# HG changeset patch # User youyuh48 # Date 1720946750 0 # Node ID 6e90a30b214fc462eb49186702789192fa8c2a5b planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty diff -r 000000000000 -r 6e90a30b214f combine_bracken_outputs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/combine_bracken_outputs.xml Sun Jul 14 08:45:50 2024 +0000 @@ -0,0 +1,33 @@ + + + bracken + + + + + + + + + + + title = {combine_bracken_outputs}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/jenniferlu717/Bracken} + + + diff -r 000000000000 -r 6e90a30b214f mytool_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mytool_conf.xml Sun Jul 14 08:45:50 2024 +0000 @@ -0,0 +1,6 @@ + + +
+ +
+ diff -r 000000000000 -r 6e90a30b214f test-data/combined.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combined.tsv Sun Jul 14 08:45:50 2024 +0000 @@ -0,0 +1,176 @@ +name taxonomy_id taxonomy_lvl S1_num S1_frac S2_num S2_frac +Streptococcus sanguinis 1305 S 21 0.00000 21 0.00000 +Streptococcus suis 1307 S 23 0.00000 23 0.00000 +Streptococcus gordonii 1302 S 10 0.00000 10 0.00000 +Vibrio cholerae 666 S 14 0.00000 14 0.00000 +Bacillus methylotrophicus 492670 S 23 0.00000 23 0.00000 +Streptococcus thermophilus 1308 S 34 0.00000 34 0.00000 +Streptococcus mutans 1309 S 10 0.00000 10 0.00000 +Burkholderia xenovorans 36873 S 34 0.00000 34 0.00000 +Sinorhizobium medicae 110321 S 54 0.00000 54 0.00000 +Burkholderia phymatum 148447 S 656706 0.02503 656706 0.02503 +Borrelia burgdorferi 139 S 36 0.00000 36 0.00000 +Nostoc punctiforme 272131 S 590648 0.02251 590648 0.02251 +Shewanella frigidimarina 56812 S 23 0.00000 23 0.00000 +Clostridium novyi 1542 S 212196 0.00809 212196 0.00809 +Mycobacterium tuberculosis 1773 S 294997 0.01124 294997 0.01124 +Mycobacterium smegmatis 1772 S 239 0.00001 239 0.00001 +Rhodopseudomonas palustris 1076 S 824296 0.03141 824296 0.03141 +Bacteroides thetaiotaomicron 818 S 395669 0.01508 395669 0.01508 +Mycobacterium abscessus 36809 S 78 0.00000 78 0.00000 +Burkholderia multivorans 87883 S 35 0.00000 35 0.00000 +Citrobacter koseri 545 S 593 0.00002 593 0.00002 +Bordetella pertussis 520 S 1364 0.00005 1364 0.00005 +Chlamydia trachomatis 813 S 72217 0.00275 72217 0.00275 +Pseudomonas aeruginosa 287 S 43 0.00000 43 0.00000 +Chlamydia pneumoniae 83558 S 78698 0.00300 78698 0.00300 +Haloquadratum walsbyi 293091 S 224017 0.00854 224017 0.00854 +Streptococcus pyogenes 1314 S 256983 0.00979 256983 0.00979 +Streptococcus pneumoniae 1313 S 178515 0.00680 178515 0.00680 +Pelodictyon luteolum 1100 S 158945 0.00606 158945 0.00606 +Streptococcus agalactiae 1311 S 164040 0.00625 164040 0.00625 +Pseudomonas protegens 380021 S 18 0.00000 18 0.00000 +Salmonella enterica 28901 S 392102 0.01494 392102 0.01494 +Francisella tularensis 263 S 120892 0.00461 120892 0.00461 +Clostridium botulinum 1491 S 282385 0.01076 282385 0.01076 +Alkaliphilus metalliredigens 208226 S 368497 0.01404 368497 0.01404 +Shewanella denitrificans 192073 S 17 0.00000 17 0.00000 +Shewanella sp. MR-7 60481 S 311044 0.01185 311044 0.01185 +Bacillus licheniformis 1402 S 13 0.00000 13 0.00000 +Burkholderia ambifaria 152480 S 30 0.00000 30 0.00000 +Alkalilimnicola ehrlichii 351052 S 226411 0.00863 226411 0.00863 +Corynebacterium jeikeium 38289 S 20 0.00000 20 0.00000 +Pediococcus pentosaceus 1255 S 13 0.00000 13 0.00000 +Bacillus anthracis 1392 S 428743 0.01634 428743 0.01634 +Hyphomonas neptunium 81032 S 262989 0.01002 262989 0.01002 +Borrelia afzelii 29518 S 37 0.00000 37 0.00000 +Pseudomonas fluorescens 294 S 22 0.00000 22 0.00000 +Corynebacterium urealyticum 43771 S 171504 0.00654 171504 0.00654 +Bacillus clausii 79880 S 281964 0.01075 281964 0.01075 +Campylobacter concisus 199 S 157990 0.00602 157990 0.00602 +Shewanella baltica 62322 S 109 