# HG changeset patch # User iuc # Date 1717501761 0 # Node ID b01d6b38f7793c5815d1f9191e1c3a03e9bb45d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli commit d093bc33200eb4b4332e0b5845ef189e48fdb37a diff -r 000000000000 -r b01d6b38f779 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,18 @@ + + 1.0.5 + + + metabuli + + + + + metabuli | grep Version | sed 's/metabuli Version: //g' + + + + + 10.1038/s41592-024-02273-y + + + \ No newline at end of file diff -r 000000000000 -r b01d6b38f779 metabuli.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metabuli.xml Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,221 @@ + + + metagenomic sequences + + + macros.xml + + + + + + '$log' + + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r b01d6b38f779 test-data/RefSeqTest/acc2taxid.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RefSeqTest/acc2taxid.map Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,3 @@ +NC_003197.2 99287 +NC_000913.3 511145 +AE004091.2 208964 diff -r 000000000000 -r b01d6b38f779 test-data/RefSeqTest/db.parameters --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RefSeqTest/db.parameters Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,8 @@ +DB_name RefSeqTest +Creation_date 2024-5-31 +Metabuli commit used to create the DB 1.0.5 +Reduced_alphabet 0 +Spaced_kmer_mask 11111111 +Accession_level 0 +Mask_mode 1 +Mask_prob 0.900000 diff -r 000000000000 -r b01d6b38f779 test-data/RefSeqTest/diffIdx Binary file test-data/RefSeqTest/diffIdx has changed diff -r 000000000000 -r b01d6b38f779 test-data/RefSeqTest/info Binary file test-data/RefSeqTest/info has changed diff -r 000000000000 -r b01d6b38f779 test-data/RefSeqTest/split Binary file test-data/RefSeqTest/split has changed diff -r 000000000000 -r b01d6b38f779 test-data/RefSeqTest/taxID_list --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RefSeqTest/taxID_list Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,3 @@ +208964 +511145 +99287 diff -r 000000000000 -r b01d6b38f779 test-data/metabuli_databases.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metabuli_databases.loc Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,4 @@ +# This file defines databases and their folder location. Each database is a line with +# three columns: value{tab}{name}{/path/to/database-folder} +# E.g. GTDB{tab}GTDB{tab}GTDB{tab}/path/to/GTDB +RefSeqTest RefSeqTest 2024 ${__HERE__}/RefSeqTest \ No newline at end of file diff -r 000000000000 -r b01d6b38f779 test-data/output/ont.r10.precision_classifications.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/ont.r10.precision_classifications.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,46 @@ +1 6afed69c-0764-187d-7701-25dbaa56fa4d 208964 14214 0.700577 strain 208964:2340 +1 cc0f07c9-8e86-392e-f794-1a4252e9fb38 99287 6180 0.657362 strain 99287:970 +1 f6611dfa-6896-0371-efec-a60a01132e83 99287 27942 0.864756 strain 99287:6265 +1 581fe12a-4956-fa3b-f64f-31d99c708716 511145 9627 0.791056 no rank 511145:1855 +1 2f1a09bf-c558-a8cc-b071-83128761e14f 208964 1812 0.584713 strain 208964:276 +1 956740a3-5b26-133c-d1a2-d2bde75f68da 511145 45297 0.301311 no rank 511145:3124 +1 c277097d-f2a7-010a-ee05-3c93b5f2b6fb 99287 15564 0.650186 strain 99287:2309 +1 7f94a381-1546-7827-286c-5800d7b14fce 511145 8064 0.645957 no rank 511145:1197 +0 42479fca-23da-2161-c636-4a3efa727e79 0 33 0 no rank +1 ee825b81-860f-2bca-1f5e-90339434a8a4 99287 28722 0.666301 strain 99287:4529 +1 fb11ddfb-d32f-5d75-f1c3-41724b7e594e 208964 19653 0.582659 strain 208964:2557 +1 91c09038-76cc-cc91-c19a-7a47204708d4 208964 10176 0.491794 strain 208964:1095 +1 d9237302-7ca1-1cb0-87b5-9bef45b7dafe 511145 15885 0.874032 no rank 511145:3671 +1 7957d890-cc56-1ca8-d0a8-674deb4f96a1 208964 633 0.775671 strain 208964:123 +1 db0e608c-27b4-198c-e5b1-ff9f70153a96 208964 1014 0.425542 strain 208964:82 +1 008b9f35-e6a4-170b-d7f4-3ff9ecc8c875 511145 6864 0.909528 no rank 511145:1785 +1 8f08681a-4a01-0c54-2dd0-3618e772370b 511145 35853 0.790659 no rank 511145:7122 +1 2c199f0c-2601-a3ec-5bff-0c33f1f18bfd 99287 3690 0.814499 strain 99287:770 +1 cd61a49b-d049-b767-3ac3-add014fe2895 208964 19470 0.759553 strain 208964:3718 +1 1f672421-5585-fb71-f73c-40283fb95a51 511145 19251 0.427328 no rank 511145:1851 +1 e5a03490-b6d8-d771-2029-fa165cc02486 208964 10941 0.734713 strain 208964:1858 +1 90d5e8c9-9992-ccad-ed13-50ae9e1f01ed 208964 6183 0.609009 strain 208964:892 +1 fcf8a78c-007a-340b-1dc2-aa07cd4f74e2 208964 10812 0.823899 strain 208964:2242 +1 3bcf93b0-d23f-dc99-60b0-58925d04121e 208964 9777 0.619617 strain 208964:1365 +1 4106b3dc-8d38-d435-04af-22a8a13519ec 511145 4356 0.789256 no rank 511145:839 +1 9419850f-7037-20f0-71c8-c37470e44974 208964 4002 0.824713 strain 208964:812 +1 16e12407-f1ea-d31c-1e78-159997a22af2 208964 4896 0.659518 strain 208964:711 +1 8160d594-20b5-54bf-3185-b420f94f2c3e 99287 2547 0.447978 strain 99287:240 +1 f60e7dc2-d87b-4689-7105-0bce5603d146 511145 17982 0.74708 no rank 511145:3307 +1 b860a965-3998-8602-b83d-1e9a17046940 208964 1122 0.530749 strain 208964:152 +1 b5411913-b5a4-6bfa-30a4-7c956ef32b3a 511145 3300 0.350152 no rank 511145:273 +1 879e0f5f-0bcb-f145-86b2-fa35b9d469a0 99287 34836 0.901323 strain 99287:8652 +1 d8a48a7d-947c-29e9-f7bc-4560053600aa 511145 1392 0.871049 no rank 511145:296 +1 d2c318b8-3227-032b-bfe1-fb011cfc260e 208964 7233 0.772155 strain 208964:1328 +1 a2a7b030-bf46-e658-60e4-949f0980b1ba 511145 3966 0.403681 no rank 511145:333 +1 d17a0751-b32c-c486-066e-4f2d0a23a25a 208964 13539 0.866201 strain 208964:3103 +1 3ab721e1-e301-4c80-8b8a-7483a2fd0619 99287 44919 0.531679 strain 99287:5404 +1 7c3c58f1-8745-92cb-6065-70ab62ac2afe 99287 4866 0.643444 strain 99287:735 +1 dd99b942-6109-7a63-2d38-7a272be96e27 511145 71058 0.482929 no rank 511145:7648 +1 20757211-06ab-db4f-e089-30d4c1aa72fa 511145 7911 0.633991 no rank 511145:1153 +1 ed31326f-5b4b-de9e-d3d7-a246a0790ea7 208964 5883 0.800697 strain 208964:1215 +1 f779b5ad-5375-ab6e-a07b-c5b8f3156bcf 208964 1110 0.633784 strain 208964:158 +1 ff46ad1a-56ec-fff8-0094-135fb400942d 208964 8154 0.610559 strain 208964:1106 +1 c8915e98-895d-b0ca-3eea-c031c9ff1918 208964 20103 0.692484 strain 208964:3358 +1 4f405c5a-5f00-7e8f-7cde-bec88c36d3cf 208964 8181 0.814631 strain 208964:1698 +1 0a5f9965-3e92-d697-cc36-cf18fb1a64a4 99287 1302 0.217742 strain 99287:78 diff -r 000000000000 -r b01d6b38f779 test-data/output/ont.r10.precision_krona.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/ont.r10.precision_krona.html Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,6620 @@ + + + + + + + + + + + + + +
+ + + magnitude + + + kt + + +46145454545452424141414141010101010212121212121
\ No newline at end of file diff -r 000000000000 -r b01d6b38f779 test-data/output/ont.r10.precision_report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/ont.r10.precision_report.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,23 @@ +2.1739 1 1 no rank 0 unclassified +97.8261 45 0 no rank 1 root +97.8261 45 0 no rank 131567 cellular organisms +97.8261 45 0 superkingdom 2 Bacteria +97.8261 45 0 phylum 1224 Pseudomonadota +97.8261 45 0 class 1236 Gammaproteobacteria +52.1739 24 0 order 91347 Enterobacterales +52.1739 24 0 family 543 Enterobacteriaceae +30.4348 14 0 genus 561 Escherichia +30.4348 14 0 species 562 Escherichia coli +30.4348 14 0 strain 83333 Escherichia coli K-12 +30.4348 14 14 no rank 511145 Escherichia coli str. K-12 substr. MG1655 +21.7391 10 0 genus 590 Salmonella +21.7391 10 0 species 28901 Salmonella enterica +21.7391 10 0 subspecies 59201 Salmonella enterica subsp. enterica +21.7391 10 0 no rank 90371 Salmonella enterica subsp. enterica serovar Typhimurium +21.7391 10 10 strain 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 +45.6522 21 0 order 72274 Pseudomonadales +45.6522 21 0 family 135621 Pseudomonadaceae +45.6522 21 0 genus 286 Pseudomonas +45.6522 21 0 species group 136841 Pseudomonas aeruginosa group +45.6522 21 0 species 287 Pseudomonas aeruginosa +45.6522 21 21 strain 208964 Pseudomonas aeruginosa PAO1 diff -r 000000000000 -r b01d6b38f779 test-data/output/ont.r10_classifications.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/ont.r10_classifications.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,46 @@ +1 6afed69c-0764-187d-7701-25dbaa56fa4d 208964 14214 0.700577 strain 208964:2340 +1 cc0f07c9-8e86-392e-f794-1a4252e9fb38 99287 6180 0.657362 strain 99287:970 +1 f6611dfa-6896-0371-efec-a60a01132e83 99287 27942 0.864756 strain 99287:6265 +1 581fe12a-4956-fa3b-f64f-31d99c708716 511145 9627 0.791056 no rank 511145:1855 +1 2f1a09bf-c558-a8cc-b071-83128761e14f 208964 1812 0.584713 strain 208964:276 +1 956740a3-5b26-133c-d1a2-d2bde75f68da 511145 45297 0.301311 no rank 511145:3124 +1 c277097d-f2a7-010a-ee05-3c93b5f2b6fb 99287 15564 0.650186 strain 99287:2309 +1 7f94a381-1546-7827-286c-5800d7b14fce 511145 8064 0.645957 no rank 511145:1197 +0 42479fca-23da-2161-c636-4a3efa727e79 0 33 0 no rank +1 ee825b81-860f-2bca-1f5e-90339434a8a4 99287 28722 0.666301 strain 99287:4529 +1 fb11ddfb-d32f-5d75-f1c3-41724b7e594e 208964 19653 0.582659 strain 208964:2557 +1 91c09038-76cc-cc91-c19a-7a47204708d4 208964 10176 0.491794 strain 208964:1095 +1 d9237302-7ca1-1cb0-87b5-9bef45b7dafe 511145 15885 0.874032 no rank 511145:3671 +1 7957d890-cc56-1ca8-d0a8-674deb4f96a1 208964 633 0.775671 strain 208964:123 +1 db0e608c-27b4-198c-e5b1-ff9f70153a96 208964 1014 0.425542 strain 208964:82 +1 008b9f35-e6a4-170b-d7f4-3ff9ecc8c875 511145 6864 0.909528 no rank 511145:1785 +1 8f08681a-4a01-0c54-2dd0-3618e772370b 511145 35853 0.790659 no rank 511145:7122 +1 2c199f0c-2601-a3ec-5bff-0c33f1f18bfd 99287 3690 0.814499 strain 99287:770 +1 cd61a49b-d049-b767-3ac3-add014fe2895 208964 19470 0.759553 strain 208964:3718 +1 1f672421-5585-fb71-f73c-40283fb95a51 511145 19251 0.427328 no rank 511145:1851 +1 e5a03490-b6d8-d771-2029-fa165cc02486 208964 10941 0.734713 strain 208964:1858 +1 90d5e8c9-9992-ccad-ed13-50ae9e1f01ed 208964 6183 0.609009 strain 208964:892 +1 fcf8a78c-007a-340b-1dc2-aa07cd4f74e2 208964 10812 0.823899 strain 208964:2242 +1 3bcf93b0-d23f-dc99-60b0-58925d04121e 208964 9777 0.619617 strain 208964:1365 +1 4106b3dc-8d38-d435-04af-22a8a13519ec 511145 4356 0.789256 no rank 511145:839 +1 9419850f-7037-20f0-71c8-c37470e44974 208964 4002 0.824713 strain 208964:812 +1 16e12407-f1ea-d31c-1e78-159997a22af2 208964 4896 0.659518 strain 208964:711 +1 8160d594-20b5-54bf-3185-b420f94f2c3e 99287 2547 0.447978 strain 99287:240 +1 f60e7dc2-d87b-4689-7105-0bce5603d146 511145 17982 0.74708 no rank 511145:3307 +1 b860a965-3998-8602-b83d-1e9a17046940 208964 1122 0.530749 strain 208964:152 +1 b5411913-b5a4-6bfa-30a4-7c956ef32b3a 511145 3300 0.350152 no rank 511145:273 +1 879e0f5f-0bcb-f145-86b2-fa35b9d469a0 99287 34836 0.901323 strain 99287:8652 +1 d8a48a7d-947c-29e9-f7bc-4560053600aa 511145 1392 0.871049 no rank 511145:296 +1 d2c318b8-3227-032b-bfe1-fb011cfc260e 208964 7233 0.772155 strain 208964:1328 +1 a2a7b030-bf46-e658-60e4-949f0980b1ba 511145 3966 0.403681 no rank 511145:333 +1 d17a0751-b32c-c486-066e-4f2d0a23a25a 208964 13539 0.866201 strain 208964:3103 +1 3ab721e1-e301-4c80-8b8a-7483a2fd0619 99287 44919 0.531679 strain 99287:5404 +1 7c3c58f1-8745-92cb-6065-70ab62ac2afe 99287 4866 0.643444 strain 99287:735 +1 dd99b942-6109-7a63-2d38-7a272be96e27 511145 71058 0.482929 no rank 511145:7648 +1 20757211-06ab-db4f-e089-30d4c1aa72fa 511145 7911 0.633991 no rank 511145:1153 +1 ed31326f-5b4b-de9e-d3d7-a246a0790ea7 208964 5883 0.800697 strain 208964:1215 +1 f779b5ad-5375-ab6e-a07b-c5b8f3156bcf 208964 1110 0.633784 strain 208964:158 +1 ff46ad1a-56ec-fff8-0094-135fb400942d 208964 8154 0.610559 strain 208964:1106 +1 c8915e98-895d-b0ca-3eea-c031c9ff1918 208964 20103 0.692484 strain 208964:3358 +1 4f405c5a-5f00-7e8f-7cde-bec88c36d3cf 208964 8181 0.814631 strain 208964:1698 +1 0a5f9965-3e92-d697-cc36-cf18fb1a64a4 99287 1302 0.217742 strain 99287:78 diff -r 000000000000 -r b01d6b38f779 test-data/output/ont.r10_krona.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/ont.r10_krona.html Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,6620 @@ + + + + + + + + + + + + + +
+ + + magnitude + + + kt + + +46145454545452424141414141010101010212121212121
