 340044, 147710, 1298859, 86662, 656024, 62153, 861208, 1217695, 1217712, 1217698, 1217697, 1217710, 861530, 640511, 697871, 563191, 366648, 546899, 1050843, 796940, 796939, 665945, 665938, 665937, 195041, 469587, 469586, 469596, 469595, 469594, 1166016, 903916, 699192, 699245, 97139, 658664, 81424, 741091, 335659, 196180, 52765, 52766, 158080, 114529, 300020, 137779, 237610, 420233, 332056, 68570, 68202, 93930, 366648, 90270, 332410
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 4 of 658 taxon IDs. The followings are left unrankd: 683756, 376164, 40136, 61655
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 3 of 11234 taxon IDs. The followings are left unrankd: 1774956, 81037, 322609
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 7 of 886 taxon IDs. The followings are left unrankd: 137779, 262776, 52766, 52765, 332056, 114529, 420233
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 12 of 1493 taxon IDs. The followings are left unrankd: 420233, 68202, 68570, 158080, 1050843, 262776, 114529, 300020, 168810, 93930, 90270, 366648
Warning: Invalid attributes in shape: square---vibriod cell---rod-shaped---coccus-shaped---filament-shaped---oval-shaped---ellipsoidal---ovoid-shaped---pleomorphic-shaped---other---sphere-shaped---spiral-shaped---curved-shaped---helical-shaped---vibrio-shaped---flask-shaped---ring-shaped---spore-shaped---crescent-shaped---star-shaped---diplococcus-shaped
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 90 of 4560 taxon IDs. The followings are left unrankd: 85643, 342610, 741091, 866775, 263820, 1331737, 355929, 289244, 228972, 376164, 1331730, 119541, 1763447, 1830421, 40136, 683756, 61655, 204473, 1400058, 1830421, 119541, 1763447, 1830421, 204473, 1763447, 1830421, 340044, 327817, 147710, 332056, 330, 1298859, 520709, 332410, 86662, 62153, 287484, 992010, 140100, 168810, 861208, 1217695, 1217693, 1217712, 1217698, 1217696, 1217697, 1217702, 1217700, 1217706, 1217710, 1217709, 62928, 640511, 697871, 644968, 911239, 546899, 1345697, 440512, 981223, 665938, 158080, 420233, 469587, 469586, 469595, 469594, 690871, 1166016, 903916, 998429, 658664, 495036, 52765, 52766, 196180, 85643, 741091, 93930, 335659, 675810, 861530, 195041, 477693, 228748, 1172, 861530, 68202, 68570
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 1 of 4413 taxon IDs. The followings are left unrankd: 322609
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 2 of 763 taxon IDs. The followings are left unrankd: 332410, 541003
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 5 of 838 taxon IDs. The followings are left unrankd: 84593, 166974, 61655, 40136, 376164
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 5 of 269 taxon IDs. The followings are left unrankd: 342610, 85643, 338187, 62153, 52765
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 6 of 971 taxon IDs. The followings are left unrankd: 866775, 1183401, 741091, 168810, 1050843, 262776
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 8 of 215 taxon IDs. The followings are left unrankd: 665938, 665937, 195041, 469587, 469586, 469596, 469594, 97139
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 2 of 92 taxon IDs. The followings are left unrankd: 1345697, 52765
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 10 of 305 taxon IDs. The followings are left unrankd: 665938, 665937, 469587, 469586, 469596, 469595, 469594, 699245, 97139, 81424
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 32 of 1280 taxon IDs. The followings are left unrankd: 327817, 82076, 332056, 332410, 86662, 62153, 992010, 140100, 684949, 1172, 931223, 62928, 1267535, 1345697, 2274, 158080, 420233, 1206751, 477693, 68202, 690871, 68570, 228748, 495036, 52765, 52766, 196180, 85643, 93930, 114529, 65497, 675810
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 2 of 25 taxon IDs. The followings are left unrankd: 52765, 52766
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 5 of 115 taxon IDs. The followings are left unrankd: 665938, 195041, 469587, 469586, 469594
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 4 of 84 taxon IDs. The followings are left unrankd: 469587, 469586, 97139, 81424
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 1 of 91 taxon IDs. The followings are left unrankd: 992010
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 1 of 47 taxon IDs. The followings are left unrankd: 195041
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 5 of 88 taxon IDs. The followings are left unrankd: 861208, 697871, 546899, 1166016, 335659
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 2 of 46 taxon IDs. The followings are left unrankd: 147710, 546899
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 1 of 5 taxon IDs. The followings are left unrankd: 546899
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 4 of 60 taxon IDs. The followings are left unrankd: 147710, 861208, 546899, 335659
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 2 of 57 taxon IDs. The followings are left unrankd: 68202, 68570
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 1 of 86 taxon IDs. The followings are left unrankd: 644968
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 1 of 61 taxon IDs. The followings are left unrankd: 86662
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 1 of 144 taxon IDs. The followings are left unrankd: 263820
Warning: Invalid attributes in habitat: Waste and sludge water
Warning: Invalid attributes in disease association: arthritis
Warning: Invalid attributes in disease association: caries
Warning: Invalid attributes in disease association: Endocarditis
Warning: Invalid attributes in disease association: Fever
Warning: There was 1 warning in `dplyr::mutate()`. ℹ In argument: `Rank = taxizedb::taxid2rank(.data$NCBI_ID, db = "ncbi")`. Caused by warning in `taxizedb::taxid2rank()`: ! No rank found for 1 of 132 taxon IDs. The followings are left unrankd: 342610
Warning: Invalid attributes in disease association: Infection
Warning: Invalid attributes in disease association: Infection caused by Escherichia coli (disorder)
Warning: Invalid attributes in disease association: Meningitis
Warning: Invalid attributes in disease association: meningitis septicemia
Warning: Invalid attributes in disease association: periodontal disorder
Warning: Invalid attributes in disease association: Periodontal Disorder
Warning: Invalid attributes in disease association: septicemia arthritis
Warning: Invalid attributes in disease association: Tetnus
Warning: Invalid attributes in disease association: tumors
Warning: Invalid attributes in disease association: urlnary tract infection
Warning: Invalid attributes in antimicrobial resistance: resistance to acinetobacter
Warning: Invalid attributes in antimicrobial resistance: resistance to beta-lactam
Warning: Invalid attributes in antimicrobial resistance: resistance to carbapenems
Warning: Invalid attributes in antimicrobial resistance: resistance to erythromycin a
Warning: Invalid attributes in antimicrobial resistance: resistance to kanamycin a
Warning: appending column names to file
Warning: appending column names to file
Warning: appending column names to file
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options
Warning: Not enough data for creating signatures. Try different filtering options