0.00000 109 0.00000 +Pseudomonas stutzeri 316 S 295131 0.01125 295131 0.01125 +Cytophaga hutchinsonii 985 S 307539 0.01172 307539 0.01172 +Cyanothece sp. ATCC 51142 43989 S 372311 0.01419 372311 0.01419 +Thermus thermophilus 274 S 152714 0.00582 152714 0.00582 +Bacillus cytotoxicus 580165 S 648 0.00002 648 0.00002 +Clostridium acetobutylicum 1488 S 13 0.00000 13 0.00000 +Burkholderia cenocepacia 95486 S 79 0.00000 79 0.00000 +Corynebacterium efficiens 152794 S 234093 0.00892 234093 0.00892 +Chromobacterium violaceum 536 S 331419 0.01263 331419 0.01263 +Ureaplasma parvum 134821 S 47617 0.00181 47617 0.00181 +Bacillus pumilus 1408 S 20 0.00000 20 0.00000 +Enterobacter sp. 638 399742 S 291 0.00001 291 0.00001 +Bordetella avium 521 S 81 0.00000 81 0.00000 +Bacillus cereus 1396 S 1288824 0.04912 1288824 0.04912 +Ochrobactrum anthropi 529 S 382895 0.01459 382895 0.01459 +Thermosipho melanesiensis 46541 S 128185 0.00489 128185 0.00489 +Mycobacterium marinum 1781 S 433344 0.01651 433344 0.01651 +Nostoc sp. PCC 7120 103690 S 254 0.00001 254 0.00001 +Pseudomonas mendocina 300 S 15 0.00000 15 0.00000 +Lactococcus lactis 1358 S 407693 0.01554 407693 0.01554 +Pseudomonas putida 303 S 515978 0.01966 515978 0.01966 +Sinorhizobium meliloti 382 S 424711 0.01619 424711 0.01619 +Clostridium beijerinckii 1520 S 419943 0.01600 419943 0.01600 +Geobacillus thermodenitrificans 33940 S 22 0.00000 22 0.00000 +Saccharopolyspora erythraea 1836 S 10 0.00000 10 0.00000 +Shewanella oneidensis 70863 S 226 0.00001 226 0.00001 +Bradyrhizobium sp. ORS 278 114615 S 19 0.00000 19 0.00000 +Rickettsia typhi 785 S 43 0.00000 43 0.00000 +Methanococcus maripaludis 39152 S 121534 0.00463 121534 0.00463 +Rickettsia prowazekii 782 S 72160 0.00275 72160 0.00275 +Listeria innocua 1642 S 34 0.00000 34 0.00000 +Bordetella petrii 94624 S 238 0.00001 238 0.00001 +Bradyrhizobium diazoefficiens 1355477 S 17 0.00000 17 0.00000 +Mycobacterium sp. KMS 189918 S 278 0.00001 278 0.00001 +Bordetella parapertussis 519 S 1494 0.00006 1494 0.00006 +Bordetella bronchiseptica 518 S 455495 0.01736 455495 0.01736 +Staphylococcus saprophyticus 29385 S 34 0.00000 34 0.00000 +Listeria monocytogenes 1639 S 44 0.00000 44 0.00000 +Cupriavidus taiwanensis 164546 S 12 0.00000 12 0.00000 +Chlamydophila caviae 83557 S 74743 0.00285 74743 0.00285 +Candidatus Blochmannia pennsylvanicus 101534 S 52530 0.00200 52530 0.00200 +Shigella flexneri 623 S 5157 0.00020 5157 0.00020 +Shigella dysenteriae 622 S 2653 0.00010 2653 0.00010 +Shigella boydii 621 S 4510 0.00017 4510 0.00017 +Rhodococcus jostii 132919 S 622314 0.02372 622314 0.02372 +Shigella sonnei 624 S 2528 0.00010 2528 0.00010 +Klebsiella pneumoniae 573 S 338 0.00001 338 0.00001 +Sodalis glossinidius 63612 S 293610 0.01119 293610 0.01119 +Nitrosococcus oceani 1229 S 13 0.00000 13 0.00000 +Shewanella sp. MR-4 60480 S 473 0.00002 473 0.00002 +Neisseria meningitidis 487 S 155179 0.00591 155179 0.00591 +Herpetosiphon aurantiacus 65 S 427306 0.01628 427306 0.01628 +Leptospira borgpetersenii 174 S 242937 0.00926 242937 0.00926 +Leptospira interrogans 173 S 13 0.00000 13 0.00000 +Photobacterium profundum 74109 S 13 0.00000 13 0.00000 +Lysinibacillus sphaericus 1421 S 47 0.00000 47 0.00000 +Clostridium perfringens 1502 S 17 0.00000 17 0.00000 +Bacillus subtilis 1423 S 267729 0.01020 267729 0.01020 +Lawsonia intracellularis 29546 S 114782 0.00437 114782 0.00437 +Lactobacillus casei 1582 S 11 0.00000 11 0.00000 +Bacillus thuringiensis 1428 S 347587 0.01325 347587 0.01325 +Psychrobacter arcticus 334543 S 78 0.00000 78 0.00000 +Oceanobacillus iheyensis 182710 S 15 0.00000 15 0.00000 +Lactobacillus helveticus 1587 S 12 0.00000 12 0.00000 +Lactobacillus delbrueckii 1584 S 157023 0.00598 157023 0.00598 +Histophilus somni 731 