Using genome dataset created in the "dataset" notebook
Simulates isotope dilution or short incubations
In [8]:
workDir = '/home/nick/notebook/SIPSim/dev/bac_genome1210/'
buildDir = os.path.join(workDir, 'percIncorpUnifRep')
genomeDir = '/home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/'
R_dir = '/home/nick/notebook/SIPSim/lib/R/'
In [9]:
import glob
from os.path import abspath
import nestly
from IPython.display import Image, display
In [10]:
%load_ext rpy2.ipython
The rpy2.ipython extension is already loaded. To reload it, use:
%reload_ext rpy2.ipython
In [11]:
%%R
library(ggplot2)
library(dplyr)
library(tidyr)
library(gridExtra)
In [12]:
if not os.path.isdir(buildDir):
os.makedirs(buildDir)
In [13]:
!cd $buildDir; \
SIPSim fragments \
$genomeDir/genome_index.txt \
--fp $genomeDir \
--fr ../../515F-806R.fna \
--fld skewed-normal,9000,2500,-5 \
--flr None,None \
--nf 10000 \
--np 24 \
2> ampFrags.log \
> ampFrags.pkl
In [14]:
!cd $buildDir; \
SIPSim fragment_kde \
ampFrags.pkl \
> ampFrags_kde.pkl
In [15]:
!cd $buildDir; \
SIPSim diffusion \
ampFrags_kde.pkl \
--np 24 \
> ampFrags_kde_dif.pkl
Processing: Vibrio_vulnificus_MO6-24_O
Processing: Dyella_japonica_A8
Processing: Citrobacter_koseri_ATCC_BAA-895
Processing: Leisingera_methylohalidivorans_DSM_14336
Processing: Arthrobacter_arilaitensis_Re117
Processing: Veillonella_parvula_DSM_2008
Processing: Rhodococcus_jostii_RHA1
Processing: Croceibacter_atlanticus_HTCC2559
Processing: Corynebacterium_diphtheriae_C7_beta
Processing: Borrelia_burgdorferi_ZS7
Processing: Desulfovibrio_salexigens_DSM_2638
Processing: Glaciecola_psychrophila_170
Processing: Mycoplasma_haemocanis_str_Illinois
Processing: Hyphomicrobium_nitrativorans_NL23
Processing: Pedobacter_heparinus_DSM_2366
Processing: Candidatus_Rickettsia_amblyommii_str_GAT-30V
Processing: Beutenbergia_cavernae_DSM_12333
Processing: Chlorobaculum_parvum_NCIB_8327
Processing: Spiroplasma_diminutum_CUAS-1
Processing: Bifidobacterium_adolescentis_ATCC_15703
Processing: Morganella_morganii_subsp_morganii_KT
Processing: Desulfurobacterium_thermolithotrophum_DSM_11699
Processing: Pseudomonas_aeruginosa_RP73
Processing: Treponema_primitia_ZAS-2
Processing: Echinicola_vietnamensis_DSM_17526
Processing: Alteromonas_macleodii_str_Balearic_Sea_AD45
Processing: Vibrio_tubiashii_ATCC_19109
Processing: Leadbetterella_byssophila_DSM_17132
Processing: Chromobacterium_violaceum_ATCC_12472
Processing: Methylovorus_glucosetrophus_SIP3-4
Processing: Klebsiella_pneumoniae_30660_NJST258_1
Processing: Meiothermus_ruber_DSM_1279
Processing: Haemophilus_somnus_129PT
Processing: Corynebacterium_efficiens_YS-314
Processing: Alkalilimnicola_ehrlichii_MLHE-1
Processing: Runella_slithyformis_DSM_19594
Processing: Caldisericum_exile_AZM16c01
Processing: Spiroplasma_taiwanense_CT-1
Processing: Candidatus_Koribacter_versatilis_Ellin345
Processing: Thalassospira_xiamenensis_M-5_DSM_17429
Processing: Prevotella_sp_oral_taxon_299_str_F0039
Processing: Burkholderia_multivorans_ATCC_17616
Processing: Corynebacterium_urealyticum_DSM_7109
Processing: Pseudomonas_denitrificans_ATCC_13867