\ No newline at end of file diff -r 000000000000 -r b01d6b38f779 test-data/output/ont.r10_report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/ont.r10_report.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,23 @@ +2.1739 1 1 no rank 0 unclassified +97.8261 45 0 no rank 1 root +97.8261 45 0 no rank 131567 cellular organisms +97.8261 45 0 superkingdom 2 Bacteria +97.8261 45 0 phylum 1224 Pseudomonadota +97.8261 45 0 class 1236 Gammaproteobacteria +52.1739 24 0 order 91347 Enterobacterales +52.1739 24 0 family 543 Enterobacteriaceae +30.4348 14 0 genus 561 Escherichia +30.4348 14 0 species 562 Escherichia coli +30.4348 14 0 strain 83333 Escherichia coli K-12 +30.4348 14 14 no rank 511145 Escherichia coli str. K-12 substr. MG1655 +21.7391 10 0 genus 590 Salmonella +21.7391 10 0 species 28901 Salmonella enterica +21.7391 10 0 subspecies 59201 Salmonella enterica subsp. enterica +21.7391 10 0 no rank 90371 Salmonella enterica subsp. enterica serovar Typhimurium +21.7391 10 10 strain 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 +45.6522 21 0 order 72274 Pseudomonadales +45.6522 21 0 family 135621 Pseudomonadaceae +45.6522 21 0 genus 286 Pseudomonas +45.6522 21 0 species group 136841 Pseudomonas aeruginosa group +45.6522 21 0 species 287 Pseudomonas aeruginosa +45.6522 21 21 strain 208964 Pseudomonas aeruginosa PAO1 diff -r 000000000000 -r b01d6b38f779 test-data/output/pb.hifi_classifications.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/pb.hifi_classifications.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,40 @@ +1 46ac816b-5257-0939-9707-d4e402ca7f66 208964 14073 0.624991 strain 208964:2034 +1 2834ee47-67d1-b9b9-a644-8d48b51ef5f0 208964 603 0.399668 strain 208964:57 +1 58130cac-3fbb-69e0-cd73-f584cea7dc94 511145 27102 0.135414 no rank 511145:866 +1 c28e35a1-5a3f-a437-6fa6-c6aca123fb7a 511145 22071 0.615559 no rank 511145:3054 +1 b1c42de6-1927-4fb4-931c-26ea9c1a125b 511145 207 0.195652 no rank 511145:9 +1 e112e5b5-4746-3cba-e53e-a16d32986d7a 208964 1020 0.731373 strain 208964:190 +1 a48e104f-ed2a-15ad-9e16-087e18062131 99287 27687 0.286037 strain 99287:1785 +1 dffb75c8-0f85-de32-360e-01c88e7519c0 99287 40410 0.524709 strain 99287:4655 +1 8c854602-9d71-7f71-0b9e-2103e53eb1f3 99287 933 0.726688 strain 99287:157 +1 88acfcc8-6092-3d67-24ff-08a0c729d292 208964 28608 0.587633 strain 208964:3750 +1 fb77e180-7d01-f781-776f-bdfcad00fbc8 99287 17943 0.475701 strain 99287:1842 +1 f71a9e94-d34a-e077-178a-d48b07507070 511145 53712 0.869238 no rank 511145:11950 +1 f964749a-6d47-6c21-e7f2-4d0835a35a3b 99287 642 0.573209 strain 99287:94 +1 406338db-9f37-0eb6-5d10-e6316ca896ea 99287 9255 0.616099 strain 99287:1302 +1 8867579d-91e4-3751-d245-1d9296fc390f 99287 28203 0.660267 strain 99287:4314 +1 aac5d808-4179-375e-edc4-fd089b7b53f8 99287 20985 0.174696 strain 99287:820 +1 f3c24ded-b4ee-3006-07b6-4859e87146e3 208964 12954 0.71503 strain 208964:2241 +1 1edb2cdb-1289-1f2a-abc6-08338f372923 208964 15972 0.31383 strain 208964:1153 +1 6345023a-4846-edaf-e9dd-a41f3dc48f53 511145 4962 0.592201 no rank 511145:694 +1 a8577a53-a35a-c6ed-4f2d-51f4e1750b93 99287 864 0.0763889 strain 99287:32 +1 bd619d24-26bc-4dfe-75b9-052f241cbf49 511145 31755 0.341553 no rank 511145:2331 +1 d61026de-c088-fac5-cf67-b76d8cf481ab 208964 4428 0.78907 strain 208964:845 +1 294128de-cb85-4061-2c9a-0d7f7248eccf 208964 4134 0.45658 strain 208964:410 +1 753335d5-a752-bde7-5a4c-13ab429f472d 208964 15255 0.0832842 strain 208964:322 +1 c1989402-f62f-21e0-e827-5c44c4d7562e 511145 32733 0.695552 no rank 511145:5320 +1 8a7703b3-9d44-ade2-1746-bb6c0bd3cc24 208964 3357 0.605302 strain 208964:437 +1 410a70bf-df52-5535-e301-822750188972 99287 7602 0.438569 strain 99287:725 +1 0b66b503-69ec-2798-2442-ebee9a26ca47 208964 22935 0.6753 strain 208964:3642 +1 b4d8e5b9-1597-48a3-f2db-5e7e37578597 208964 6225 0.356466 strain 208964:474 +1 c514c133-303c-ceaf-cfdc-b70536c26e32 99287 9018 0.478598 strain 99287:913 +1 518f3cec-ce4a-3a0f-d6bf-03a4433c7612 208964 33669 0.67531 strain 208964:5315 +1 7c871d7a-5122-b779-a6fe-24b3417b0d4d 511145 10275 0.341655 no rank 511145:759 +1 de93f009-2707-a131-b038-108e8373cea7 99287 19668 0.577435 strain 99287:2579 +1 3a62aec2-7254-e342-ea17-e43f2e3c933a 99287 25908 0.259476 strain 99287:1501 +1 0b62d3c8-5482-b549-457a-ffeca8907812 511145 10296 0.316191 no rank 511145:686 +1 8323893b-d729-09be-770b-c0697f571c28 511145 3924 0.771789 no rank 511145:707 +1 a4d8d18d-afde-b01a-d552-476bc9831614 208964 5094 0.736455 strain 208964:931 +1 2bc1c4e3-a780-9ba8-dbbf-66336e0c1b9a 511145 1944 0.343621 no rank 511145:117 +0 cbebaff1-ab59-f0cd-9854-fca99cb223e7 0 13575 0 no rank +1 3b93efb1-3066-00d4-566f-64c1fecc6951 511145 18780 0.464457 no rank 511145:2020 diff -r 000000000000 -r b01d6b38f779 test-data/output/pb.hifi_krona.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/pb.hifi_krona.html Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,6620 @@ + + + + + + + + + + + + + +
+ + + magnitude + + + kt + + +40139393939392525131313131312121212141414141414
\ No newline at end of file diff -r 000000000000 -r b01d6b38f779 test-data/output/pb.hifi_report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/pb.hifi_report.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,23 @@ +2.5000 1 1 no rank 0 unclassified +97.5000 39 0 no rank 1 root +97.5000 39 0 no rank 131567 cellular organisms +97.5000 39 0 superkingdom 2 Bacteria +97.5000 39 0 phylum 1224 Pseudomonadota +97.5000 39 0 class 1236 Gammaproteobacteria +62.5000 25 0 order 91347 Enterobacterales +62.5000 25 0 family 543 Enterobacteriaceae +32.5000 13 0 genus 590 Salmonella +32.5000 13 0 species 28901 Salmonella enterica +32.5000 13 0 subspecies 59201 Salmonella enterica subsp. enterica +32.5000 13 0 no rank 90371 Salmonella enterica subsp. enterica serovar Typhimurium +32.5000 13 13 strain 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 +30.0000 12 0 genus 561 Escherichia +30.0000 12 0 species 562 Escherichia coli +30.0000 12 0 strain 83333 Escherichia coli K-12 +30.0000 12 12 no rank 511145 Escherichia coli str. K-12 substr. MG1655 +35.0000 14 0 order 72274 Pseudomonadales +35.0000 14 0 family 135621 Pseudomonadaceae +35.0000 14 0 genus 286 Pseudomonas +35.0000 14 0 species group 136841 Pseudomonas aeruginosa group +35.0000 14 0 species 287 Pseudomonas aeruginosa +35.0000 14 14 strain 208964 Pseudomonas aeruginosa PAO1 diff -r 000000000000 -r b01d6b38f779 test-data/output/sr_classifications.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/sr_classifications.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,1500 @@ +1 AE004091.2_0_0/1 208964 594 0.984848 strain 208964:167 +1 AE004091.2_1_0/1 208964 594 0.89899 strain 208964:150 +1 AE004091.2_2_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_3_0/1 208964 594 0.946128 strain 208964:176 +1 AE004091.2_4_0/1 208964 594 0.95202 strain 208964:161 +1 AE004091.2_5_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_6_0/1 208964 594 0.699495 strain 208964:94 +1 AE004091.2_7_0/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_8_0/1 208964 594 0.936869 strain 208964:151 +1 AE004091.2_9_0/1 208964 594 0.957071 strain 208964:169 +1 AE004091.2_10_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_11_0/1 208964 594 0.974747 strain 208964:172 +1 AE004091.2_12_0/1 208964 594 0.999158 strain 208964:184 +1 AE004091.2_13_0/1 208964 594 0.936869 strain 208964:166 +1 AE004091.2_14_0/1 208964 594 0.767677 strain 208964:125 +1 AE004091.2_15_0/1 208964 594 0.893939 strain 208964:158 +1 AE004091.2_16_0/1 208964 594 0.881313 strain 208964:133 +1 AE004091.2_17_0/1 208964 594 0.949495 strain 208964:153 +1 AE004091.2_18_0/1 208964 594 0.964646 strain 208964:179 +1 AE004091.2_19_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_20_0/1 208964 594 0.878788 strain 208964:156 +1 AE004091.2_21_0/1 208964 594 0.920034 strain 208964:157 +1 AE004091.2_22_0/1 208964 594 0.992424 strain 208964:176 +1 AE004091.2_23_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_24_0/1 208964 594 0.631313 strain 208964:111 +1 AE004091.2_25_0/1 208964 594 0.846801 strain 208964:142 +1 AE004091.2_26_0/1 208964 594 0.996633 strain 208964:176 +1 AE004091.2_27_0/1 208964 594 0.992424 strain 208964:183 +1 AE004091.2_28_0/1 208964 594 0.949495 strain 208964:160 +1 AE004091.2_29_0/1 208964 594 0.992424 strain 208964:176 +1 AE004091.2_30_0/1 208964 594 0.94697 strain 208964:168 +1 AE004091.2_31_0/1 208964 594 0.924242 strain 208964:151 +1 AE004091.2_32_0/1 208964 594 0.944444 strain 208964:160 +1 AE004091.2_33_0/1 208964 594 0.818182 strain 208964:137 +1 AE004091.2_34_0/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_35_0/1 208964 594 0.934343 strain 208964:150 +1 AE004091.2_36_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_37_0/1 208964 594 0.939394 strain 208964:160 +1 AE004091.2_38_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_39_0/1 208964 594 0.964646 strain 208964:177 +1 AE004091.2_40_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_41_0/1 208964 594 0.940236 strain 208964:152 +1 AE004091.2_42_0/1 208964 594 0.974747 strain 208964:172 +1 AE004091.2_43_0/1 208964 594 0.987374 strain 208964:169 +1 AE004091.2_44_0/1 208964 594 0.982323 strain 208964:160 +1 AE004091.2_45_0/1 208964 594 0.954545 strain 208964:175 +1 AE004091.2_46_0/1 208964 594 0.998317 strain 208964:176 +1 AE004091.2_47_0/1 208964 594 0.974747 strain 208964:159 +1 AE004091.2_48_0/1 208964 594 0.934343 strain 208964:172 +1 AE004091.2_49_0/1 208964 594 0.984848 strain 208964:175 +1 AE004091.2_50_0/1 208964 594 0.978114 strain 208964:152 +1 AE004091.2_51_0/1 208964 594 0.969697 strain 208964:164 +1 AE004091.2_52_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_53_0/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_54_0/1 208964 594 0.90404 strain 208964:151 +1 AE004091.2_55_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_56_0/1 208964 594 0.955387 strain 208964:176 +1 AE004091.2_57_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_58_0/1 208964 594 0.949495 strain 208964:153 +1 AE004091.2_59_0/1 208964 594 0.993266 strain 208964:176 +1 AE004091.2_60_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_61_0/1 208964 594 0.761784 strain 208964:134 +1 AE004091.2_62_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_63_0/1 208964 594 0.924242 strain 208964:149 +1 AE004091.2_64_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_65_0/1 208964 594 0.992424 strain 208964:176 +1 AE004091.2_66_0/1 208964 594 0.902357 strain 208964:158 +1 AE004091.2_67_0/1 208964 594 0.941077 strain 208964:152 +1 AE004091.2_68_0/1 208964 594 0.962121 strain 208964:142 +1 AE004091.2_69_0/1 208964 594 0.881313 strain 208964:148 +1 AE004091.2_70_0/1 208964 594 0.881313 strain 208964:148 +1 AE004091.2_71_0/1 208964 594 0.883838 strain 208964:155 +1 AE004091.2_72_0/1 208964 594 0.825758 strain 208964:148 +1 AE004091.2_73_0/1 208964 594 0.968855 strain 208964:162 +1 AE004091.2_74_0/1 208964 594 0.956229 strain 208964:176 +1 AE004091.2_75_0/1 208964 594 0.998317 strain 208964:176 +1 AE004091.2_76_0/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_77_0/1 208964 594 0.89899 strain 208964:151 +1 AE004091.2_78_0/1 208964 594 0.993266 strain 208964:175 +1 AE004091.2_79_0/1 208964 594 0.967172 strain 208964:150 +1 AE004091.2_80_0/1 208964 594 0.988216 strain 208964:175 +1 AE004091.2_81_0/1 208964 594 0.977273 strain 208964:166 +1 AE004091.2_82_0/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_83_0/1 208964 594 0.972222 strain 208964:172 +1 AE004091.2_84_0/1 208964 594 0.984848 strain 208964:160 +1 AE004091.2_85_0/1 208964 594 0.99495 strain 208964:183 +1 AE004091.2_86_0/1 208964 594 0.97138 strain 208964:177 +1 AE004091.2_87_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_88_0/1 208964 594 0.979798 strain 208964:166 +1 AE004091.2_89_0/1 208964 594 0.757576 strain 208964:119 +1 AE004091.2_90_0/1 208964 594 0.967172 strain 208964:171 +1 AE004091.2_91_0/1 208964 594 0.990741 strain 208964:168 +1 AE004091.2_92_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_93_0/1 208964 594 0.992424 strain 208964:176 +1 AE004091.2_94_0/1 208964 594 0.902357 strain 208964:145 +1 AE004091.2_95_0/1 208964 594 0.968013 strain 208964:163 +1 AE004091.2_96_0/1 208964 594 0.993266 strain 208964:176 +1 AE004091.2_97_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_98_0/1 208964 594 0.996633 strain 208964:176 +1 AE004091.2_99_0/1 208964 594 0.896465 strain 208964:168 +1 AE004091.2_100_0/1 208964 594 0.944444 strain 208964:176 +1 AE004091.2_101_0/1 208964 594 0.988216 strain 208964:168 +1 AE004091.2_102_0/1 208964 594 0.883838 strain 208964:161 +1 AE004091.2_103_0/1 208964 594 0.962963 strain 208964:163 +1 AE004091.2_104_0/1 208964 594 0.961279 strain 208964:169 +1 AE004091.2_105_0/1 208964 594 0.957071 strain 208964:148 +1 AE004091.2_106_0/1 208964 594 0.95202 strain 208964:161 +1 AE004091.2_107_0/1 208964 594 0.993266 strain 208964:176 +1 AE004091.2_108_0/1 208964 594 0.976431 strain 208964:158 +1 AE004091.2_109_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_110_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_111_0/1 208964 594 0.910774 strain 208964:169 +1 AE004091.2_112_0/1 208964 594 0.878788 strain 208964:153 +1 AE004091.2_113_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_114_0/1 208964 594 0.919192 strain 208964:156 +1 AE004091.2_115_0/1 208964 594 0.991583 strain 208964:176 +1 AE004091.2_116_0/1 208964 594 0.99495 strain 208964:183 +1 AE004091.2_117_0/1 208964 594 0.957071 strain 208964:169 +1 AE004091.2_118_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_119_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_120_0/1 208964 594 0.991583 strain 208964:182 +1 AE004091.2_121_0/1 208964 594 0.977273 strain 208964:173 +1 AE004091.2_122_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_123_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_124_0/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_125_0/1 208964 594 0.85101 strain 208964:127 +1 AE004091.2_126_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_127_0/1 208964 594 0.996633 strain 208964:184 +1 AE004091.2_128_0/1 208964 594 0.959596 strain 208964:177 +1 AE004091.2_129_0/1 208964 594 0.989057 strain 208964:173 +1 AE004091.2_130_0/1 208964 594 0.781987 strain 208964:124 +1 AE004091.2_131_0/1 208964 594 0.990741 strain 208964:168 +1 AE004091.2_132_0/1 208964 594 0.89899 strain 208964:166 +1 AE004091.2_133_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_134_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_135_0/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_136_0/1 208964 594 0.941919 strain 208964:162 +1 AE004091.2_137_0/1 208964 594 0.894781 strain 208964:152 +1 AE004091.2_138_0/1 208964 594 0.912458 strain 208964:167 +1 AE004091.2_139_0/1 208964 594 0.853535 strain 208964:130 +1 AE004091.2_140_0/1 208964 594 0.772727 strain 208964:137 +1 AE004091.2_141_0/1 208964 594 0.964646 strain 208964:177 +1 AE004091.2_142_0/1 208964 594 0.959596 strain 208964:176 +1 AE004091.2_143_0/1 208964 594 0.934343 strain 208964:164 +1 AE004091.2_144_0/1 208964 594 0.863636 strain 208964:149 +1 AE004091.2_145_0/1 208964 594 0.956229 strain 208964:154 +1 AE004091.2_146_0/1 208964 594 0.909091 strain 208964:160 +1 AE004091.2_147_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_148_0/1 208964 594 0.89899 strain 208964:133 +1 AE004091.2_149_0/1 208964 594 0.982323 strain 208964:160 +1 AE004091.2_150_0/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_151_0/1 208964 594 0.989899 strain 208964:176 +1 AE004091.2_152_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_153_0/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_154_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_155_0/1 208964 594 0.921717 strain 208964:162 +1 AE004091.2_156_0/1 208964 594 0.919192 strain 208964:171 +1 AE004091.2_157_0/1 208964 594 0.947811 strain 208964:176 +1 AE004091.2_158_0/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_159_0/1 