S 136592 0.00521 136592 0.00521 +Wigglesworthia glossinidia 51229 S 66276 0.00253 66276 0.00253 +Cronobacter sakazakii 28141 S 273 0.00001 273 0.00001 +Yersinia enterocolitica 630 S 101 0.00000 101 0.00000 +Bacillus halodurans 86665 S 269935 0.01029 269935 0.01029 +Yersinia pestis 632 S 314256 0.01198 314256 0.01198 +Burkholderia vietnamiensis 60552 S 31 0.00000 31 0.00000 +Photorhabdus luminescens 29488 S 51 0.00000 51 0.00000 +Bacillus weihenstephanensis 86662 S 1985 0.00008 1985 0.00008 +Idiomarina loihiensis 135577 S 187662 0.00715 187662 0.00715 +Prochlorococcus marinus 1219 S 307285 0.01171 307285 0.01171 +Ignicoccus hospitalis 160233 S 87457 0.00333 87457 0.00333 +Burkholderia lata 482957 S 18 0.00000 18 0.00000 +Lactobacillus salivarius 1624 S 139568 0.00532 139568 0.00532 +Syntrophomonas wolfei 863 S 193746 0.00738 193746 0.00738 +Burkholderia thailandensis 57975 S 1182 0.00005 1182 0.00005 +Haemophilus influenzae 727 S 118512 0.00452 118512 0.00452 +Cupriavidus necator 106590 S 29197 0.00111 29197 0.00111 +Acinetobacter sp. ADP1 62977 S 11 0.00000 11 0.00000 +Ruminiclostridium thermocellum 1515 S 260196 0.00992 260196 0.00992 +Erwinia tasmaniensis 338565 S 323258 0.01232 323258 0.01232 +Clostridium tetani 1513 S 16 0.00000 16 0.00000 +Psychrobacter cryohalolentis 330922 S 417930 0.01593 417930 0.01593 +Borrelia bavariensis 664662 S 80060 0.00305 80060 0.00305 +Shewanella loihica 359303 S 10 0.00000 10 0.00000 +Pasteurella multocida 747 S 12 0.00000 12 0.00000 +Treponema denticola 158 S 183767 0.00700 183767 0.00700 +Yersinia pseudotuberculosis 633 S 2033 0.00008 2033 0.00008 +Pseudomonas entomophila 312306 S 52 0.00000 52 0.00000 +Halorhodospira halophila 1053 S 11 0.00000 11 0.00000 +Lachnoclostridium phytofermentans 66219 S 10 0.00000 10 0.00000 +Buchnera aphidicola 9 S 26206 0.00100 26206 0.00100 +Escherichia coli 562 S 1449813 0.05525 1449813 0.05525 +Coxiella burnetii 777 S 135528 0.00516 135528 0.00516 +Geobacter sulfurreducens 35554 S 244296 0.00931 244296 0.00931 +Anabaena variabilis 1172 S 446471 0.01701 446471 0.01701 +Synechococcus elongatus 32046 S 466493 0.01778 466493 0.01778 +Serratia proteamaculans 28151 S 117 0.00000 117 0.00000 +Burkholderia pseudomallei 28450 S 453210 0.01727 453210 0.01727 +Neisseria gonorrhoeae 485 S 152524 0.00581 152524 0.00581 +Thiobacillus denitrificans 36861 S 227011 0.00865 227011 0.00865 +Burkholderia mallei 13373 S 3268 0.00012 3268 0.00012 +Pectobacterium atrosepticum 29471 S 96 0.00000 96 0.00000 +Listeria welshimeri 1643 S 180835 0.00689 180835 0.00689 +Mycobacterium gilvum 1804 S 244 0.00001 244 0.00001 +Mycobacterium sp. JLS 164757 S 699935 0.02667 699935 0.02667 +Staphylococcus aureus 1280 S 1212241 0.04620 1212241 0.04620 +Staphylococcus haemolyticus 1283 S 33 0.00000 33 0.00000 +Staphylococcus epidermidis 1282 S 55 0.00000 55 0.00000 +Psychromonas ingrahamii 357794 S 287771 0.01097 287771 0.01097 +Shewanella amazonensis 60478 S 18 0.00000 18 0.00000 +Mycobacterium vanbaalenii 110539 S 248 0.00001 248 0.00001 +Shewanella sediminis 271097 S 12 0.00000 12 0.00000 +Acinetobacter baumannii 470 S 258028 0.00983 258028 0.00983 +Mycobacterium leprae 1769 S 31 0.00000 31 0.00000 +Mycobacterium bovis 1765 S 279394 0.01065 279394 0.01065 +Mycobacterium ulcerans 1809 S 901 0.00003 901 0.00003 +Vibrio campbellii 680 S 14 0.00000 14 0.00000 +Mycobacterium avium 1764 S 311211 0.01186 311211 0.01186 +Shewanella sp. ANA-3 94122 S 447 0.00002 447 0.00002 diff -r 000000000000 -r 6e90a30b214f test-data/sample1_output_species_abundance.