Processing: Acidiphilium_multivorum_AIU301
Processing: Helicobacter_cetorum_MIT_00-7128
Processing: Capnocytophaga_ochracea_DSM_7271
Processing: Thermodesulfatator_indicus_DSM_15286
Processing: Polymorphum_gilvum_SL003B-26A1
Processing: Lactococcus_garvieae_ATCC_49156
Processing: Flavobacterium_johnsoniae_UW101
Processing: Magnetospirillum_gryphiswaldense_MSR-1_v2
Processing: Vibrio_parahaemolyticus_RIMD_2210633
Processing: Hyphomicrobium_denitrificans_1NES1
Processing: Treponema_paraluiscuniculi_Cuniculi_A
Processing: Enterococcus_faecalis_D32
Processing: Campylobacter_lari_RM2100
Processing: Microlunatus_phosphovorus_NM-1
Processing: Enterobacter_aerogenes_KCTC_2190
Processing: Nitrosococcus_watsonii_C-113
Processing: Chloroflexus_aurantiacus_J-10-fl
Processing: Candidatus_Kinetoplastibacterium_galatii_TCC219
Processing: Prevotella_intermedia_17
Processing: Aequorivita_sublithincola_DSM_14238
Processing: Treponema_brennaborense_DSM_12168
Processing: Rickettsia_sibirica_246
Processing: Janthinobacterium_agaricidamnosum_NBRC_102515_DSM_9628
Processing: Isosphaera_pallida_ATCC_43644
Processing: Gallionella_capsiferriformans_ES-2
Processing: Erysipelothrix_rhusiopathiae_SY1027
Processing: Thermoanaerobacter_wiegelii_Rt8_B1
Processing: Castellaniella_defragrans_65Phen
Processing: Liberibacter_crescens_BT-1
Processing: Rickettsia_helvetica_C9P9
Processing: Enterococcus_casseliflavus_EC20
Processing: Rhodobacter_capsulatus_SB_1003
Processing: Capnocytophaga_canimorsus_Cc5
Processing: Sphingomonas_wittichii_RW1
Processing: Erwinia_pyrifoliae_Ep1_96
Processing: Tropheryma_whipplei_str_Twist
Processing: Blattabacterium_sp_Blatta_orientalis_str_Tarazona
Processing: Shewanella_sediminis_HAW-EB3
Processing: Phaeobacter_gallaeciensis_2_10
Processing: Burkholderia_cepacia_GG4
Processing: Syntrophothermus_lipocalidus_DSM_12680
Processing: Leuconostoc_kimchii_IMSNU_11154
Processing: Mycoplasma_crocodyli_MP145
Processing: Spirochaeta_thermophila_DSM_6578
Processing: Bibersteinia_trehalosi_USDA-ARS-USMARC-189
Processing: Treponema_azotonutricium_ZAS-9
Processing: Corynebacterium_argentoratense_DSM_44202
Processing: Enterobacter_cloacae_subsp_cloacae_ATCC_13047
Processing: Helicobacter_cinaedi_PAGU611
Processing: Geobacter_uraniireducens_Rf4
Processing: Lactobacillus_amylovorus_GRL1118
Processing: Pantoea_ananatis_PA13
Processing: Thermobaculum_terrenum_ATCC_BAA-798
Processing: Dehalogenimonas_lykanthroporepellens_BL-DC-9
Processing: Serratia_symbiotica_str_Cinara_cedri
Processing: Rhodospirillum_photometricum_DSM_122
Processing: Mycoplasma_arthritidis_158L3-1
Processing: Brucella_ceti_TE28753-12
Processing: Anabaena_cylindrica_PCC_7122
Processing: Pseudomonas_syringae_pv_tomato_str_DC3000
Processing: Micavibrio_aeruginosavorus_EPB
Processing: Rickettsia_philipii_str_364D
Processing: Methylotenera_versatilis_301
Processing: Mesoplasma_florum_L1
Processing: Orientia_tsutsugamushi_str_Boryong
Processing: Dactylococcopsis_salina_PCC_8305
Processing: Desulfomonile_tiedjei_DSM_6799
Processing: Staphylococcus_warneri_SG1