208964 594 0.939394 strain 208964:173 +1 AE004091.2_160_0/1 208964 594 0.833333 strain 208964:127 +1 AE004091.2_161_0/1 208964 594 0.611111 strain 208964:100 +1 AE004091.2_162_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_163_0/1 208964 594 0.959596 strain 208964:169 +1 AE004091.2_164_0/1 208964 594 0.888889 strain 208964:152 +1 AE004091.2_165_0/1 208964 594 0.974747 strain 208964:172 +1 AE004091.2_166_0/1 208964 594 0.930976 strain 208964:172 +1 AE004091.2_167_0/1 208964 594 0.984848 strain 208964:181 +1 AE004091.2_168_0/1 208964 594 0.962121 strain 208964:142 +1 AE004091.2_169_0/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_170_0/1 208964 594 0.914141 strain 208964:148 +1 AE004091.2_171_0/1 208964 594 0.929293 strain 208964:163 +1 AE004091.2_172_0/1 208964 594 0.996633 strain 208964:184 +1 AE004091.2_173_0/1 208964 594 0.996633 strain 208964:176 +1 AE004091.2_174_0/1 208964 594 0.972222 strain 208964:172 +1 AE004091.2_175_0/1 208964 594 0.916667 strain 208964:141 +1 AE004091.2_176_0/1 208964 594 0.948653 strain 208964:160 +1 AE004091.2_177_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_178_0/1 208964 594 0.949495 strain 208964:160 +1 AE004091.2_179_0/1 208964 594 0.984848 strain 208964:174 +1 AE004091.2_180_0/1 208964 594 0.922559 strain 208964:165 +1 AE004091.2_181_0/1 208964 594 0.991583 strain 208964:176 +1 AE004091.2_182_0/1 208964 594 0.988216 strain 208964:168 +1 AE004091.2_183_0/1 208964 594 0.924242 strain 208964:157 +1 AE004091.2_184_0/1 208964 594 0.969697 strain 208964:171 +1 AE004091.2_185_0/1 208964 594 0.959596 strain 208964:176 +1 AE004091.2_186_0/1 208964 594 0.893939 strain 208964:150 +1 AE004091.2_187_0/1 208964 594 0.808081 strain 208964:149 +1 AE004091.2_188_0/1 208964 594 0.989057 strain 208964:176 +1 AE004091.2_189_0/1 208964 594 0.888889 strain 208964:156 +1 AE004091.2_190_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_191_0/1 208964 594 0.95202 strain 208964:175 +1 AE004091.2_192_0/1 208964 594 0.954545 strain 208964:162 +1 AE004091.2_193_0/1 208964 594 0.964646 strain 208964:177 +1 AE004091.2_194_0/1 208964 594 0.936027 strain 208964:158 +1 AE004091.2_195_0/1 208964 594 0.967172 strain 208964:171 +1 AE004091.2_196_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_197_0/1 208964 594 0.984848 strain 208964:168 +1 AE004091.2_198_0/1 208964 594 0.883838 strain 208964:119 +1 AE004091.2_199_0/1 208964 594 0.979798 strain 208964:180 +1 AE004091.2_200_0/1 208964 594 0.969697 strain 208964:164 +1 AE004091.2_201_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_202_0/1 208964 594 0.949495 strain 208964:160 +1 AE004091.2_203_0/1 208964 594 0.93266 strain 208964:174 +1 AE004091.2_204_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_205_0/1 208964 594 0.959596 strain 208964:169 +1 AE004091.2_206_0/1 208964 594 0.989057 strain 208964:168 +1 AE004091.2_207_0/1 208964 594 0.964646 strain 208964:170 +1 AE004091.2_208_0/1 208964 594 0.964646 strain 208964:173 +1 AE004091.2_209_0/1 208964 594 0.984848 strain 208964:168 +1 AE004091.2_210_0/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_211_0/1 208964 594 0.888889 strain 208964:165 +1 AE004091.2_212_0/1 208964 594 0.989899 strain 208964:175 +1 AE004091.2_213_0/1 208964 594 0.982323 strain 208964:160 +1 AE004091.2_214_0/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_215_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_216_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_217_0/1 208964 594 0.830808 strain 208964:133 +1 AE004091.2_218_0/1 208964 594 0.969697 strain 208964:171 +1 AE004091.2_219_0/1 208964 594 0.991583 strain 208964:175 +1 AE004091.2_220_0/1 208964 594 0.908249 strain 208964:141 +1 AE004091.2_221_0/1 208964 594 0.967172 strain 208964:173 +1 AE004091.2_222_0/1 208964 594 0.926768 strain 208964:135 +1 AE004091.2_223_0/1 208964 594 0.969697 strain 208964:178 +1 AE004091.2_224_0/1 208964 594 0.80303 strain 208964:141 +1 AE004091.2_225_0/1 208964 594 0.949495 strain 208964:153 +1 AE004091.2_226_0/1 208964 594 0.911616 strain 208964:153 +1 AE004091.2_227_0/1 208964 594 0.964646 strain 208964:163 +1 AE004091.2_228_0/1 208964 594 0.924242 strain 208964:171 +1 AE004091.2_229_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_230_0/1 208964 594 0.984848 strain 208964:174 +1 AE004091.2_231_0/1 208964 594 0.737374 strain 208964:127 +1 AE004091.2_232_0/1 208964 594 0.611111 strain 208964:108 +1 AE004091.2_233_0/1 208964 594 0.909091 strain 208964:146 +1 AE004091.2_234_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_235_0/1 208964 594 0.888889 strain 208964:149 +1 AE004091.2_236_0/1 208964 594 0.921717 strain 208964:157 +1 AE004091.2_237_0/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_238_0/1 208964 594 0.957071 strain 208964:176 +1 AE004091.2_239_0/1 208964 594 0.939394 strain 208964:176 +1 AE004091.2_240_0/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_241_0/1 208964 594 0.959596 strain 208964:176 +1 AE004091.2_242_0/1 208964 594 0.959596 strain 208964:176 +1 AE004091.2_243_0/1 208964 594 0.982323 strain 208964:181 +1 AE004091.2_244_0/1 208964 594 0.977273 strain 208964:168 +1 AE004091.2_245_0/1 208964 594 1 strain 208964:184 +1 AE004091.2_246_0/1 208964 594 0.868687 strain 208964:144 +1 AE004091.2_247_0/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_248_0/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_249_0/1 208964 594 0.950337 strain 208964:175 +1 AE004091.2_0_1/1 208964 594 0.988216 strain 208964:175 +1 AE004091.2_1_1/1 208964 594 0.883838 strain 208964:140 +1 AE004091.2_2_1/1 208964 594 0.972222 strain 208964:179 +1 AE004091.2_3_1/1 208964 594 0.959596 strain 208964:176 +1 AE004091.2_4_1/1 208964 594 0.876263 strain 208964:156 +1 AE004091.2_5_1/1 208964 594 0.944444 strain 208964:168 +1 AE004091.2_6_1/1 208964 594 0.90404 strain 208964:154 +1 AE004091.2_7_1/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_8_1/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_9_1/1 208964 594 0.731481 strain 208964:118 +1 AE004091.2_10_1/1 208964 594 0.99495 strain 208964:184 +1 AE004091.2_11_1/1 208964 594 0.806397 strain 208964:125 +1 AE004091.2_12_1/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_13_1/1 208964 594 0.93266 strain 208964:164 +1 AE004091.2_14_1/1 208964 594 0.964646 strain 208964:156 +1 AE004091.2_15_1/1 208964 594 0.984848 strain 208964:176 +1 AE004091.2_16_1/1 208964 594 0.972222 strain 208964:151 +1 AE004091.2_17_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_18_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_19_1/1 208964 594 0.944444 strain 208964:160 +1 AE004091.2_20_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_21_1/1 208964 594 0.815657 strain 208964:142 +1 AE004091.2_22_1/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_23_1/1 208964 594 0.984848 strain 208964:181 +1 AE004091.2_24_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_25_1/1 208964 594 0.964646 strain 208964:163 +1 AE004091.2_26_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_27_1/1 208964 594 0.939394 strain 208964:172 +1 AE004091.2_28_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_29_1/1 208964 594 0.964646 strain 208964:158 +1 AE004091.2_30_1/1 208964 594 0.957071 strain 208964:169 +1 AE004091.2_31_1/1 208964 594 0.99495 strain 208964:183 +1 AE004091.2_32_1/1 208964 594 0.358586 strain 208964:52 +1 AE004091.2_33_1/1 208964 594 0.969697 strain 208964:172 +1 AE004091.2_34_1/1 208964 594 0.944444 strain 208964:166 +1 AE004091.2_35_1/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_36_1/1 208964 594 0.977273 strain 208964:173 +1 AE004091.2_37_1/1 208964 594 0.959596 strain 208964:162 +1 AE004091.2_38_1/1 208964 594 0.967172 strain 208964:178 +1 AE004091.2_39_1/1 208964 594 0.962121 strain 208964:163 +1 AE004091.2_40_1/1 208964 594 0.5 strain 208964:92 +1 AE004091.2_41_1/1 208964 594 0.959596 strain 208964:176 +1 AE004091.2_42_1/1 208964 594 0.941919 strain 208964:166 +1 AE004091.2_43_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_44_1/1 208964 594 0.981481 strain 208964:166 +1 AE004091.2_45_1/1 208964 594 0.921717 strain 208964:134 +1 AE004091.2_46_1/1 208964 594 0.501683 strain 208964:95 +1 AE004091.2_47_1/1 208964 594 0.93771 strain 208964:158 +1 AE004091.2_48_1/1 208964 594 0.792929 strain 208964:143 +1 AE004091.2_49_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_50_1/1 208964 594 0.998317 strain 208964:176 +1 AE004091.2_51_1/1 208964 594 0.941077 strain 208964:168 +1 AE004091.2_52_1/1 208964 594 0.987374 strain 208964:168 +1 AE004091.2_53_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_54_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_55_1/1 208964 594 0.992424 strain 208964:176 +1 AE004091.2_56_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_57_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_58_1/1 208964 594 0.996633 strain 208964:176 +1 AE004091.2_59_1/1 208964 594 0.976431 strain 208964:165 +1 AE004091.2_60_1/1 208964 594 0.989899 strain 208964:176 +1 AE004091.2_61_1/1 208964 594 0.929293 strain 208964:156 +1 AE004091.2_62_1/1 208964 594 0.901515 strain 208964:137 +1 AE004091.2_63_1/1 208964 594 0.923401 strain 208964:171 +1 AE004091.2_64_1/1 208964 594 0.808081 strain 208964:137 +1 AE004091.2_65_1/1 208964 594 0.878788 strain 208964:149 +1 AE004091.2_66_1/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_67_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_68_1/1 208964 594 0.909091 strain 208964:152 +1 AE004091.2_69_1/1 208964 594 0.958754 strain 208964:160 +1 AE004091.2_70_1/1 208964 594 0.973906 strain 208964:172 +1 AE004091.2_71_1/1 208964 594 0.984848 strain 208964:174 +1 AE004091.2_72_1/1 208964 594 0.949495 strain 208964:168 +1 AE004091.2_73_1/1 208964 594 0.957912 strain 208964:161 +1 AE004091.2_74_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_75_1/1 208964 594 0.979798 strain 208964:180 +1 AE004091.2_76_1/1 208964 594 0.99495 strain 208964:184 +1 AE004091.2_77_1/1 208964 594 0.986532 strain 208964:181 +1 AE004091.2_78_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_79_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_80_1/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_81_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_82_1/1 208964 594 0.957912 strain 208964:175 +1 AE004091.2_83_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_84_1/1 208964 594 0.957071 strain 208964:176 +1 AE004091.2_85_1/1 208964 594 0.987374 strain 208964:168 +1 AE004091.2_86_1/1 208964 594 0.993266 strain 208964:176 +1 AE004091.2_87_1/1 208964 594 0.964646 strain 208964:177 +1 AE004091.2_88_1/1 208964 594 0.775253 strain 208964:121 +1 AE004091.2_89_1/1 208964 594 0.914141 strain 208964:170 +1 AE004091.2_90_1/1 208964 594 0.964646 strain 208964:177 +1 AE004091.2_91_1/1 208964 594 0.988216 strain 208964:168 +1 AE004091.2_92_1/1 208964 594 0.97138 strain 208964:178 +1 AE004091.2_93_1/1 208964 594 0.973064 strain 208964:165 +1 AE004091.2_94_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_95_1/1 208964 594 0.915825 strain 208964:147 +1 AE004091.2_96_1/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_97_1/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_98_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_99_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_100_1/1 208964 594 0.888047 strain 208964:156 +1 AE004091.2_101_1/1 208964 594 0.981481 strain 208964:166 +1 AE004091.2_102_1/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_103_1/1 208964 594 0.993266 strain 208964:176 +1 AE004091.2_104_1/1 208964 594 0.64899 strain 208964:110 +1 AE004091.2_105_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_106_1/1 208964 594 0.888889 strain 208964:155 +1 AE004091.2_107_1/1 208964 594 0.934343 strain 208964:176 +1 AE004091.2_108_1/1 208964 594 0.934343 strain 208964:174 +1 AE004091.2_109_1/1 208964 594 0.984848 strain 208964:181 +1 AE004091.2_110_1/1 208964 594 0.934343 strain 208964:164 +1 AE004091.2_111_1/1 208964 594 0.804714 strain 208964:135 +1 AE004091.2_112_1/1 208964 594 0.976431 strain 208964:179 +1 AE004091.2_113_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_114_1/1 208964 594 0.957912 strain 208964:169 +1 AE004091.2_115_1/1 208964 594 0.988216 strain 208964:160 +1 AE004091.2_116_1/1 208964 594 0.979798 strain 208964:168 +1 AE004091.2_117_1/1 208964 594 0.782828 strain 208964:127 +1 AE004091.2_118_1/1 208964 594 0.968855 strain 208964:166 +1 AE004091.2_119_1/1 208964 594 0.927609 strain 208964:165 +1 AE004091.2_120_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_121_1/1 208964 594 0.949495 strain 208964:154 +1 AE004091.2_122_1/1 208964 594 0.727273 strain 208964:130 +1 AE004091.2_123_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_124_1/1 208964 594 0.941919 strain 208964:168 +1 AE004091.2_125_1/1 208964 594 0.876263 strain 208964:139 +1 AE004091.2_126_1/1 208964 594 0.984848 strain 208964:168 +1 AE004091.2_127_1/1 208964 594 0.925084 strain 208964:156 +1 AE004091.2_128_1/1 208964 594 0.962121 strain 208964:177 +1 AE004091.2_129_1/1 208964 594 0.924242 strain 208964:169 +1 AE004091.2_130_1/1 208964 594 0.934343 strain 208964:152 +1 AE004091.2_131_1/1 208964 594 0.951178 strain 208964:168 +1 AE004091.2_132_1/1 208964 594 0.989899 strain 208964:175 +1 AE004091.2_133_1/1 208964 594 0.651515 strain 208964:107 +1 AE004091.2_134_1/1 208964 594 0.963805 strain 208964:170 +1 AE004091.2_135_1/1 208964 594 0.934343 strain 208964:164 +1 AE004091.2_136_1/1 208964 594 0.492424 strain 208964:84 +1 AE004091.2_137_1/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_138_1/1 208964 594 0.848485 strain 208964:141 +1 AE004091.2_139_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_140_1/1 208964 594 0.97138 strain 208964:173 +1 AE004091.2_141_1/1 208964 594 0.926768 strain 208964:156 +1 AE004091.2_142_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_143_1/1 208964 594 0.861111 strain 208964:131 +1 AE004091.2_144_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_145_1/1 208964 594 0.934343 strain 208964:157 +1 AE004091.2_146_1/1 208964 594 0.924242 