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample1_output_species_abundance.txt Sun Jul 14 08:45:50 2024 +0000 @@ -0,0 +1,176 @@ +name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads +Streptococcus sanguinis 1305 S 21 0 21 0.00000 +Streptococcus suis 1307 S 22 1 23 0.00000 +Streptococcus gordonii 1302 S 10 0 10 0.00000 +Vibrio cholerae 666 S 10 4 14 0.00000 +Bacillus methylotrophicus 492670 S 23 0 23 0.00000 +Streptococcus thermophilus 1308 S 34 0 34 0.00000 +Streptococcus mutans 1309 S 10 0 10 0.00000 +Burkholderia xenovorans 36873 S 34 0 34 0.00000 +Sinorhizobium medicae 110321 S 54 0 54 0.00000 +Burkholderia phymatum 148447 S 655478 1228 656706 0.02503 +Borrelia burgdorferi 139 S 36 0 36 0.00000 +Nostoc punctiforme 272131 S 590086 562 590648 0.02251 +Shewanella frigidimarina 56812 S 23 0 23 0.00000 +Clostridium novyi 1542 S 211808 388 212196 0.00809 +Mycobacterium tuberculosis 1773 S 20647 274350 294997 0.01124 +Mycobacterium smegmatis 1772 S 239 0 239 0.00001 +Rhodopseudomonas palustris 1076 S 823190 1106 824296 0.03141 +Bacteroides thetaiotaomicron 818 S 392179 3490 395669 0.01508 +Mycobacterium abscessus 36809 S 78 0 78 0.00000 +Burkholderia multivorans 87883 S 30 5 35 0.00000 +Citrobacter koseri 545 S 576 17 593 0.00002 +Bordetella pertussis 520 S 632 732 1364 0.00005 +Chlamydia trachomatis 813 S 71933 284 72217 0.00275 +Pseudomonas aeruginosa 287 S 42 1 43 0.00000 +Chlamydia pneumoniae 83558 S 78615 83 78698 0.00300 +Haloquadratum walsbyi 293091 S 223986 31 224017 0.00854 +Streptococcus pyogenes 1314 S 252007 4976 256983 0.00979 +Streptococcus pneumoniae 1313 S 177347 1168 178515 0.00680 +Pelodictyon luteolum 1100 S 157283 1662 158945 0.00606 +Streptococcus agalactiae 1311 S 159789 4251 164040 0.00625 +Pseudomonas protegens 380021 S 18 0 18 0.00000 +Salmonella enterica 28901 S 387186 4916 392102 0.01494 +Francisella tularensis 263 S 120338 554 120892 0.00461 +Clostridium botulinum 1491 S 281791 594 282385 0.01076 +Alkaliphilus metalliredigens 208226 S 368065 432 368497 0.01404 +Shewanella denitrificans 192073 S 17 0 17 0.00000 +Shewanella sp. MR-7 60481 S 224465 86579 311044 0.01185 +Bacillus licheniformis 1402 S 13 0 13 0.00000 +Burkholderia ambifaria 152480 S 27 3 30 0.00000 +Alkalilimnicola ehrlichii 351052 S 226337 74 226411 0.00863 +Corynebacterium jeikeium 38289 S 20 0 20 0.00000 +Pediococcus pentosaceus 1255 S 13 0 13 0.00000 +Bacillus anthracis 1392 S 151306 277437 428743 0.01634 +Hyphomonas neptunium 81032 S 262956 33 262989 0.01002 +Borrelia afzelii 29518 S 37 0 37 0.00000 +Pseudomonas fluorescens 294 S 21 1 22 0.00000 +Corynebacterium urealyticum 43771 S 168078 3426 171504 0.00654 +Bacillus clausii 79880 S 281618 346 281964 0.01075 +Campylobacter concisus 199 S 157661 329 157990 0.00602 +Shewanella baltica 62322 S 108 1 109 0.00000 +Pseudomonas stutzeri 316 S 293151 1980 295131 0.01125 +Cytophaga hutchinsonii 985 S 307508 31 307539 0.01172 +Cyanothece sp. ATCC 51142 43989 S 372257 54 372311 0.01419 +Thermus thermophilus 274 S 152701 13 152714 0.00582 +Bacillus cytotoxicus 580165 S 643 5 648 0.00002 +Clostridium acetobutylicum 1488 S 13 0 13 0.00000 +Burkholderia cenocepacia 95486 S 29 50 79 0.00000 +Corynebacterium efficiens 152794 S 233423 670 234093 0.00892 +Chromobacterium violaceum 536 S 330985 434 331419 0.01263 +Ureaplasma parvum 134821 S 47612 5 47617 0.00181 +Bacillus pumilus 1408 S 20 0 20 0.00000 +Enterobacter sp. 638 399742 S 290 1 291 0.00001 +Bordetella avium 521 S 81 0 81 0.00000 +Bacillus cereus 1396 S 1086754 202070 1288824 0.04912 +Ochrobactrum anthropi 529 S 381841 1054 382895 0.01459 +Thermosipho melanesiensis 46541 S 128132 53 128185 0.00489 +Mycobacterium marinum 1781 S 281340 152004 433344 0.01651 +Nostoc sp. PCC 7120 103690 S 247 7 254 0.00001 +Pseudomonas mendocina 300 S 14 1 15 0.00000 +Lactococcus lactis 1358 S 404921 2772 407693 0.01554 +Pseudomonas putida 303 S 511201 4777 515978 0.01966 +Sinorhizobium meliloti 382 S 420783 