Processing: Rickettsia_africae_ESF-5
Processing: Candidatus_Mycoplasma_haemolamae_str_Purdue
Processing: Alcanivorax_pacificus_W11-5
Processing: Desulfitobacterium_metallireducens_DSM_15288
Processing: Mycoplasma_yeatsii_GM274B
Processing: Clostridium_perfringens_str_13
Processing: Mycobacterium_vanbaalenii_PYR-1
Processing: Raoultella_ornithinolytica_B6
Processing: Acinetobacter_oleivorans_DR1
Processing: Streptomyces_pratensis_ATCC_33331
Processing: Geobacillus_thermoglucosidasius_C56-YS93
Processing: Corynebacterium_glycinophilum_AJ_3170
Processing: Escherichia_albertii_KF1
Processing: Rothia_mucilaginosa_DY-18
Processing: Pseudomonas_poae_RE*1-1-14
Processing: Chromohalobacter_salexigens_DSM_3043
Processing: Chloroherpeton_thalassium_ATCC_35110
Processing: Amycolatopsis_methanolica_239
Processing: Hirschia_baltica_ATCC_49814
Processing: Brachyspira_hyodysenteriae_WA1
Processing: Bifidobacterium_indicum_LMG_11587_DSM_20214
Processing: Haemophilus_parainfluenzae_T3T1
Processing: Listeria_seeligeri_serovar_1_2b_str_SLCC3954
Processing: Mycoplasma_genitalium_M6320
Processing: Rhizobium_etli_bv_phaseoli_str_IE4803
Processing: Lactobacillus_sanfranciscensis_TMW_1_1304
Processing: Mycoplasma_bovis_HB0801
Processing: Chlorobium_luteolum_DSM_273
Processing: Sebaldella_termitidis_ATCC_33386
Processing: Rickettsia_canadensis_str_McKiel
Processing: Serratia_liquefaciens_ATCC_27592
Processing: Beijerinckia_indica_subsp_indica_ATCC_9039
Processing: Agrobacterium_vitis_S4
Processing: Actinobacillus_equuli_subsp_equuli
Processing: Thermotoga_caldifontis_AZM44c09
Processing: Bacillus_anthracis_str_H9401
Processing: Nakamurella_multipartita_DSM_44233
Processing: Treponema_pedis_str_T_A4
Processing: Acidaminococcus_intestini_RyC-MR95
Processing: Caldanaerobacter_subterraneus_subsp_tengcongensis_MB4
Processing: Cyanobacterium_aponinum_PCC_10605
Processing: Ehrlichia_ruminantium_str_Welgevonden
Processing: _Clostridium_stercorarium_subsp_stercorarium_DSM_8532
Processing: Mycobacterium_neoaurum_VKM_Ac-1815D
Processing: Paenibacillus_mucilaginosus_KNP414
Processing: Spiroplasma_mirum_ATCC_29335
Processing: Streptococcus_thermophilus_LMG_18311
Processing: Aggregatibacter_aphrophilus_NJ8700
Processing: Burkholderia_phymatum_STM815
Processing: Paenibacillus_larvae_subsp_larvae_DSM_25430
Processing: Rickettsia_massiliae_MTU5
Processing: Bifidobacterium_kashiwanohense_PV20-2
Processing: Gloeobacter_kilaueensis_JS1
Processing: Bacillus_cytotoxicus_NVH_391-98
Processing: Candidatus_Moranella_endobia_PCVAL
Processing: Streptosporangium_roseum_DSM_43021
Processing: Pelagibacterium_halotolerans_B2
Processing: Delftia_acidovorans_SPH-1
Processing: Chlamydia_muridarum_str_Nigg3_CMUT3-5
Processing: Cycloclasticus_zancles_7-ME
Processing: Rickettsia_conorii_str_Malish_7
Processing: Thermobacillus_composti_KWC4
Processing: Mesorhizobium_ciceri_biovar_biserrulae_WSM1271
Processing: Cellulophaga_baltica_NN016038
Processing: Bacillus_infantis_NRRL_B-14911
Processing: Desulfosporosinus_meridiei_DSM_13257
Processing: Marinomonas_mediterranea_MMB-1
Processing: Mycoplasma_hyorhinis_SK76