strain 208964:152 +1 AE004091.2_147_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_148_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_149_1/1 208964 594 0.996633 strain 208964:176 +1 AE004091.2_150_1/1 208964 594 0.929293 strain 208964:165 +1 AE004091.2_151_1/1 208964 594 0.989899 strain 208964:182 +1 AE004091.2_152_1/1 208964 594 0.643939 strain 208964:100 +1 AE004091.2_153_1/1 208964 594 0.975589 strain 208964:180 +1 AE004091.2_154_1/1 208964 594 0.820707 strain 208964:139 +1 AE004091.2_155_1/1 208964 594 0.86532 strain 208964:145 +1 AE004091.2_156_1/1 208964 594 0.998317 strain 208964:176 +1 AE004091.2_157_1/1 208964 594 0.995791 strain 208964:184 +1 AE004091.2_158_1/1 208964 594 0.949495 strain 208964:175 +1 AE004091.2_159_1/1 208964 594 0.969697 strain 208964:157 +1 AE004091.2_160_1/1 208964 594 0.939394 strain 208964:151 +1 AE004091.2_161_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_162_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_163_1/1 208964 594 0.969697 strain 208964:166 +1 AE004091.2_164_1/1 208964 594 0.909091 strain 208964:161 +1 AE004091.2_165_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_166_1/1 208964 594 0.996633 strain 208964:184 +1 AE004091.2_167_1/1 208964 594 0.976431 strain 208964:166 +1 AE004091.2_168_1/1 208964 594 0.868687 strain 208964:148 +1 AE004091.2_169_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_170_1/1 208964 594 0.957912 strain 208964:162 +1 AE004091.2_171_1/1 208964 594 0.97138 strain 208964:164 +1 AE004091.2_172_1/1 208964 594 0.921717 strain 208964:172 +1 AE004091.2_173_1/1 208964 594 0.919192 strain 208964:173 +1 AE004091.2_174_1/1 208964 594 0.934343 strain 208964:157 +1 AE004091.2_175_1/1 208964 594 0.989057 strain 208964:175 +1 AE004091.2_176_1/1 208964 594 0.5 strain 208964:92 +1 AE004091.2_177_1/1 208964 594 0.931818 strain 208964:151 +1 AE004091.2_178_1/1 208964 594 0.953704 strain 208964:168 +1 AE004091.2_179_1/1 208964 594 0.983165 strain 208964:166 +1 AE004091.2_180_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_181_1/1 208964 594 0.998317 strain 208964:176 +1 AE004091.2_182_1/1 208964 594 0.984848 strain 208964:160 +1 AE004091.2_183_1/1 208964 594 0.979798 strain 208964:173 +1 AE004091.2_184_1/1 208964 594 0.957912 strain 208964:169 +1 AE004091.2_185_1/1 208964 594 0.86532 strain 208964:134 +1 AE004091.2_186_1/1 208964 594 0.973064 strain 208964:165 +1 AE004091.2_187_1/1 208964 594 0.972222 strain 208964:172 +1 AE004091.2_188_1/1 208964 594 0.939394 strain 208964:172 +1 AE004091.2_189_1/1 208964 594 0.998317 strain 208964:184 +1 AE004091.2_190_1/1 208964 594 0.925084 strain 208964:157 +1 AE004091.2_191_1/1 208964 594 0.991583 strain 208964:176 +1 AE004091.2_192_1/1 208964 594 0.979798 strain 208964:168 +1 AE004091.2_193_1/1 208964 594 0.99495 strain 208964:184 +1 AE004091.2_194_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_195_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_196_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_197_1/1 208964 594 0.995791 strain 208964:184 +1 AE004091.2_198_1/1 208964 594 0.984848 strain 208964:174 +1 AE004091.2_199_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_200_1/1 208964 594 0.964646 strain 208964:171 +1 AE004091.2_201_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_202_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_203_1/1 208964 594 0.939394 strain 208964:159 +1 AE004091.2_204_1/1 208964 594 0.99495 strain 208964:184 +1 AE004091.2_205_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_206_1/1 208964 594 0.959596 strain 208964:176 +1 AE004091.2_207_1/1 208964 594 0.964646 strain 208964:170 +1 AE004091.2_208_1/1 208964 594 0.974747 strain 208964:165 +1 AE004091.2_209_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_210_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_211_1/1 208964 594 0.960438 strain 208964:163 +1 AE004091.2_212_1/1 208964 594 0.987374 strain 208964:182 +1 AE004091.2_213_1/1 208964 594 0.99495 strain 208964:183 +1 AE004091.2_214_1/1 208964 594 0.994108 strain 208964:176 +1 AE004091.2_215_1/1 208964 594 0.905724 strain 208964:153 +1 AE004091.2_216_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_217_1/1 208964 594 0.954545 strain 208964:175 +1 AE004091.2_218_1/1 208964 594 0.989899 strain 208964:168 +1 AE004091.2_219_1/1 208964 594 0.926768 strain 208964:165 +1 AE004091.2_220_1/1 208964 594 0.886364 strain 208964:158 +1 AE004091.2_221_1/1 208964 594 0.934343 strain 208964:168 +1 AE004091.2_222_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_223_1/1 208964 594 0.929293 strain 208964:172 +1 AE004091.2_224_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_225_1/1 208964 594 0.984848 strain 208964:181 +1 AE004091.2_226_1/1 208964 594 0.914141 strain 208964:153 +1 AE004091.2_227_1/1 208964 594 0.987374 strain 208964:168 +1 AE004091.2_228_1/1 208964 594 0.914141 strain 208964:154 +1 AE004091.2_229_1/1 208964 594 0.939394 strain 208964:158 +1 AE004091.2_230_1/1 208964 594 0.994108 strain 208964:184 +1 AE004091.2_231_1/1 208964 594 0.992424 strain 208964:176 +1 AE004091.2_232_1/1 208964 594 0.916667 strain 208964:155 +1 AE004091.2_233_1/1 208964 594 0.676768 strain 208964:120 +1 AE004091.2_234_1/1 208964 594 0.996633 strain 208964:183 +1 AE004091.2_235_1/1 208964 594 0.997475 strain 208964:184 +1 AE004091.2_236_1/1 208964 594 0.991583 strain 208964:176 +1 AE004091.2_237_1/1 208964 594 0.988216 strain 208964:168 +1 AE004091.2_238_1/1 208964 594 0.941919 strain 208964:152 +1 AE004091.2_239_1/1 208964 594 0.949495 strain 208964:167 +1 AE004091.2_240_1/1 208964 594 0.996633 strain 208964:184 +1 AE004091.2_241_1/1 208964 594 0.967172 strain 208964:171 +1 AE004091.2_242_1/1 208964 594 0.924242 strain 208964:162 +1 AE004091.2_243_1/1 208964 594 0.960438 strain 208964:171 +1 AE004091.2_244_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_245_1/1 208964 594 1 strain 208964:184 +1 AE004091.2_246_1/1 208964 594 0.936869 strain 208964:160 +1 AE004091.2_247_1/1 208964 594 0.99495 strain 208964:176 +1 AE004091.2_248_1/1 208964 594 0.973064 strain 208964:158 +1 AE004091.2_249_1/1 208964 594 0.979798 strain 208964:180 +1 NC_000913.3_0_0/1 511145 594 0.974747 no rank 511145:179 +1 NC_000913.3_1_0/1 511145 594 0.826599 no rank 511145:140 +1 NC_000913.3_2_0/1 511145 594 0.939394 no rank 511145:152 +1 NC_000913.3_3_0/1 511145 594 0.954545 no rank 511145:176 +1 NC_000913.3_4_0/1 511145 594 0.979798 no rank 511145:173 +1 NC_000913.3_5_0/1 511145 594 0.997475 no rank 511145:184 +1 NC_000913.3_6_0/1 511145 594 0.939394 no rank 511145:168 +1 NC_000913.3_7_0/1 511145 594 0.992424 no rank 511145:183 +1 NC_000913.3_8_0/1 511145 594 0.99495 no rank 511145:184 +1 NC_000913.3_9_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_10_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_11_0/1 511145 594 0.618687 no rank 511145:83 +1 NC_000913.3_12_0/1 511145 594 0.989899 no rank 511145:182 +1 NC_000913.3_13_0/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_14_0/1 511145 594 0.939394 no rank 511145:165 +1 NC_000913.3_15_0/1 511145 594 0.99495 no rank 511145:176 +1 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NC_000913.3_49_0/1 511145 594 0.919192 no rank 511145:165 +1 NC_000913.3_50_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_51_0/1 511145 594 0.991583 no rank 511145:182 +1 NC_000913.3_52_0/1 511145 594 0.909091 no rank 511145:161 +1 NC_000913.3_53_0/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_54_0/1 511145 594 0.93771 no rank 511145:174 +1 NC_000913.3_55_0/1 511145 594 0.885522 no rank 511145:152 +1 NC_000913.3_56_0/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_57_0/1 511145 594 0.992424 no rank 511145:183 +1 NC_000913.3_58_0/1 511145 594 0.732323 no rank 511145:127 +1 NC_000913.3_59_0/1 511145 594 0.819865 no rank 511145:136 +1 NC_000913.3_60_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_61_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_62_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_63_0/1 511145 594 0.967172 no rank 511145:178 +1 NC_000913.3_64_0/1 511145 594 0.899832 no rank 511145:151 +1 NC_000913.3_65_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_66_0/1 511145 594 0.964646 no rank 511145:177 +1 NC_000913.3_67_0/1 511145 594 0.964646 no rank 511145:165 +1 NC_000913.3_68_0/1 511145 594 0.975589 no rank 511145:180 +1 NC_000913.3_69_0/1 511145 594 0.915825 no rank 511145:133 +1 NC_000913.3_70_0/1 511145 594 0.964646 no rank 511145:170 +1 NC_000913.3_71_0/1 511145 594 0.984848 no rank 511145:174 +1 NC_000913.3_72_0/1 511145 594 0.954545 no rank 511145:162 +1 NC_000913.3_73_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_74_0/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_75_0/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_76_0/1 511145 594 0.984848 no rank 511145:174 +1 NC_000913.3_77_0/1 511145 594 0.94697 no rank 511145:160 +1 NC_000913.3_78_0/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_79_0/1 511145 594 0.964646 no rank 511145:177 +1 NC_000913.3_80_0/1 511145 594 0.923401 no rank 511145:156 +1 NC_000913.3_81_0/1 511145 594 0.886364 no rank 511145:142 +1 NC_000913.3_82_0/1 511145 594 1 no 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NC_000913.3_99_0/1 511145 594 0.992424 no rank 511145:176 +1 NC_000913.3_100_0/1 511145 594 0.991583 no rank 511145:168 +1 NC_000913.3_101_0/1 511145 594 0.962121 no rank 511145:170 +1 NC_000913.3_102_0/1 511145 594 0.996633 no rank 511145:176 +1 NC_000913.3_103_0/1 511145 594 0.986532 no rank 511145:181 +1 NC_000913.3_104_0/1 511145 594 0.753367 no rank 511145:127 +1 NC_000913.3_105_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_106_0/1 511145 594 0.954545 no rank 511145:161 +1 NC_000913.3_107_0/1 511145 594 0.941919 no rank 511145:138 +1 NC_000913.3_108_0/1 511145 594 0.919192 no rank 511145:161 +1 NC_000913.3_109_0/1 511145 594 0.994108 no rank 511145:184 +1 NC_000913.3_110_0/1 511145 594 0.995791 no rank 511145:184 +1 NC_000913.3_111_0/1 511145 594 0.977273 no rank 511145:173 +1 NC_000913.3_112_0/1 511145 594 0.99495 no rank 511145:183 +1 NC_000913.3_113_0/1 511145 594 0.961279 no rank 511145:177 +1 NC_000913.3_114_0/1 511145 594 0.99495 no rank 511145:184 +1 NC_000913.3_115_0/1 511145 594 0.944444 no rank 511145:176 +1 NC_000913.3_116_0/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_117_0/1 511145 594 0.974747 no rank 511145:172 +1 NC_000913.3_118_0/1 511145 594 0.962121 no rank 511145:163 +1 NC_000913.3_119_0/1 511145 594 0.997475 no rank 511145:184 +1 NC_000913.3_120_0/1 511145 594 0.992424 no rank 511145:183 +1 NC_000913.3_121_0/1 511145 594 0.901515 no rank 511145:160 +1 NC_000913.3_122_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_123_0/1 511145 594 0.954545 no rank 511145:176 +1 NC_000913.3_124_0/1 511145 594 0.997475 no rank 511145:184 +1 NC_000913.3_125_0/1 511145 594 0.978114 no rank 511145:173 +1 NC_000913.3_126_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_127_0/1 511145 594 0.987374 no rank 511145:176 +1 NC_000913.3_128_0/1 511145 594 0.891414 no rank 511145:159 +1 NC_000913.3_129_0/1 511145 594 0.997475 no rank 511145:184 +1 NC_000913.3_130_0/1 511145 594 0.94697 no rank 511145:168 +1 NC_000913.3_131_0/1 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NC_000913.3_164_0/1 511145 594 0.969697 no rank 511145:164 +1 NC_000913.3_165_0/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_166_0/1 511145 594 0.989899 no rank 511145:168 +1 NC_000913.3_167_0/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_168_0/1 511145 594 0.99495 no rank 511145:184 +1 NC_000913.3_169_0/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_170_0/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_171_0/1 511145 594 0.995791 no rank 511145:184 +1 NC_000913.3_172_0/1 511145 594 0.993266 no rank 511145:176 +1 NC_000913.3_173_0/1 511145 594 0.997475 no rank 511145:184 +1 NC_000913.3_174_0/1 511145 594 0.888889 no rank 511145:157 +1 NC_000913.3_175_0/1 511145 594 0.934343 no rank 511145:165 +1 NC_000913.3_176_0/1 511145 594 0.954545 no rank 511145:176 +1 NC_000913.3_177_0/1 511145 594 0.998317 no rank 511145:176 +1 NC_000913.3_178_0/1 511145 594 0.928451 no rank 511145:159 +1 NC_000913.3_179_0/1 511145 594 0.957071 no rank 511145:169 +1 NC_000913.3_180_0/1 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NC_000913.3_226_1/1 511145 594 0.987374 no rank 511145:168 +1 NC_000913.3_227_1/1 511145 594 0.992424 no rank 511145:176 +1 NC_000913.3_228_1/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_229_1/1 511145 594 0.994108 no rank 511145:176 +1 NC_000913.3_230_1/1 511145 594 0.927609 no rank 511145:150 +1 NC_000913.3_231_1/1 511145 594 0.984848 no rank 511145:176 +1 NC_000913.3_232_1/1 511145 594 0.969697 no rank 511145:178 +1 NC_000913.3_233_1/1 511145 594 0.977273 no rank 511145:173 +1 NC_000913.3_234_1/1 511145 594 0.992424 no rank 511145:176 +1 NC_000913.3_235_1/1 511145 594 0.997475 no rank 511145:184 +1 NC_000913.3_236_1/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_237_1/1 511145 594 0.992424 no rank 511145:176 +1 NC_000913.3_238_1/1 511145 594 0.989899 no rank 511145:168 +1 NC_000913.3_239_1/1 511145 594 0.869529 no rank 511145:139 +1 NC_000913.3_240_1/1 511145 594 0.998317 no rank 511145:184 +1 NC_000913.3_241_1/1 511145 594 0.959596 no rank 511145:176 +1 NC_000913.3_242_1/1 511145 594 0.997475 no rank 511145:184 +1 NC_000913.3_243_1/1 511145 594 0.944444 no rank 511145:163 +1 NC_000913.3_244_1/1 511145 594 0.922559 no rank 511145:169 +1 NC_000913.3_245_1/1 511145 594 0.825758 no rank 511145:139 +1 NC_000913.3_246_1/1 511145 594 0.992424 no rank 511145:184 +1 NC_000913.3_247_1/1 511145 594 0.99495 no rank 511145:176 +1 NC_000913.3_248_1/1 511145 594 1 no rank 511145:184 +1 NC_000913.3_249_1/1 511145 594 0.944444 no rank 511145:176 +1 NC_003197.2_0_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_1_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_2_0/1 99287 594 0.996633 strain 99287:184 +1 NC_003197.2_3_0/1 99287 594 0.969697 strain 99287:171 +1 NC_003197.2_4_0/1 99287 594 0.961279 strain 99287:163 +1 NC_003197.2_5_0/1 99287 594 0.868687 strain 99287:135 +1 NC_003197.2_6_0/1 99287 594 0.929293 strain 99287:172 +1 NC_003197.2_7_0/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_8_0/1 99287 594 0.871212 strain 99287:147 +1 NC_003197.2_9_0/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_10_0/1 99287 594 0.988216 strain 99287:168 +1 NC_003197.2_11_0/1 99287 594 0.96633 strain 99287:178 +1 NC_003197.2_12_0/1 99287 594 0.891414 strain 99287:151 +1 NC_003197.2_13_0/1 99287 594 0.98064 strain 99287:160 +1 NC_003197.2_14_0/1 99287 594 0.919192 strain 99287:162 +1 NC_003197.2_15_0/1 99287 594 0.986532 strain 99287:174 +1 NC_003197.2_16_0/1 99287 594 0.949495 strain 99287:176 +1 NC_003197.2_17_0/1 99287 594 0.984848 strain 99287:181 +1 NC_003197.2_18_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_19_0/1 99287 594 0.959596 strain 99287:169 +1 NC_003197.2_20_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_21_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_22_0/1 99287 594 0.866162 strain 99287:131 +1 NC_003197.2_23_0/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_24_0/1 99287 594 0.984848 strain 99287:167 +1 NC_003197.2_25_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_26_0/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_27_0/1 99287 594 0.981481 strain 99287:180 +1 NC_003197.2_28_0/1 99287 594 0.981481 strain 99287:175 +1 NC_003197.2_29_0/1 99287 594 0.936869 strain 99287:166 +1 NC_003197.2_30_0/1 99287 594 0.987374 strain 99287:168 +1 NC_003197.2_31_0/1 99287 594 0.873737 strain 99287:147 +1 NC_003197.2_32_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_33_0/1 99287 594 0.959596 strain 99287:176 +1 NC_003197.2_34_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_35_0/1 99287 594 0.981481 strain 99287:160 +1 NC_003197.2_36_0/1 99287 594 0.962963 strain 99287:176 +1 NC_003197.2_37_0/1 99287 594 0.996633 strain 99287:176 +1 NC_003197.2_38_0/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_39_0/1 99287 594 0.987374 strain 99287:168 +1 NC_003197.2_40_0/1 99287 594 0.952862 strain 99287:168 +1 NC_003197.2_41_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_42_0/1 99287 594 0.979798 strain 99287:180 +1 NC_003197.2_43_0/1 99287 594 0.979798 strain 99287:180 +1 NC_003197.2_44_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_45_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_46_0/1 99287 594 0.995791 strain 99287:184 +1 NC_003197.2_47_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_48_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_49_0/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_50_0/1 99287 594 0.999158 strain 99287:184 +1 NC_003197.2_51_0/1 99287 594 0.957912 strain 99287:169 +1 NC_003197.2_52_0/1 99287 594 0.993266 strain 99287:176 +1 NC_003197.2_53_0/1 99287 594 0.99495 strain 99287:183 +1 NC_003197.2_54_0/1 99287 594 0.959596 strain 99287:163 +1 NC_003197.2_55_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_56_0/1 99287 594 0.842593 strain 99287:149 +1 NC_003197.2_57_0/1 99287 594 0.951178 strain 99287:161 +1 NC_003197.2_58_0/1 99287 594 0.979798 strain 99287:159 +1 NC_003197.2_59_0/1 99287 594 0.977273 strain 99287:173 +1 NC_003197.2_60_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_61_0/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_62_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_63_0/1 99287 594 0.974747 strain 99287:179 +1 NC_003197.2_64_0/1 99287 594 0.959596 strain 99287:169 +1 NC_003197.2_65_0/1 99287 594 0.940236 strain 99287:160 +1 NC_003197.2_66_0/1 99287 594 0.936869 strain 99287:158 +1 NC_003197.2_67_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_68_0/1 99287 594 0.994108 strain 99287:176 +1 NC_003197.2_69_0/1 99287 594 0.982323 strain 99287:160 +1 NC_003197.2_70_0/1 99287 594 0.893939 strain 99287:136 +1 NC_003197.2_71_0/1 99287 594 0.996633 strain 99287:181 +1 NC_003197.2_72_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_73_0/1 99287 594 0.973906 strain 99287:172 +1 NC_003197.2_74_0/1 99287 594 0.967172 strain 99287:171 +1 NC_003197.2_75_0/1 99287 594 0.962121 strain 99287:170 +1 NC_003197.2_76_0/1 99287 594 0.967172 strain 99287:171 +1 NC_003197.2_77_0/1 99287 594 0.939394 strain 99287:168 +1 NC_003197.2_78_0/1 99287 594 0.893939 strain 99287:152 +1 NC_003197.2_79_0/1 99287 594 0.989899 strain 99287:182 +1 NC_003197.2_80_0/1 99287 594 0.986532 strain 99287:168 +1 NC_003197.2_81_0/1 99287 594 0.944444 strain 99287:173 +1 NC_003197.2_82_0/1 99287 594 0.990741 strain 99287:176 +1 NC_003197.2_83_0/1 99287 594 0.96633 strain 99287:177 +1 NC_003197.2_84_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_85_0/1 99287 594 1 strain 99287:183 +1 NC_003197.2_86_0/1 99287 594 0.898148 strain 99287:160 +1 NC_003197.2_87_0/1 99287 594 0.878788 strain 99287:153 +1 NC_003197.2_88_0/1 99287 594 0.974747 strain 99287:158 +1 NC_003197.2_89_0/1 99287 594 0.990741 strain 99287:183 +1 NC_003197.2_90_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_91_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_92_0/1 99287 594 0.949495 strain 99287:176 +1 NC_003197.2_93_0/1 99287 594 0.996633 strain 99287:184 +1 NC_003197.2_94_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_95_0/1 99287 594 0.967172 strain 99287:172 +1 NC_003197.2_96_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_97_0/1 99287 594 0.982323 strain 99287:160 +1 NC_003197.2_98_0/1 99287 594 0.949495 strain 99287:176 +1 NC_003197.2_99_0/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_100_0/1 99287 594 0.973064 strain 99287:173 +1 NC_003197.2_101_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_102_0/1 99287 594 0.928451 strain 99287:152 +1 NC_003197.2_103_0/1 99287 594 0.996633 strain 99287:176 +1 NC_003197.2_104_0/1 99287 594 0.989899 strain 99287:175 +1 NC_003197.2_105_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_106_0/1 99287 594 0.957071 strain 99287:169 +1 NC_003197.2_107_0/1 99287 594 0.98569 strain 99287:168 +1 NC_003197.2_108_0/1 99287 594 0.949495 strain 99287:140 +1 NC_003197.2_109_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_110_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_111_0/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_112_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_113_0/1 99287 594 0.959596 strain 99287:176 +1 NC_003197.2_114_0/1 99287 594 0.964646 strain 99287:170 +1 NC_003197.2_115_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_116_0/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_117_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_118_0/1 99287 594 0.959596 strain 99287:169 +1 NC_003197.2_119_0/1 99287 594 0.99495 strain 99287:184 +1 NC_003197.2_120_0/1 99287 594 0.949495 strain 99287:168 +1 NC_003197.2_121_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_122_0/1 99287 594 0.987374 strain 99287:168 +1 NC_003197.2_123_0/1 99287 594 0.99495 strain 99287:184 +1 NC_003197.2_124_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_125_0/1 99287 594 0.793771 strain 99287:134 +1 NC_003197.2_126_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_127_0/1 99287 594 0.993266 strain 99287:176 +1 NC_003197.2_128_0/1 99287 594 0.878788 strain 99287:153 +1 NC_003197.2_129_0/1 99287 594 0.909091 strain 99287:162 +1 NC_003197.2_130_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_131_0/1 99287 594 0.957071 strain 99287:162 +1 NC_003197.2_132_0/1 99287 594 0.957071 strain 99287:176 +1 NC_003197.2_133_0/1 99287 594 0.959596 strain 99287:176 +1 NC_003197.2_134_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_135_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_136_0/1 99287 594 0.968013 strain 99287:165 +1 NC_003197.2_137_0/1 99287 594 0.993266 strain 99287:184 +1 NC_003197.2_138_0/1 99287 594 0.929293 strain 99287:165 +1 NC_003197.2_139_0/1 99287 594 0.96633 strain 99287:170 +1 NC_003197.2_140_0/1 99287 594 0.90404 strain 99287:154 +1 NC_003197.2_141_0/1 99287 594 0.984848 strain 99287:168 +1 NC_003197.2_142_0/1 99287 594 0.974747 strain 99287:172 +1 NC_003197.2_143_0/1 99287 594 0.776094 strain 99287:121 +1 NC_003197.2_144_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_145_0/1 99287 594 0.993266 strain 99287:168 +1 NC_003197.2_146_0/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_147_0/1 99287 594 0.961279 strain 99287:171 +1 NC_003197.2_148_0/1 99287 594 0.893939 strain 99287:142 +1 NC_003197.2_149_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_150_0/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_151_0/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_152_0/1 99287 594 0.964646 strain 99287:163 +1 NC_003197.2_153_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_154_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_155_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_156_0/1 99287 594 0.936869 strain 99287:165 +1 NC_003197.2_157_0/1 99287 594 0.957912 strain 99287:168 +1 NC_003197.2_158_0/1 99287 594 0.969697 strain 99287:171 +1 NC_003197.2_159_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_160_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_161_0/1 99287 594 0.989057 strain 99287:176 +1 NC_003197.2_162_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_163_0/1 99287 594 0.981481 strain 99287:181 +1 NC_003197.2_164_0/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_165_0/1 99287 594 0.959596 strain 99287:155 +1 NC_003197.2_166_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_167_0/1 99287 594 0.939394 strain 99287:168 +1 NC_003197.2_168_0/1 99287 594 0.984848 strain 99287:174 +1 NC_003197.2_169_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_170_0/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_171_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_172_0/1 99287 594 0.979798 strain 99287:174 +1 NC_003197.2_173_0/1 99287 594 0.949495 strain 99287:168 +1 NC_003197.2_174_0/1 99287 594 0.934343 strain 99287:176 +1 NC_003197.2_175_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_176_0/1 99287 594 0.963805 strain 99287:164 +1 NC_003197.2_177_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_178_0/1 99287 594 0.998317 strain 99287:183 +1 NC_003197.2_179_0/1 99287 594 0.944444 strain 99287:160 +1 NC_003197.2_180_0/1 99287 594 0.964646 strain 99287:170 +1 NC_003197.2_181_0/1 99287 594 0.949495 strain 99287:176 +1 NC_003197.2_182_0/1 99287 594 0.964646 strain 99287:177 +1 NC_003197.2_183_0/1 99287 594 0.848485 strain 99287:147 +1 NC_003197.2_184_0/1 99287 594 0.979798 strain 99287:173 +1 NC_003197.2_185_0/1 99287 594 0.983165 strain 99287:182 +1 NC_003197.2_186_0/1 99287 594 0.954545 strain 99287:175 +1 NC_003197.2_187_0/1 99287 594 0.96633 strain 99287:170 +1 NC_003197.2_188_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_189_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_190_0/1 99287 594 0.949495 strain 99287:167 +1 NC_003197.2_191_0/1 99287 594 0.962121 strain 99287:177 +1 NC_003197.2_192_0/1 99287 594 0.909091 strain 99287:140 +1 NC_003197.2_193_0/1 99287 594 0.949495 strain 99287:168 +1 NC_003197.2_194_0/1 99287 594 0.911616 strain 99287:167 +1 NC_003197.2_195_0/1 99287 594 0.951178 strain 99287:168 +1 NC_003197.2_196_0/1 99287 594 0.957071 strain 99287:149 +1 NC_003197.2_197_0/1 99287 594 0.882155 strain 99287:149 +1 NC_003197.2_198_0/1 99287 594 0.987374 strain 99287:175 +1 NC_003197.2_199_0/1 99287 594 0.972222 strain 99287:179 +1 NC_003197.2_200_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_201_0/1 99287 594 0.94697 strain 99287:175 +1 NC_003197.2_202_0/1 99287 594 0.876263 strain 99287:141 +1 NC_003197.2_203_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_204_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_205_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_206_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_207_0/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_208_0/1 99287 594 0.929293 strain 99287:163 +1 NC_003197.2_209_0/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_210_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_211_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_212_0/1 99287 594 0.954545 strain 99287:155 +1 NC_003197.2_213_0/1 99287 594 0.949495 strain 99287:167 +1 NC_003197.2_214_0/1 99287 594 0.95202 strain 99287:150 +1 NC_003197.2_215_0/1 99287 594 0.93771 strain 99287:158 +1 NC_003197.2_216_0/1 99287 594 0.976431 strain 99287:173 +1 NC_003197.2_217_0/1 99287 594 0.927609 strain 99287:152 +1 NC_003197.2_218_0/1 99287 594 0.99495 strain 99287:184 +1 NC_003197.2_219_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_220_0/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_221_0/1 99287 594 0.964646 strain 99287:170 +1 NC_003197.2_222_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_223_0/1 99287 594 0.931818 strain 99287:129 +1 NC_003197.2_224_0/1 99287 594 0.990741 strain 99287:168 +1 NC_003197.2_225_0/1 99287 594 0.949495 strain 99287:168 +1 NC_003197.2_226_0/1 99287 594 0.893939 strain 99287:143 +1 NC_003197.2_227_0/1 99287 594 0.915825 strain 99287:149 +1 NC_003197.2_228_0/1 99287 594 0.989899 strain 99287:176 +1 NC_003197.2_229_0/1 99287 594 0.949495 strain 99287:168 +1 NC_003197.2_230_0/1 99287 594 0.989899 strain 99287:175 +1 NC_003197.2_231_0/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_232_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_233_0/1 99287 594 0.919192 strain 99287:149 +1 NC_003197.2_234_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_235_0/1 99287 594 0.926768 strain 99287:156 +1 NC_003197.2_236_0/1 99287 594 0.977273 strain 99287:180 +1 NC_003197.2_237_0/1 99287 594 0.984848 strain 99287:175 +1 NC_003197.2_238_0/1 99287 594 0.979798 strain 99287:173 +1 NC_003197.2_239_0/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_240_0/1 99287 594 0.947811 strain 99287:168 +1 NC_003197.2_241_0/1 99287 594 0.929293 strain 99287:157 +1 NC_003197.2_242_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_243_0/1 99287 594 0.93771 strain 99287:158 +1 NC_003197.2_244_0/1 99287 594 0.949495 strain 99287:168 +1 NC_003197.2_245_0/1 99287 594 0.969697 strain 99287:165 +1 