3928 424711 0.01619 +Clostridium beijerinckii 1520 S 418932 1011 419943 0.01600 +Geobacillus thermodenitrificans 33940 S 11 11 22 0.00000 +Saccharopolyspora erythraea 1836 S 10 0 10 0.00000 +Shewanella oneidensis 70863 S 222 4 226 0.00001 +Bradyrhizobium sp. ORS 278 114615 S 14 5 19 0.00000 +Rickettsia typhi 785 S 43 0 43 0.00000 +Methanococcus maripaludis 39152 S 121232 302 121534 0.00463 +Rickettsia prowazekii 782 S 70541 1619 72160 0.00275 +Listeria innocua 1642 S 33 1 34 0.00000 +Bordetella petrii 94624 S 233 5 238 0.00001 +Bradyrhizobium diazoefficiens 1355477 S 17 0 17 0.00000 +Mycobacterium sp. KMS 189918 S 11 267 278 0.00001 +Bordetella parapertussis 519 S 348 1146 1494 0.00006 +Bordetella bronchiseptica 518 S 128479 327016 455495 0.01736 +Staphylococcus saprophyticus 29385 S 34 0 34 0.00000 +Listeria monocytogenes 1639 S 43 1 44 0.00000 +Cupriavidus taiwanensis 164546 S 12 0 12 0.00000 +Chlamydophila caviae 83557 S 74403 340 74743 0.00285 +Candidatus Blochmannia pennsylvanicus 101534 S 52480 50 52530 0.00200 +Shigella flexneri 623 S 1022 4135 5157 0.00020 +Shigella dysenteriae 622 S 1206 1447 2653 0.00010 +Shigella boydii 621 S 1035 3475 4510 0.00017 +Rhodococcus jostii 132919 S 622004 310 622314 0.02372 +Shigella sonnei 624 S 605 1923 2528 0.00010 +Klebsiella pneumoniae 573 S 333 5 338 0.00001 +Sodalis glossinidius 63612 S 292996 614 293610 0.01119 +Nitrosococcus oceani 1229 S 13 0 13 0.00000 +Shewanella sp. MR-4 60480 S 336 137 473 0.00002 +Neisseria meningitidis 487 S 143635 11544 155179 0.00591 +Herpetosiphon aurantiacus 65 S 427279 27 427306 0.01628 +Leptospira borgpetersenii 174 S 242592 345 242937 0.00926 +Leptospira interrogans 173 S 13 0 13 0.00000 +Photobacterium profundum 74109 S 12 1 13 0.00000 +Lysinibacillus sphaericus 1421 S 47 0 47 0.00000 +Clostridium perfringens 1502 S 17 0 17 0.00000 +Bacillus subtilis 1423 S 265462 2267 267729 0.01020 +Lawsonia intracellularis 29546 S 114759 23 114782 0.00437 +Lactobacillus casei 1582 S 11 0 11 0.00000 +Bacillus thuringiensis 1428 S 187882 159705 347587 0.01325 +Psychrobacter arcticus 334543 S 78 0 78 0.00000 +Oceanobacillus iheyensis 182710 S 15 0 15 0.00000 +Lactobacillus helveticus 1587 S 12 0 12 0.00000 +Lactobacillus delbrueckii 1584 S 153860 3163 157023 0.00598 +Histophilus somni 731 S 136275 317 136592 0.00521 +Wigglesworthia glossinidia 51229 S 66219 57 66276 0.00253 +Cronobacter sakazakii 28141 S 270 3 273 0.00001 +Yersinia enterocolitica 630 S 101 0 101 0.00000 +Bacillus halodurans 86665 S 269485 450 269935 0.01029 +Yersinia pestis 632 S 61383 252873 314256 0.01198 +Burkholderia vietnamiensis 60552 S 26 5 31 0.00000 +Photorhabdus luminescens 29488 S 51 0 51 0.00000 +Bacillus weihenstephanensis 86662 S 1934 51 1985 0.00008 +Idiomarina loihiensis 135577 S 187227 435 187662 0.00715 +Prochlorococcus marinus 1219 S 307019 266 307285 0.01171 +Ignicoccus hospitalis 160233 S 87443 14 87457 0.00333 +Burkholderia lata 482957 S 16 2 18 0.00000 +Lactobacillus salivarius 1624 S 139242 326 139568 0.00532 +Syntrophomonas wolfei 863 S 193716 30 193746 0.00738 +Burkholderia thailandensis 57975 S 1133 49 1182 0.00005 +Haemophilus influenzae 727 S 117883 629 118512 0.00452 +Cupriavidus necator 106590 S 29061 136 29197 0.00111 +Acinetobacter sp. ADP1 62977 S 11 0 11 0.00000 +Ruminiclostridium thermocellum 1515 S 260096 100 260196 0.00992 +Erwinia tasmaniensis 338565 S 322076 1182 323258 0.01232 +Clostridium tetani 1513 S 16 0 16 0.00000 +Psychrobacter cryohalolentis 330922 S 413504 4426 417930 0.01593 +Borrelia bavariensis 664662 S 78122 1938 80060 0.00305 +Shewanella loihica 359303 S 10 0 10 0.00000 +Pasteurella multocida 747 S 12 0 12 0.00000 +Treponema denticola 158 S 183744 23 183767 0.00700 +Yersinia pseudotuberculosis 633 S 