NC_003197.2_246_0/1 99287 594 0.987374 strain 99287:168 +1 NC_003197.2_247_0/1 99287 594 0.988216 strain 99287:168 +1 NC_003197.2_248_0/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_249_0/1 99287 594 1 strain 99287:184 +1 NC_003197.2_0_1/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_1_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_2_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_3_1/1 99287 594 0.984848 strain 99287:174 +1 NC_003197.2_4_1/1 99287 594 0.93771 strain 99287:173 +1 NC_003197.2_5_1/1 99287 594 0.858586 strain 99287:151 +1 NC_003197.2_6_1/1 99287 594 0.982323 strain 99287:181 +1 NC_003197.2_7_1/1 99287 594 0.974747 strain 99287:168 +1 NC_003197.2_8_1/1 99287 594 0.928451 strain 99287:160 +1 NC_003197.2_9_1/1 99287 594 0.993266 strain 99287:176 +1 NC_003197.2_10_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_11_1/1 99287 594 0.911616 strain 99287:140 +1 NC_003197.2_12_1/1 99287 594 0.967172 strain 99287:178 +1 NC_003197.2_13_1/1 99287 594 0.984848 strain 99287:160 +1 NC_003197.2_14_1/1 99287 594 0.967172 strain 99287:179 +1 NC_003197.2_15_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_16_1/1 99287 594 0.944444 strain 99287:168 +1 NC_003197.2_17_1/1 99287 594 0.995791 strain 99287:184 +1 NC_003197.2_18_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_19_1/1 99287 594 0.939394 strain 99287:174 +1 NC_003197.2_20_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_21_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_22_1/1 99287 594 0.89899 strain 99287:127 +1 NC_003197.2_23_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_24_1/1 99287 594 0.979798 strain 99287:168 +1 NC_003197.2_25_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_26_1/1 99287 594 0.944444 strain 99287:168 +1 NC_003197.2_27_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_28_1/1 99287 594 0.753367 strain 99287:126 +1 NC_003197.2_29_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_30_1/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_31_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_32_1/1 99287 594 0.961279 strain 99287:176 +1 NC_003197.2_33_1/1 99287 594 0.974747 strain 99287:165 +1 NC_003197.2_34_1/1 99287 594 0.984848 strain 99287:174 +1 NC_003197.2_35_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_36_1/1 99287 594 0.959596 strain 99287:169 +1 NC_003197.2_37_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_38_1/1 99287 594 0.944444 strain 99287:166 +1 NC_003197.2_39_1/1 99287 594 0.95202 strain 99287:176 +1 NC_003197.2_40_1/1 99287 594 0.90404 strain 99287:160 +1 NC_003197.2_41_1/1 99287 594 0.999158 strain 99287:184 +1 NC_003197.2_42_1/1 99287 594 0.982323 strain 99287:181 +1 NC_003197.2_43_1/1 99287 594 0.962121 strain 99287:156 +1 NC_003197.2_44_1/1 99287 594 0.984848 strain 99287:160 +1 NC_003197.2_45_1/1 99287 594 0.989899 strain 99287:182 +1 NC_003197.2_46_1/1 99287 594 1 strain 99287:183 +1 NC_003197.2_47_1/1 99287 594 0.996633 strain 99287:184 +1 NC_003197.2_48_1/1 99287 594 0.873737 strain 99287:145 +1 NC_003197.2_49_1/1 99287 594 0.974747 strain 99287:172 +1 NC_003197.2_50_1/1 99287 594 0.987374 strain 99287:176 +1 NC_003197.2_51_1/1 99287 594 0.979798 strain 99287:176 +1 NC_003197.2_52_1/1 99287 594 0.878788 strain 99287:163 +1 NC_003197.2_53_1/1 99287 594 0.977273 strain 99287:173 +1 NC_003197.2_54_1/1 99287 594 0.939394 strain 99287:165 +1 NC_003197.2_55_1/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_56_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_57_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_58_1/1 99287 594 0.964646 strain 99287:157 +1 NC_003197.2_59_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_60_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_61_1/1 99287 594 0.954545 strain 99287:175 +1 NC_003197.2_62_1/1 99287 594 0.977273 strain 99287:173 +1 NC_003197.2_63_1/1 99287 594 0.984848 strain 99287:174 +1 NC_003197.2_64_1/1 99287 594 0.711279 strain 99287:116 +1 NC_003197.2_65_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_66_1/1 99287 594 0.987374 strain 99287:182 +1 NC_003197.2_67_1/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_68_1/1 99287 594 0.998317 strain 99287:176 +1 NC_003197.2_69_1/1 99287 594 0.956229 strain 99287:176 +1 NC_003197.2_70_1/1 99287 594 0.994108 strain 99287:176 +1 NC_003197.2_71_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_72_1/1 99287 594 0.949495 strain 99287:174 +1 NC_003197.2_73_1/1 99287 594 0.989899 strain 99287:176 +1 NC_003197.2_74_1/1 99287 594 0.989899 strain 99287:175 +1 NC_003197.2_75_1/1 99287 594 0.722222 strain 99287:128 +1 NC_003197.2_76_1/1 99287 594 0.934343 strain 99287:150 +1 NC_003197.2_77_1/1 99287 594 0.959596 strain 99287:169 +1 NC_003197.2_78_1/1 99287 594 0.90404 strain 99287:158 +1 NC_003197.2_79_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_80_1/1 99287 594 0.995791 strain 99287:184 +1 NC_003197.2_81_1/1 99287 594 0.961279 strain 99287:170 +1 NC_003197.2_82_1/1 99287 594 0.984848 strain 99287:160 +1 NC_003197.2_83_1/1 99287 594 0.863636 strain 99287:152 +1 NC_003197.2_84_1/1 99287 594 0.934343 strain 99287:171 +1 NC_003197.2_85_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_86_1/1 99287 594 0.967172 strain 99287:171 +1 NC_003197.2_87_1/1 99287 594 0.944444 strain 99287:176 +1 NC_003197.2_88_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_89_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_90_1/1 99287 594 0.990741 strain 99287:176 +1 NC_003197.2_91_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_92_1/1 99287 594 0.964646 strain 99287:177 +1 NC_003197.2_93_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_94_1/1 99287 594 0.969697 strain 99287:171 +1 NC_003197.2_95_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_96_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_97_1/1 99287 594 0.974747 strain 99287:168 +1 NC_003197.2_98_1/1 99287 594 0.981481 strain 99287:173 +1 NC_003197.2_99_1/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_100_1/1 99287 594 0.95202 strain 99287:168 +1 NC_003197.2_101_1/1 99287 594 0.967172 strain 99287:171 +1 NC_003197.2_102_1/1 99287 594 0.977273 strain 99287:173 +1 NC_003197.2_103_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_104_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_105_1/1 99287 594 0.912458 strain 99287:161 +1 NC_003197.2_106_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_107_1/1 99287 594 0.949495 strain 99287:176 +1 NC_003197.2_108_1/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_109_1/1 99287 594 0.929293 strain 99287:170 +1 NC_003197.2_110_1/1 99287 594 0.810606 strain 99287:146 +1 NC_003197.2_111_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_112_1/1 99287 594 0.95202 strain 99287:168 +1 NC_003197.2_113_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_114_1/1 99287 594 0.964646 strain 99287:163 +1 NC_003197.2_115_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_116_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_117_1/1 99287 594 0.939394 strain 99287:165 +1 NC_003197.2_118_1/1 99287 594 0.996633 strain 99287:184 +1 NC_003197.2_119_1/1 99287 594 0.882155 strain 99287:147 +1 NC_003197.2_120_1/1 99287 594 0.960438 strain 99287:176 +1 NC_003197.2_121_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_122_1/1 99287 594 0.969697 strain 99287:178 +1 NC_003197.2_123_1/1 99287 594 0.924242 strain 99287:135 +1 NC_003197.2_124_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_125_1/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_126_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_127_1/1 99287 594 0.959596 strain 99287:176 +1 NC_003197.2_128_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_129_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_130_1/1 99287 594 0.967172 strain 99287:152 +1 NC_003197.2_131_1/1 99287 594 0.989899 strain 99287:169 +1 NC_003197.2_132_1/1 99287 594 0.972222 strain 99287:172 +1 NC_003197.2_133_1/1 99287 594 0.959596 strain 99287:163 +1 NC_003197.2_134_1/1 99287 594 0.992424 strain 99287:184 +1 NC_003197.2_135_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_136_1/1 99287 594 0.934343 strain 99287:157 +1 NC_003197.2_137_1/1 99287 594 0.84596 strain 99287:135 +1 NC_003197.2_138_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_139_1/1 99287 594 0.95202 strain 99287:161 +1 NC_003197.2_140_1/1 99287 594 0.991583 strain 99287:175 +1 NC_003197.2_141_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_142_1/1 99287 594 0.996633 strain 99287:176 +1 NC_003197.2_143_1/1 99287 594 0.982323 strain 99287:168 +1 NC_003197.2_144_1/1 99287 594 0.977273 strain 99287:180 +1 NC_003197.2_145_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_146_1/1 99287 594 0.988216 strain 99287:168 +1 NC_003197.2_147_1/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_148_1/1 99287 594 0.891414 strain 99287:152 +1 NC_003197.2_149_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_150_1/1 99287 594 0.941077 strain 99287:160 +1 NC_003197.2_151_1/1 99287 594 0.949495 strain 99287:160 +1 NC_003197.2_152_1/1 99287 594 0.984848 strain 99287:160 +1 NC_003197.2_153_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_154_1/1 99287 594 0.933502 strain 99287:165 +1 NC_003197.2_155_1/1 99287 594 0.979798 strain 99287:159 +1 NC_003197.2_156_1/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_157_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_158_1/1 99287 594 0.934343 strain 99287:150 +1 NC_003197.2_159_1/1 99287 594 0.944444 strain 99287:174 +1 NC_003197.2_160_1/1 99287 594 0.994108 strain 99287:183 +1 NC_003197.2_161_1/1 99287 594 0.993266 strain 99287:176 +1 NC_003197.2_162_1/1 99287 594 0.988216 strain 99287:168 +1 NC_003197.2_163_1/1 99287 594 0.916667 strain 99287:156 +1 NC_003197.2_164_1/1 99287 594 0.99495 strain 99287:183 +1 NC_003197.2_165_1/1 99287 594 0.914141 strain 99287:147 +1 NC_003197.2_166_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_167_1/1 99287 594 0.996633 strain 99287:176 +1 NC_003197.2_168_1/1 99287 594 0.998317 strain 99287:176 +1 NC_003197.2_169_1/1 99287 594 0.775253 strain 99287:132 +1 NC_003197.2_170_1/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_171_1/1 99287 594 0.772727 strain 99287:135 +1 NC_003197.2_172_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_173_1/1 99287 594 0.924242 strain 99287:171 +1 NC_003197.2_174_1/1 99287 594 0.939394 strain 99287:161 +1 NC_003197.2_175_1/1 99287 594 0.984848 strain 99287:167 +1 NC_003197.2_176_1/1 99287 594 0.895623 strain 99287:163 +1 NC_003197.2_177_1/1 99287 594 0.972222 strain 99287:172 +1 NC_003197.2_178_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_179_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_180_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_181_1/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_182_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_183_1/1 99287 594 0.993266 strain 99287:176 +1 NC_003197.2_184_1/1 99287 594 0.949495 strain 99287:176 +1 NC_003197.2_185_1/1 99287 594 0.974747 strain 99287:158 +1 NC_003197.2_186_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_187_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_188_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_189_1/1 99287 594 0.989899 strain 99287:175 +1 NC_003197.2_190_1/1 99287 594 0.808081 strain 99287:134 +1 NC_003197.2_191_1/1 99287 594 0.958754 strain 99287:169 +1 NC_003197.2_192_1/1 99287 594 0.949495 strain 99287:168 +1 NC_003197.2_193_1/1 99287 594 0.95202 strain 99287:175 +1 NC_003197.2_194_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_195_1/1 99287 594 0.991583 strain 99287:168 +1 NC_003197.2_196_1/1 99287 594 0.988216 strain 99287:168 +1 NC_003197.2_197_1/1 99287 594 0.984848 strain 99287:160 +1 NC_003197.2_198_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_199_1/1 99287 594 0.914141 strain 99287:169 +1 NC_003197.2_200_1/1 99287 594 0.964646 strain 99287:170 +1 NC_003197.2_201_1/1 99287 594 0.939394 strain 99287:160 +1 NC_003197.2_202_1/1 99287 594 0.774411 strain 99287:127 +1 NC_003197.2_203_1/1 99287 594 0.964646 strain 99287:172 +1 NC_003197.2_204_1/1 99287 594 0.974747 strain 99287:179 +1 NC_003197.2_205_1/1 99287 594 0.979798 strain 99287:179 +1 NC_003197.2_206_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_207_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_208_1/1 99287 594 0.996633 strain 99287:184 +1 NC_003197.2_209_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_210_1/1 99287 594 0.987374 strain 99287:168 +1 NC_003197.2_211_1/1 99287 594 0.989899 strain 99287:182 +1 NC_003197.2_212_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_213_1/1 99287 594 0.979798 strain 99287:180 +1 NC_003197.2_214_1/1 99287 594 0.853535 strain 99287:142 +1 NC_003197.2_215_1/1 99287 594 0.974747 strain 99287:172 +1 NC_003197.2_216_1/1 99287 594 0.992424 strain 99287:183 +1 NC_003197.2_217_1/1 99287 594 0.997475 strain 99287:180 +1 NC_003197.2_218_1/1 99287 594 0.944444 strain 99287:166 +1 NC_003197.2_219_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_220_1/1 99287 594 0.95202 strain 99287:161 +1 NC_003197.2_221_1/1 99287 594 0.982323 strain 99287:181 +1 NC_003197.2_222_1/1 99287 594 0.967172 strain 99287:164 +1 NC_003197.2_223_1/1 99287 594 0.998317 strain 99287:184 +1 NC_003197.2_224_1/1 99287 594 0.989899 strain 99287:168 +1 NC_003197.2_225_1/1 99287 594 0.99495 strain 99287:183 +1 NC_003197.2_226_1/1 99287 594 0.979798 strain 99287:180 +1 NC_003197.2_227_1/1 99287 594 0.944444 strain 99287:166 +1 NC_003197.2_228_1/1 99287 594 0.993266 strain 99287:176 +1 NC_003197.2_229_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_230_1/1 99287 594 0.949495 strain 99287:176 +1 NC_003197.2_231_1/1 99287 594 0.934343 strain 99287:171 +1 NC_003197.2_232_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_233_1/1 99287 594 0.982323 strain 99287:181 +1 NC_003197.2_234_1/1 99287 594 0.90404 strain 99287:147 +1 NC_003197.2_235_1/1 99287 594 0.931818 strain 99287:176 +1 NC_003197.2_236_1/1 99287 594 1 strain 99287:184 +1 NC_003197.2_237_1/1 99287 594 0.914141 strain 99287:155 +1 NC_003197.2_238_1/1 99287 594 0.997475 strain 99287:184 +1 NC_003197.2_239_1/1 99287 594 0.992424 strain 99287:176 +1 NC_003197.2_240_1/1 99287 594 0.982323 strain 99287:160 +1 NC_003197.2_241_1/1 99287 594 0.992424 strain 99287:183 +1 NC_003197.2_242_1/1 99287 594 0.968855 strain 99287:171 +1 NC_003197.2_243_1/1 99287 594 0.95202 strain 99287:149 +1 NC_003197.2_244_1/1 99287 594 0.99495 strain 99287:176 +1 NC_003197.2_245_1/1 99287 594 0.670034 strain 99287:116 +1 NC_003197.2_246_1/1 99287 594 0.972222 strain 99287:165 +1 NC_003197.2_247_1/1 99287 594 0.979798 strain 99287:173 +1 NC_003197.2_248_1/1 99287 594 0.951178 strain 99287:168 +1 NC_003197.2_249_1/1 99287 594 0.997475 strain 99287:184 diff -r 000000000000 -r b01d6b38f779 test-data/output/sr_krona.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/sr_krona.html Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,6620 @@ + + + + + + + + + + + + + +
+ + + magnitude + + + kt + + +15001500150015001500150010001000500500500500500500500500500500500500500500500
\ No newline at end of file diff -r 000000000000 -r b01d6b38f779 test-data/output/sr_report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output/sr_report.tsv Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,22 @@ +100.0000 1500 0 no rank 1 root +100.0000 1500 0 no rank 131567 cellular organisms +100.0000 1500 0 superkingdom 2 Bacteria +100.0000 1500 0 phylum 1224 Pseudomonadota +100.0000 1500 0 class 1236 Gammaproteobacteria +66.6667 1000 0 order 91347 Enterobacterales +66.6667 1000 0 family 543 Enterobacteriaceae +33.3333 500 0 genus 561 Escherichia +33.3333 500 0 species 562 Escherichia coli +33.3333 500 0 strain 83333 Escherichia coli K-12 +33.3333 500 500 no rank 511145 Escherichia coli str. K-12 substr. MG1655 +33.3333 500 0 genus 590 Salmonella +33.3333 500 0 species 28901 Salmonella enterica +33.3333 500 0 subspecies 59201 Salmonella enterica subsp. enterica +33.3333 500 0 no rank 90371 Salmonella enterica subsp. enterica serovar Typhimurium +33.3333 500 500 strain 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 +33.3333 500 0 order 72274 Pseudomonadales +33.3333 500 0 family 135621 Pseudomonadaceae +33.3333 500 0 genus 286 Pseudomonas +33.3333 500 0 species group 136841 Pseudomonas aeruginosa group +33.3333 500 0 species 287 Pseudomonas aeruginosa +33.3333 500 500 strain 208964 Pseudomonas aeruginosa PAO1 diff -r 000000000000 -r b01d6b38f779 test-data/reads/illumina_R1.fastq.gz Binary file test-data/reads/illumina_R1.fastq.gz has changed diff -r 000000000000 -r b01d6b38f779 test-data/reads/illumina_R2.fastq.gz Binary file test-data/reads/illumina_R2.fastq.gz has changed diff -r 000000000000 -r b01d6b38f779 test-data/reads/ont.r10.4.1.fastq.gz Binary file test-data/reads/ont.r10.4.1.fastq.gz has changed diff -r 000000000000 -r b01d6b38f779 test-data/reads/pacbio.hifi.fastq.gz Binary file test-data/reads/pacbio.hifi.fastq.gz has changed diff -r 000000000000 -r b01d6b38f779 test-data/taxonomy.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy.loc Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,4 @@ +# This file defines databases and their folder location. Each database is a line with +# three columns: value{tab}{name}{/path/to/database-folder} +# E.g. GTDB{tab}GTDB{tab}/path/to/GTDB +taxonomy taxonomy ${__HERE__}/taxonomy diff -r 000000000000 -r b01d6b38f779 test-data/taxonomy/merged.dmp diff -r 000000000000 -r b01d6b38f779 test-data/taxonomy/names.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy/names.dmp Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,397 @@ +1 | all | | synonym | +1 | root | | scientific name | +2 | Bacteria | Bacteria | scientific name | +2 | bacteria | | blast name | +2 |" ""Bacteria"" Cavalier-Smith 1987 "| | authority | +2 | Bacteria (ex Cavalier-Smith 1987) | | synonym | +2 | Bacteria Woese et al. 2024 | | synonym | +2 |" ""Bacteriobiota"" Luketa 2012 "| | authority | +2 | Bacteriobiota | | synonym | +2 | eubacteria | | genbank common name | +2 | Monera | Monera | in-part | +2 | Procaryotae | Procaryotae | in-part | +2 | Prokaryotae | Prokaryotae | in-part | +2 | Prokaryota | Prokaryota | in-part | +2 | prokaryote | prokaryote | in-part | +2 | prokaryotes | prokaryotes | in-part | +286 |" ""Chlorobacterium"" Guillebeau 1890, nom. rejic. Opin. 6 (not ""Chlorobacterium"" Lauterborn 1916) "| | synonym | +286 | Chryseomonas Holmes et al. 1986 | | authority | +286 | Chryseomonas | | synonym | +286 | Flavimonas Holmes et al. 1987 | | authority | +286 | Flavimonas | | synonym | +286 |" ""Liquidomonas"" Orla-Jensen 1909 "| | authority | +286 | Liquidomonas | | synonym | +286 |" ""Loefflerella"" Holden 1935 "| | authority | +286 | Loefflerella | | synonym | +286 | Pseudomonas Migula 1894 (Approved Lists 1980) | | authority | +286 | Pseudomonas Migula 1894 emend. Yang et al. 2013 | | authority | +286 | Pseudomonas | | scientific name | +286 | RNA similarity group I | | common name | +286 | Serpens Hespell 1977 (Approved Lists 1980) | | authority | +286 | Serpens | | synonym | +287 |" ""Bacillus aeruginosus"" (Schroeter 1872) Trevisan 1885 "| | authority | +287 | Bacillus aeruginosus | | synonym | +287 | Bacillus pyocyaneus | | synonym | +287 |" ""Bacillus pyocyaneus"" (Zopf 1884) Flugge 1886 "| | authority | +287 |" ""Bacterium aeruginosum"" Cohn 1872 "| | authority | +287 |" ""Bacterium aeruginosum"" Schroeter 1872 "| | authority | +287 | Bacterium aeruginosum | | synonym | +287 | bacterium ASFP-37 | | includes | +287 | bacterium ASFP-38 | | includes | +287 | bacterium ASFP-45 | | includes | +287 | bacterium ASFP-46 | | includes | +287 | bacterium ASFP-48 | | includes | +287 | bacterium CRM125 | | includes | +287 | Bacterium pyocyaneum | | synonym | +287 |" ""Bacterium pyocyaneum"" (Zopf 1884) Lehmann and Neumann 1896 "| | authority | +287 | Micrococcus pyocyaneus | | synonym | +287 |" ""Micrococcus pyocyaneus"" Zopf 1884 "| | authority | +287 |" probable synonym or variety: ""Pseudomonas polycolor"" Clara 1930 "| | synonym | +287 | Pseudomonas aeruginosa (Schroeter 1872) Migula 1900 (Approved Lists 1980) | | authority | +287 | Pseudomonas aeruginosa (Schroeter 1872) Migula 1900 (Approved Lists 1980) emend. Rudra et al. 2022 | | authority | +287 | Pseudomonas aeruginosa | | scientific name | +287 | Pseudomonas polycolor | | synonym | +287 | Pseudomonas pyocyanea | | synonym | +287 |" ""Pseudomonas pyocyanea"" (Zopf 1884) Migula 1895 "| | authority | +287 | Pseudomonas sp. 2_1_26 | | includes | +287 | Pseudomonas sp. ACP_02 | | includes | +287 | Pseudomonas sp. CRRI 93 | | includes | +287 | Pseudomonas sp. HSA1/2016 | | includes | +287 | Pseudomonas sp. NCIM 2036 | | includes | +287 | Pseudomonas sp. NCIM 2862 | | includes | +287 | Pseudomonas sp. PR_01 | | includes | +287 | Pseudomonas sp. PSE5 | | includes | +287 | Pseudomonas sp. RV3 | | includes | +287 | Pseudomonas sp. UFT2/2016 | | includes | +543 | Enterobacteraceae (ex Lapage 1979) Lapage 1982 | | authority | +543 | Enterobacteraceae | | synonym | +543 | enterobacteria | | blast name | +543 | Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980 | | authority | +543 | Enterobacteriaceae Rahn 1937 (Approved Lists 1980) emend. Adeolu et al. 2016 | | authority | +543 | Enterobacteriaceae | | scientific name | +543 | gamma-3 proteobacteria | gamma-3 proteobacteria | in-part | +561 | Escherichia Castellani and Chalmers 1919 | | authority | +561 | Escherichia | | scientific name | +562 | Achromobacter sp. ATCC 35328 | | includes | +562 |" ""Bacillus coli"" Migula 1895 "| | authority | +562 | Bacillus coli | | synonym | +562 | bacterium 10a | | includes | +562 |" ""Bacterium coli commune"" Escherich 1885 "| | authority | +562 | Bacterium coli commune | | synonym | +562 |" ""Bacterium coli"" (Migula 1895) Lehmann and Neumann 1896 "| | authority | +562 | Bacterium coli | | synonym | +562 | bacterium E3 | | includes | +562 | E. coli | | common name | +562 | Enterococcus coli | | synonym | +562 | Escherichia coli (Migula 1895) Castellani and Chalmers 1919 (Approved Lists 1980) | | authority | +562 | Escherichia coli | | scientific name | +562 | Escherichia/Shigella coli | | equivalent name | +562 | Escherichia sp. 3_2_53FAA | | includes | +562 | Escherichia sp. MAR | | includes | +590 | Salmonella Lignieres 1900 | | authority | +590 | Salmonella | | scientific name | +1224 | Alphaproteobacteriota | | synonym | +1224 |" ""Alphaproteobacteriota"" Whitman et al. 2018 "| | synonym | +1224 | proteobacteria | | blast name | +1224 |" ""Proteobacteria"" Garrity et al. 2005 "| | authority | +1224 | Proteobacteria Stackebrandt et al. 1988 | | authority | +1224 | Proteobacteria | | synonym | +1224 |" ""Proteobacteriota"" Panda et al. 2022 "| | authority | +1224 | Proteobacteriota | | synonym | +1224 | Pseudomonadota corrig. Garrity et al. 2021 | | authority | +1224 | Pseudomonadota | | scientific name | +1224 | purple photosynthetic bacteria and relatives | | common name | +1236 | Gammaproteobacteria Garrity et al. 2005 emend. Williams and Kelly 2013 | | authority | +1236 | Gammaproteobacteria | | scientific name | +1236 | gamma proteobacteria | | synonym | +1236 | gamma subdivision | | synonym | +1236 | gamma subgroup | | synonym | +1236 | g-proteobacteria | | blast name | +1236 | Proteobacteria gamma subdivision | | synonym | +1236 |" ""Pseudomonadia"" Oren et al. 2016 "| | authority | +1236 | Pseudomonadia | | synonym | +1236 | Purple bacteria, gamma subdivision | | synonym | +28901 |" ""Bacillus cholerae-suis"" Smith 1894 "| | authority | +28901 | Bacillus cholerae-suis | | synonym | +28901 | Salmonella choleraesuis corrig. (Smith 1894) Weldin 1927 (Approved Lists 1980) | | authority | +28901 | Salmonella cholerae-suis | | synonym | +28901 | Salmonella choleraesuis | | synonym | +28901 | Salmonella enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987 | | authority | +28901 |" ""Salmonella enterica"" Kauffmann and Edwards 1952 "| | authority | +28901 | Salmonella enterica | | scientific name | +28901 | Salmonella enterica ser. choleraesuis | | synonym | +28901 | Salmonella sp. 22OH10_CL01-S1 | | includes | +28901 | Salmonella sp. 22OH12_PC07-S1 | | includes | +28901 | Salmonella sp. 23OH01_CG01-S1 | | includes | +28901 | Salmonella sp. 23OH01_GT01-S1 | | includes | +28901 | Salmonella sp. 23OH01_GT02-S1 | | includes | +28901 | Salmonella sp. 23OH02_GT02-S1 | | includes | +28901 | Salmonella sp. 23OH04_CG01-S1 | | includes | +28901 | Salmonella sp. 23OH05_CB01-S1 | | includes | +28901 | Salmonella sp. 23OH06_CG01-S1 | | includes | +28901 | Salmonella sp. 23OH06_CH01-S1 | | includes | +28901 | Salmonella sp. 23OH06_GT01-S1 | | includes | +28901 | Salmonella sp. 23OH07_CB02-S1 | | includes | +28901 | Salmonella sp. 23OH07_GT04-S1 | | includes | +28901 | Salmonella sp. 23OH08_CG01-S1 | | includes | +28901 | Salmonella sp. 23OH10_CB03-S1 | | includes | +28901 | Salmonella sp. 23OH10_CG01-S1 | | includes | +28901 | Salmonella sp. AMC 200 | | includes | +28901 | Salmonella sp. AMC 238 | | includes | +28901 | Salmonella sp. AMC 239 | | includes | +28901 | Salmonella sp. AMC 240 | | includes | +28901 | Salmonella sp. AMC 253 | | includes | +28901 | Salmonella sp. AMC 257 | | includes | +28901 | Salmonella sp. AMC 265 | | includes | +28901 | Salmonella sp. AMC 266 | | includes | +28901 | Salmonella sp. AMC 267 | | includes | +28901 | Salmonella sp. AMC 268 | | includes | +28901 | Salmonella sp. AMC 270 | | includes | +28901 | Salmonella sp. AMC 289 | | includes | +28901 | Salmonella sp. AMC 28 | | includes | +28901 | Salmonella sp. AMC 291 | | includes | +28901 | Salmonella sp. AMC 294 | | includes | +28901 | Salmonella sp. AMC 299 | | includes | +28901 | Salmonella sp. AMC 301 | | includes | +28901 | Salmonella sp. AMC 327 | | includes | +28901 | Salmonella sp. AMC 90 | | includes | +28901 | Salmonella sp. FDA00013420 | | includes | +28901 | Salmonella sp. FDA00013433 | | includes | +28901 | Salmonella sp. FDA00013434 | | includes | +28901 | Salmonella sp. FDA00013435 | | includes | +28901 | Salmonella sp. FDA00013436 | | includes | +28901 | Salmonella sp. FDA00013437 | | includes | +28901 | Salmonella sp. FDA00013438 | | includes | +28901 | Salmonella sp. FDA00013439 | | includes | +28901 | Salmonella sp. FDA00013440 | | includes | +28901 | Salmonella sp. FDA00013468 | | includes | +28901 | Salmonella sp. FDA00013469 | | includes | +28901 | Salmonella sp. FDA00013470 | | includes | +28901 | Salmonella sp. FDA00013495 | | includes | +28901 | Salmonella sp. FDA00013496 | | includes | +28901 | Salmonella sp. FDA00013499 | | includes | +28901 | Salmonella sp. FDA00013500 | | includes | +28901 | Salmonella sp. FDA00013513 | | includes | +28901 | Salmonella sp. FDA00013514 | | includes | +28901 | Salmonella sp. FDA00013515 | | includes | +28901 | Salmonella sp. FDA00013516 | | includes | +28901 | Salmonella sp. FDA00013517 | | includes | +28901 | Salmonella sp. FDA00013518 | | includes | +28901 | Salmonella sp. FDA00013519 | | includes | +28901 | Salmonella sp. FDA00013520 | | includes | +28901 | Salmonella sp. FDA00013521 | | includes | +28901 | Salmonella sp. FDA00013522 | | includes | +28901 | Salmonella sp. FDA00013523 | | includes | +28901 | Salmonella sp. FDA00013524 | | includes | +28901 | Salmonella sp. FDA00013525 | | includes | +28901 | Salmonella sp. FDA00013526 | | includes | +28901 | Salmonella sp. FDA00013597 | | includes | +28901 | Salmonella sp. HC-257 | | includes | +28901 | Salmonella sp. IA1-174 | | includes | +28901 | Salmonella sp. MH3-A1 | | includes | +28901 | Salmonella sp. MH3-A2 | | includes | +28901 | Salmonella sp. MH3-A3 | | includes | +28901 | Salmonella sp. MH3-C | | includes | +28901 | Salmonella sp. MH3-D1 | | includes | +28901 | Salmonella sp. MH3-D2 | | includes | +28901 | Salmonella sp. MH3-D3 | | includes | +28901 | Salmonella sp. MH3-D4 | | includes | +28901 | Salmonella sp. MH3-Z1 | | includes | +28901 | Salmonella sp. MH3-Z2 | | includes | +28901 | Salmonella sp. MH4-A2 | | includes | +28901 | Salmonella sp. MH4-A3 | | includes | +28901 | Salmonella sp. MH4-A4 | | includes | +28901 | Salmonella sp. MH4-Z2 | | includes | +28901 | Salmonella sp. NYVetLIRN-85 | | includes | +28901 | Salmonella sp. NYVetLIRN-86 | | includes | +28901 | Salmonella sp. NYVetLIRN-87 | | includes | +28901 | Salmonella sp. NYVetLIRN-88 | | includes | +28901 | Salmonella sp. OH-18-15149 | | includes | +28901 | Salmonella sp. OH-18-15334 | | includes | +28901 | Salmonella sp. OH-18-15363 | | includes | +28901 | Salmonella sp. OH-18-16886 | | includes | +28901 | Salmonella sp. OH-18-16934 | | includes | +28901 | Salmonella sp. OH-18-18132-10 | | includes | +28901 | Salmonella sp. OH-18-18132-11 | | includes | +28901 | Salmonella sp. OH-18-18132-12 | | includes | +28901 | Salmonella sp. OH-18-18132-13 | | includes | +28901 | Salmonella sp. OH-18-18132-14 | | includes | +28901 | Salmonella sp. OH-18-18132-15 | | includes | +28901 | Salmonella sp. OH-18-18132-1 | | includes | +28901 | Salmonella sp. OH-18-18132-2 | | includes | +28901 | Salmonella sp. OH-18-18132-3 | | includes | +28901 | Salmonella sp. OH-18-18132-4 | | includes | +28901 | Salmonella sp. OH-18-18132-5 | | includes | +28901 | Salmonella sp. OH-18-18132-6 | | includes | +28901 | Salmonella sp. OH-18-18132-7 | | includes | +28901 | Salmonella sp. OH-18-18132-8 | | includes | +28901 | Salmonella sp. OH-18-18132-9 | | includes | +28901 | Salmonella sp. OH-18-18281-1 | | includes | +28901 | Salmonella sp. OH-18-18281-2 | | includes | +28901 | Salmonella sp. OH-18-18411 | | includes | +28901 | Salmonella sp. OH-18-18446 | | includes | +28901 | Salmonella sp. OH-18-18447 | | includes | +28901 | Salmonella sp. OH-18-18941 | | includes | +28901 | Salmonella sp. OH-18-19201 | | includes | +28901 | Salmonella sp. OH-18-19951-1 | | includes | +28901 | Salmonella sp. OH-18-20073-2T | | includes | +28901 | Salmonella sp. OH-18-20117-1 | | includes | +28901 | Salmonella sp. OH-18-20132-7 | | includes | +28901 | Salmonella sp. OH-18-20225-1-S | | includes | +28901 | Salmonella sp. OH-18-20225-2-S | | includes | +28901 | Salmonella sp. OH-18-20299-1 | | includes | +28901 | Salmonella sp. OH-18-20299-2 | | includes | +28901 | Salmonella sp. OH-18-20299-3 | | includes | +28901 | Salmonella sp. OH-18-20299-4 | | includes | +28901 | Salmonella sp. OH-18-20299-5 | | includes | +28901 | Salmonella sp. OH-18-20299-6 | | includes | +28901 | Salmonella sp. OH-18-20299-7 | | includes | +28901 | Salmonella sp. OH-18-20299-8 | | includes | +28901 | Salmonella sp. OH-18-20386 | | includes | +28901 | Salmonella sp. OH-18-20895 | | includes | +28901 | Salmonella sp. OH-18-20897 | | includes | +28901 | Salmonella sp. OH-18-21102 | | includes | +28901 | Salmonella sp. OH-18-21112 | | includes | +28901 | Salmonella sp. OH-18-21175 | | includes | +28901 | Salmonella sp. OH-18-21493-S | | includes | +28901 | Salmonella sp. OH-18-21628 | | includes | +28901 | Salmonella sp. OH-18-21629 | | includes | +28901 | Salmonella sp. OH-18-21765 | | includes | +28901 | Salmonella sp. OH-18-21865-2 | | includes | +28901 | Salmonella sp. OH-18-22026 | | includes | +28901 | Salmonella sp. OH-18-22045 | | includes | +28901 | Salmonella sp. OH-18-22168 | | includes | +28901 | Salmonella sp. OH-18-22269-1 | | includes | +28901 | Salmonella sp. OH-18-22479 | | includes | +28901 | Salmonella sp. SAL-18-VL-LA-TX-0007 | | includes | +28901 | Salmonella sp. SAL-18-VL-LA-TX-0008 | | includes | +28901 | Salmonella sp. SAL-18-VL-LA-TX-0009 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-MS-0001 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-MS-0002 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-MS-0003 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-NJ-0001 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-UP-NBC-0001 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-UP-NBC-0004 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-UP-NBC-0005 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-UP-NBC-0006 | | includes | +28901 | Salmonella sp. SAL-18-VL-NY-UP-NBC-0007 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-IN-0001 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-IN-0002 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-IN-0003 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-IN-0005 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-IN-0007 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-WA-0012 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-WA-0013 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-WA-0014 | | includes | +28901 | Salmonella sp. SAL-18-VL-OH-WA-0017 | | includes | +28901 | Salmonella sp. TTU_251 | | includes | +28901 | Salmonella sp. TTU_258 | | includes | +28901 | Salmonella sp. TTU_262 | | includes | +28901 | Salmonella sp. TTU_264 | | includes | +28901 | Salmonella sp. TTU_265 | | includes | +28901 | Salmonella sp. TTU_266 | | includes | +28901 | Salmonella sp. TTU_267 | | includes | +28901 | Salmonella sp. TTU_269 | | includes | +28901 | Salmonella sp. TTU_274 | | includes | +28901 | Salmonella sp. TTU_279 | | includes | +28901 | Salmonella sp. TTU_282 | | includes | +28901 | Salmonella sp. TTU_284 | | includes | +28901 | Salmonella sp. TTU_287 | | includes | +28901 | Salmonella sp. TTU_289 | | includes | +28901 | Salmonella sp. TTU_297 | | includes | +28901 | Salmonella sp. TTU_298 | | includes | +28901 | Salmonella sp. TTU_299 | | includes | +28901 | Salmonella sp. TTU_303 | | includes | +28901 | Salmonella sp. TTU_304 | | includes | +28901 | Salmonella sp. TTU_305 | | includes | +28901 | Salmonella sp. TTU_306 | | includes | +28901 | Salmonella sp. TTU_307 | | includes | +28901 | Salmonella sp. TTU_308 | | includes | +28901 | Salmonella sp. TTU_309 | | includes | +28901 | Salmonella sp. TTU_310 | | includes | +28901 | Salmonella sp. TTU_311 | | includes | +28901 | Salmonella sp. TTU_312 | | includes | +28901 | Salmonella sp. TTU_313 | | includes | +28901 | Salmonella sp. TTU_314 | | includes | +28901 | Salmonella sp. TTU_315 | | includes | +28901 | Salmonella sp. TTU_316 | | includes | +28901 | Salmonella sp. TTU_317 | | includes | +28901 | Salmonella sp. TTU_318 | | includes | +28901 | Salmonella sp. TTU_319 | | includes | +28901 | Salmonella sp. TTU_320 | | includes | +28901 | Salmonella sp. TTU_321 | | includes | +28901 | Salmonella sp. TTU_322 | | includes | +28901 | Salmonella sp. TTU_323 | | includes | +28901 | Salmonella sp. TTU_324 | | includes | +28901 | Salmonella sp. TTU_325 | | includes | +28901 | Salmonella sp. TTU_326 | | includes | +28901 | Salmonella sp. TTU_327 | | includes | +28901 | Salmonella sp. TTU_328 | | includes | +28901 | Salmonella sp. TTU_329 | | includes | +28901 | Salmonella sp. TTU_330 | | includes | +28901 | Salmonella sp. TTU_331 | | includes | +28901 | Salmonella sp. TTU_332 | | includes | +28901 | Salmonella sp. TTU_333 | | includes | +28901 | Salmonella sp. TTU_334 | | includes | +28901 | Salmonella sp. TTU_335 | | includes | +28901 | Salmonella sp. TTU_338 | | includes | +28901 | Salmonella sp. TTU_345 | | includes | +28901 | Salmonella sp. TTU_352 | | includes | +28901 | Salmonella sp. TTU_353 | | includes | +28901 | Salmonella sp. TTU_357 | | includes | +28901 | Salmonella sp. TTU_358 | | includes | +28901 | Salmonella sp. TTU_359 | | includes | +28901 | Salmonella sp. TXACF1801691 | | includes | +28901 | Salmonella sp. Z-172 | | includes | +28901 | Salmonella sp. ZH-248 | | includes | +59201 | Salmonella choleraesuis subsp. choleraesuis corrig. (Smith 1894) Weldin 1927 | | authority | +59201 | Salmonella cholerae-suis subsp. cholerae-suis | | synonym | +59201 | Salmonella choleraesuis subsp. choleraesuis | | synonym | +59201 | Salmonella enterica I | | synonym | +59201 | Salmonella enterica subsp. enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987 | | authority | +59201 | Salmonella enterica subsp. enterica | | scientific name | +59201 | Salmonella enterica subsp. I | | synonym | +59201 | Salmonella enterica subsp. Subsp. I | | synonym | +59201 | Salmonella enterica subsp. Subsp. Ixxx | | synonym | +72274 | gamma-3 proteobacteria | gamma-3 proteobacteria | in-part | +72274 | Pseudomonaceae/Moraxellaceae group | | synonym | +72274 | Pseudomonadales Orla-Jensen 1921 emend. Liao et al. 2020 | | authority | +72274 | Pseudomonadales | | scientific name | +83333 | Escherichia coli K12 | | equivalent name | +83333 | Escherichia coli K-12 | | scientific name | +90371 |" ""Bacillus typhimurium"" Loeffler 1892 "| | authority | +90371 | Bacillus typhimurium | | synonym | +90371 | Salmonella choleraesuis serotype typhimurium | | synonym | +90371 | Salmonella enterica 1,4,[5],12,:i:1,2 | | synonym | +90371 | Salmonella enterica serotype Typhimurium | | synonym | +90371 | Salmonella enterica serovar Typhimurium | | synonym | +90371 | Salmonella enterica ser. typhimurium | | synonym | +90371 | Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:1,2 | | synonym | +90371 | Salmonella enterica subsp. enterica serovar Typhimurium | | scientific name | +90371 | Salmonella typhimurium (Loeffler 1892) Castellani and Chalmers 1919 | | authority | +90371 |" ""Salmonella typhi-murium"" (sic) (Loeffler 1892) Castellani and Chalmers 1919 "| | authority | +90371 | Salmonella typhi-murium | | synonym | +90371 | Salmonella typhimurium | | synonym | +91347 | Enterobacterales Adeolu et al. 2016 | | authority | +91347 | Enterobacterales | | scientific name | +91347 | Enterobacteriaceae and related endosymbionts | | synonym | +91347 | Enterobacteriaceae group | | synonym | +91347 | Enterobacteriales | | synonym | +91347 | gamma-3 proteobacteria | gamma-3 proteobacteria | in-part | +99287 | Salmonella enterica subsp. enterica serovar Typhimurium LT2 | | equivalent name | +99287 | Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 | | equivalent name | +99287 | Salmonella enterica subsp. enterica serovar Typhimurium strain LT2-LTL2 | | equivalent name | +99287 | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | | scientific name | +99287 | Salmonella typhimurium LT2 | | synonym | +131567 | biota | | synonym | +131567 | cellular organisms | | scientific name | +135621 | Pseudomonadaceae | | scientific name | +135621 | Pseudomonadaceae Winslow et al. 1917 | | authority | +136841 | Pseudomonas aeruginosa group | | scientific name | +208964 | Pseudomonas aeruginosa PAO1 | | scientific name | +208964 | Pseudomonas sp. PAO1 | | equivalent name | +511145 | Escherichia coli MG1655 | | synonym | +511145 | Escherichia coli strain MG1655 | | equivalent name | +511145 | Escherichia coli str. K12 substr. MG1655 | | equivalent name | +511145 | Escherichia coli str. K-12 substr. MG1655 | | scientific name | +511145 | Escherichia coli str. MG1655 | | equivalent name | diff -r 000000000000 -r b01d6b38f779 test-data/taxonomy/nodes.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy/nodes.dmp Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,22 @@ +1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | | | 0 | 0 | 0 | +2 | 131567 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | | | | 0 | 0 | 1 | +286 | 135621 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +287 | 136841 | species | PA | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | code compliant; specified | | | 1 | 0 | 1 | +543 | 91347 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +561 | 543 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +562 | 561 | species | EC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | code compliant; specified | | | 1 | 0 | 1 | +590 | 543 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +1224 | 2 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | | | 0 | 0 | 1 | +1236 | 1224 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +28901 | 590 | species | SE | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | code compliant; specified | | | 1 | 0 | 1 | +59201 | 28901 | subspecies | SE | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | code compliant; specified | | | 1 | 0 | 1 | +72274 | 1236 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +83333 | 562 | strain | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | | | 0 | 0 | 1 | +90371 | 59201 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | | | 0 | 0 | 1 | +91347 | 1236 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +99287 | 90371 | strain | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | | | 0 | 0 | 1 | +131567 | 1 | no rank | | 8 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | | | 0 | 0 | 1 | +135621 | 72274 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | code compliant | | | 0 | 0 | 1 | +136841 | 286 | species group | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | | | 0 | 0 | 1 | +208964 | 287 | strain | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | | | 0 | 0 | 1 | +511145 | 83333 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | | | 0 | 0 | 1 | diff -r 000000000000 -r b01d6b38f779 tool-data/metabuli_databases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/metabuli_databases.loc.sample Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,3 @@ +# This file defines databases and their folder location. Each database is a line with +# three columns: value{tab}{name}{/path/to/database-folder} +# E.g. GTDB{tab}GTDB{tab}/path/to/GTDB diff -r 000000000000 -r b01d6b38f779 tool-data/taxonomy.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/taxonomy.loc.sample Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,3 @@ +# This file defines databases and their folder location. Each database is a line with +# three columns: value{tab}{name}{/path/to/database-folder} +# E.g. GTDB{tab}GTDB{tab}/path/to/GTDB \ No newline at end of file diff -r 000000000000 -r b01d6b38f779 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,12 @@ + + + + + value, name, version, path + +
+ + value, name, path + +
+
diff -r 000000000000 -r b01d6b38f779 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Jun 04 11:49:21 2024 +0000 @@ -0,0 +1,13 @@ + + + + + value, name, version, path + +
+ + + value, name, path + +
+