709 1324 2033 0.00008 +Pseudomonas entomophila 312306 S 52 0 52 0.00000 +Halorhodospira halophila 1053 S 11 0 11 0.00000 +Lachnoclostridium phytofermentans 66219 S 10 0 10 0.00000 +Buchnera aphidicola 9 S 26192 14 26206 0.00100 +Escherichia coli 562 S 717629 732184 1449813 0.05525 +Coxiella burnetii 777 S 135506 22 135528 0.00516 +Geobacter sulfurreducens 35554 S 244079 217 244296 0.00931 +Anabaena variabilis 1172 S 433603 12868 446471 0.01701 +Synechococcus elongatus 32046 S 466278 215 466493 0.01778 +Serratia proteamaculans 28151 S 117 0 117 0.00000 +Burkholderia pseudomallei 28450 S 224374 228836 453210 0.01727 +Neisseria gonorrhoeae 485 S 135601 16923 152524 0.00581 +Thiobacillus denitrificans 36861 S 226889 122 227011 0.00865 +Burkholderia mallei 13373 S 193 3075 3268 0.00012 +Pectobacterium atrosepticum 29471 S 96 0 96 0.00000 +Listeria welshimeri 1643 S 176044 4791 180835 0.00689 +Mycobacterium gilvum 1804 S 236 8 244 0.00001 +Mycobacterium sp. JLS 164757 S 326114 373821 699935 0.02667 +Staphylococcus aureus 1280 S 1192940 19301 1212241 0.04620 +Staphylococcus haemolyticus 1283 S 33 0 33 0.00000 +Staphylococcus epidermidis 1282 S 53 2 55 0.00000 +Psychromonas ingrahamii 357794 S 287498 273 287771 0.01097 +Shewanella amazonensis 60478 S 18 0 18 0.00000 +Mycobacterium vanbaalenii 110539 S 244 4 248 0.00001 +Shewanella sediminis 271097 S 12 0 12 0.00000 +Acinetobacter baumannii 470 S 257301 727 258028 0.00983 +Mycobacterium leprae 1769 S 31 0 31 0.00000 +Mycobacterium bovis 1765 S 15035 264359 279394 0.01065 +Mycobacterium ulcerans 1809 S 525 376 901 0.00003 +Vibrio campbellii 680 S 11 3 14 0.00000 +Mycobacterium avium 1764 S 310855 356 311211 0.01186 +Shewanella sp. ANA-3 94122 S 405 42 447 0.00002 diff -r 000000000000 -r 6e90a30b214f test-data/sample2_output_species_abundance.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample2_output_species_abundance.txt Sun Jul 14 08:45:50 2024 +0000 @@ -0,0 +1,176 @@ +name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads +Streptococcus sanguinis 1305 S 21 0 21 0.00000 +Streptococcus suis 1307 S 22 1 23 0.00000 +Streptococcus gordonii 1302 S 10 0 10 0.00000 +Vibrio cholerae 666 S 10 4 14 0.00000 +Bacillus methylotrophicus 492670 S 23 0 23 0.00000 +Streptococcus thermophilus 1308 S 34 0 34 0.00000 +Streptococcus mutans 1309 S 10 0 10 0.00000 +Burkholderia xenovorans 36873 S 34 0 34 0.00000 +Sinorhizobium medicae 110321 S 54 0 54 0.00000 +Burkholderia phymatum 148447 S 655478 1228 656706 0.02503 +Borrelia burgdorferi 139 S 36 0 36 0.00000 +Nostoc punctiforme 272131 S 590086 562 590648 0.02251 +Shewanella frigidimarina 56812 S 23 0 23 0.00000 +Clostridium novyi 1542 S 211808 388 212196 0.00809 +Mycobacterium tuberculosis 1773 S 20647 274350 294997 0.01124 +Mycobacterium smegmatis 1772 S 239 0 239 0.00001 +Rhodopseudomonas palustris 1076 S 823190 1106 824296 0.03141 +Bacteroides thetaiotaomicron 818 S 392179 3490 395669 0.01508 +Mycobacterium abscessus 36809 S 78 0 78 0.00000 +Burkholderia multivorans 87883 S 30 5 35 0.00000 +Citrobacter koseri 545 S 576 17 593 0.00002 +Bordetella pertussis 520 S 632 732 1364 0.00005 +Chlamydia trachomatis 813 S 71933 284 72217 0.00275 +Pseudomonas aeruginosa 287 S 42 1 43 0.00000 +Chlamydia pneumoniae 83558 S 78615 83 78698 0.00300 +Haloquadratum walsbyi 293091 S 223986 31 224017 0.00854 +Streptococcus pyogenes 1314 S 252007 4976 256983 0.00979 +Streptococcus pneumoniae 1313 S 177347 1168 178515 0.00680 +Pelodictyon luteolum 1100 S 157283 1662 158945 0.00606 +Streptococcus agalactiae 1311 S 159789 4251 164040 0.00625 +Pseudomonas protegens 380021 S 18 0 18 0.00000 +Salmonella enterica 28901 S 387186 4916 392102 0.01494 +Francisella tularensis 263 S 120338 554 120892 0.00461 +Clostridium botulinum 1491 S 281791 594 282385 0.01076 +Alkaliphilus metalliredigens 208226 S 368065 432 368497 0.01404 +Shewanella denitrificans 192073 S 17 0 17 0.00000 +Shewanella sp. MR-7 60481 S 224465 86579 311044 0.01185 +Bacillus licheniformis 1402 S 13 0 13 0.00000 +Burkholderia ambifaria 152480 S 27 3 30 0.00000 +Alkalilimnicola ehrlichii 351052 S 226337 74 226411 0.00863 +Corynebacterium jeikeium 38289 S 20 0 20 0.00000 +Pediococcus pentosaceus 1255 S 13 0 13 0.00000 +Bacillus anthracis 1392 S 151306 277437 428743 0.01634 +Hyphomonas neptunium 81032 S 262956 33 262989 0.01002 +Borrelia afzelii 29518 S 37 0 37 0.00000 +Pseudomonas fluorescens 294 S 21 1 22 0.00000 +Corynebacterium urealyticum 43771 S 168078 3426 171504 0.00654 +Bacillus clausii 79880 S 281618 346 281964 0.01075 +Campylobacter concisus 199 S 157661 329 157990 0.00602 +Shewanella baltica 62322 S 108 1 109 0.00000 +Pseudomonas stutzeri 316 S 293151 1980 295131 0.01125 +Cytophaga hutchinsonii 985 S 307508 31 307539 0.01172 +Cyanothece sp. ATCC 51142 43989 S 372257 54 372311 0.01419 +Thermus thermophilus 274 S 152701 13 152714 0.00582 +Bacillus cytotoxicus 580165 S 643 5 648 0.00002 +Clostridium acetobutylicum 1488 S 13 0 13 0.00000 +Burkholderia cenocepacia 95486 S 29 50 79 0.00000 +Corynebacterium efficiens 152794 S 233423 670 234093 0.00892 +Chromobacterium violaceum 536 S 330985 434 331419 0.01263 +Ureaplasma parvum 134821 S 47612 5 47617 0.00181 +Bacillus pumilus 1408 S 20 0 20 0.00000 +Enterobacter sp. 638 399742 S 290 1 291 0.00001 +Bordetella avium 521 S 81 0 81 0.00000 +Bacillus cereus 1396 S 1086754 202070 1288824 0.04912 +Ochrobactrum anthropi 529 S 381841 1054 382895 0.01459 +Thermosipho melanesiensis 46541 S 128132 53 128185 0.00489 +Mycobacterium marinum 1781 S 281340 152004 433344 0.01651 +Nostoc sp. PCC 7120 103690 S 247 7 254 0.00001 +Pseudomonas mendocina 300 S 14 1 15 0.00000 +Lactococcus lactis 1358 S 404921 2772 407693 0.01554 +Pseudomonas putida 303 S 511201 4777 515978 0.01966 +Sinorhizobium meliloti 382 S 420783 3928 424711 0.01619 +Clostridium beijerinckii 1520 S 418932 1011 419943 0.01600 +Geobacillus thermodenitrificans 33940 S 11 11 22 0.00000 +Saccharopolyspora erythraea 1836 S 10 0 10 0.00000 +Shewanella oneidensis 70863 S 222 4 226 0.00001 +Bradyrhizobium sp. ORS 278 114615 S 14 5 19 0.00000 +Rickettsia typhi 785 S 43 0 43 0.00000 +Methanococcus maripaludis 39152 S 121232 302 121534 0.00463 +Rickettsia prowazekii 782 S 70541 1619 72160 0.00275 +Listeria innocua 1642 S 33 1 34 0.00000 +Bordetella petrii 94624 S 233 5 238 0.00001 +Bradyrhizobium diazoefficiens 1355477 S 17 0 17 0.00000 +Mycobacterium sp. KMS 189918 S 11 267 278 0.00001 +Bordetella parapertussis 519 S 348 1146 1494 0.00006 +Bordetella bronchiseptica 518 S 128479 327016 455495 0.01736 +Staphylococcus saprophyticus 29385 S 34 0 34 0.00000 +Listeria monocytogenes 1639 S 43 1 44 0.00000 +Cupriavidus taiwanensis 164546 S 12 0 12 0.00000 +Chlamydophila caviae 83557 S 74403 340 74743 0.00285 +Candidatus Blochmannia pennsylvanicus 101534 S 52480 50 52530 0.00200 +Shigella flexneri 623 S 1022 4135 5157 0.00020 +Shigella dysenteriae 622 S 1206 1447 2653 0.00010 +Shigella boydii 621 S 1035 3475 4510 0.00017 +Rhodococcus jostii 132919 S 622004 310 622314 0.02372 +Shigella sonnei 624 S 605 1923 2528 0.00010 +Klebsiella pneumoniae 573 S 333 5 338 0.00001 +Sodalis glossinidius 63612 S 292996 614 293610 0.01119 +Nitrosococcus oceani 1229 S 13 0 13 0.00000 +Shewanella sp. MR-4 60480 S 336 137 473 0.00002 +Neisseria meningitidis 487 S 143635 11544 155179 0.00591 +Herpetosiphon aurantiacus 65 S 427279 27 427306 0.01628 +Leptospira borgpetersenii 174 S 242592 345 242937 0.00926 +Leptospira interrogans 173 S 13 0 13 0.00000 +Photobacterium profundum 74109 S 12 1 13 0.00000 +Lysinibacillus sphaericus 1421 S 47 0 47 0.00000 +Clostridium perfringens 1502 S 17 0 17 0.00000 +Bacillus subtilis 1423 S 265462 2267 267729 0.01020 +Lawsonia intracellularis 29546 S 114759 23 114782 0.00437 +Lactobacillus casei 1582 S 11 0 11 0.00000 +Bacillus thuringiensis 1428 S 187882 159705 347587 0.01325 +Psychrobacter arcticus 334543 S 78 0 78 0.00000 +Oceanobacillus iheyensis 182710 S 15 0 15 0.00000 +Lactobacillus helveticus 1587 S 12 0 12 0.00000 +Lactobacillus delbrueckii 1584 S 153860 3163 157023 0.00598 +Histophilus somni 731 S 136275 317 136592 0.00521 +Wigglesworthia glossinidia 51229 S 66219 57 66276 0.00253 +Cronobacter sakazakii 28141 S 270 3 273 0.00001 +Yersinia enterocolitica 630 S 101 0 101 0.00000 +Bacillus halodurans 86665 S 269485 450 269935 0.01029 +Yersinia pestis 632 S 61383 252873 314256 0.01198 +Burkholderia vietnamiensis 60552 S 26 5 31 0.00000 +Photorhabdus luminescens 29488 S 51 0 51 0.00000 +Bacillus weihenstephanensis 86662 S 1934 51 1985 0.00008 +Idiomarina loihiensis 135577 S 187227 435 187662 0.00715 +Prochlorococcus marinus 1219 S 307019 266 307285 0.01171 +Ignicoccus hospitalis 160233 S 87443 14 87457 0.00333 +Burkholderia lata 482957 S 16 2 18 0.00000 +Lactobacillus salivarius 1624 S 139242 326 139568 0.00532 +Syntrophomonas wolfei 863 S 193716 30 193746 0.00738 +Burkholderia thailandensis 57975 S 1133 49 1182 0.00005 +Haemophilus influenzae 727 S 117883 629 118512 0.00452 +Cupriavidus necator 106590 S 29061 136 29197 0.00111 +Acinetobacter sp. ADP1 62977 S 11 0 11 0.00000 +Ruminiclostridium thermocellum 1515 S 260096 100 260196 0.00992 +Erwinia tasmaniensis 338565 S 322076 1182 323258 0.01232 +Clostridium tetani 1513 S 16 0 16 0.00000 +Psychrobacter cryohalolentis 330922 S 413504 4426 417930 0.01593 +Borrelia bavariensis 664662 S 78122 1938 80060 0.00305 +Shewanella loihica 359303 S 10 0 10 0.00000 +Pasteurella multocida 747 S 12 0 12 0.00000 +Treponema denticola 158 S 183744 23 183767 0.00700 +Yersinia pseudotuberculosis 633 S 709 1324 2033 0.00008 +Pseudomonas entomophila 312306 S 52 0 52 0.00000 +Halorhodospira halophila 1053 S 11 0 11 0.00000 +Lachnoclostridium phytofermentans 66219 S 10 0 10 0.00000 +Buchnera aphidicola 9 S 26192 14 26206 0.00100 +Escherichia coli 562 S 717629 732184 1449813 0.05525 +Coxiella burnetii 777 S 135506 22 135528 0.00516 +Geobacter sulfurreducens 35554 S 244079 217 244296 0.00931 +Anabaena variabilis 1172 S 433603 12868 446471 0.01701 +Synechococcus elongatus 32046 S 466278 215 466493 0.01778 +Serratia proteamaculans 28151 S 117 0 117 0.00000 +Burkholderia pseudomallei 28450 S 224374 228836 453210 0.01727 +Neisseria gonorrhoeae 485 S 135601 16923 152524 0.00581 +Thiobacillus denitrificans 36861 S 226889 122 227011 0.00865 +Burkholderia mallei 13373 S 193 3075 3268 0.00012 +Pectobacterium atrosepticum 29471 S 96 0 96 0.00000 +Listeria welshimeri 1643 S 176044 4791 180835 0.00689 +Mycobacterium gilvum 1804 S 236 8 244 0.00001 +Mycobacterium sp. JLS 164757 S 326114 373821 699935 0.02667 +Staphylococcus aureus 1280 S 1192940 19301 1212241 0.04620 +Staphylococcus haemolyticus 1283 S 33 0 33 0.00000 +Staphylococcus epidermidis 1282 S 53 2 55 0.00000 +Psychromonas ingrahamii 357794 S 287498 273 287771 0.01097 +Shewanella amazonensis 60478 S 18 0 18 0.00000 +Mycobacterium vanbaalenii 110539 S 244 4 248 0.00001 +Shewanella sediminis 271097 S 12 0 12 0.00000 +Acinetobacter baumannii 470 S 257301 727 258028 0.00983 +Mycobacterium leprae 1769 S 31 0 31 0.00000 +Mycobacterium bovis 1765 S 15035 264359 279394 0.01065 +Mycobacterium ulcerans 1809 S 525 376 901 0.00003 +Vibrio campbellii 680 S 11 3 14 0.00000 +Mycobacterium avium 1764 S 310855 356 311211 0.01186 +Shewanella sp. ANA-3 94122 S 405 42 447 0.00002