Processing: Pleurocapsa_sp_PCC_7327
Processing: Bacillus_coagulans_DSM_1_ATCC_7050
Processing: Bifidobacterium_thermophilum_RBL67
Processing: Bartonella_vinsonii_subsp_berkhoffii_str_Winnie
Processing: Caulobacter_crescentus_NA1000
Processing: Saccharothrix_espanaensis_DSM_44229
Processing: Aster_yellows_witches-broom_phytoplasma_AYWB
Processing: Escherichia_fergusonii_ATCC_35469
Processing: Xanthobacter_autotrophicus_Py2
Processing: Leuconostoc_carnosum_JB16
Processing: Pasteurella_multocida_subsp_multocida_str_HN06
Processing: Rickettsia_australis_str_Cutlack
Processing: cyanobacterium_endosymbiont_of_Epithemia_turgida_isolate_EtSB_Lake_Yunoko
Processing: Eggerthella_lenta_DSM_2243
Processing: Spiroplasma_apis_B31
Processing: Tetragenococcus_halophilus_NBRC_12172
Processing: Prosthecochloris_aestuarii_DSM_271
Processing: Candidatus_Blochmannia_chromaiodes_str_640
Processing: Sulfurimonas_gotlandica_GD1
Processing: Nocardiopsis_alba_ATCC_BAA-2165
Processing: Persephonella_marina_EX-H1
Processing: Gardnerella_vaginalis_ATCC_14019
Processing: Candidatus_Liberibacter_americanus_str_Sao_Paulo
Processing: Enterobacter_asburiae_LF7a
Processing: Rhizobium_tropici_CIAT_899
Processing: Leptospira_borgpetersenii_serovar_Hardjo-bovis_str_L550
Processing: Bacillus_cereus_G9241
Processing: Desulfotomaculum_ruminis_DSM_2154
Processing: Terriglobus_roseus_DSM_18391
Processing: Alcanivorax_dieselolei_B5
Processing: Candidatus_Riesia_pediculicola_USDA
Processing: Kribbella_flavida_DSM_17836
Processing: Alkaliphilus_oremlandii_OhILAs
Processing: Aerococcus_urinae_ACS-120-V-Col10a
Processing: Mycoplasma_agalactiae_PG2
Processing: Octadecabacter_arcticus_238
Processing: Weeksella_virosa_DSM_16922
Processing: Bacillus_pumilus_SAFR-032
Processing: Roseobacter_litoralis_Och_149
Processing: Blastococcus_saxobsidens_DD2
Processing: Roseobacter_denitrificans_OCh_114
Processing: Sphaerobacter_thermophilus_DSM_20745
Processing: Thermosipho_africanus_TCF52B
Processing: Pseudomonas_resinovorans_NBRC_106553
Processing: Candidatus_Symbiobacter_mobilis_CR
Processing: Lawsonia_intracellularis_N343
Processing: Rubrobacter_xylanophilus_DSM_9941
Processing: Halothiobacillus_neapolitanus_c2
Processing: Rhodopseudomonas_palustris_BisB5
Processing: Acidiphilium_cryptum_JF-5
Processing: Pseudomonas_knackmussii_B13
Processing: Desulfovibrio_vulgaris_str_Miyazaki_F
Processing: Spiribacter_salinus_M19-40
Processing: Zymomonas_mobilis_subsp_mobilis_NRRL_B-12526
Processing: Clavibacter_michiganensis_subsp_sepedonicus
Processing: Sulfurihydrogenibium_azorense_Az-Fu1
Processing: Neorickettsia_risticii_str_Illinois
Processing: Denitrovibrio_acetiphilus_DSM_12809
Processing: Gloeobacter_violaceus_PCC_7421
Processing: Desulfobacula_toluolica_Tol2
Processing: Candidatus_Hodgkinia_cicadicola_Dsem
Processing: Sulfurospirillum_deleyianum_DSM_6946
Processing: Mycoplasma_wenyonii_str_Massachusetts
Processing: Caldicellulosiruptor_lactoaceticus_6A
Processing: Deinococcus_radiodurans_R1
Processing: Polynucleobacter_necessarius_subsp_necessarius_STIR1
Processing: Marinomonas_posidonica_IVIA-Po-181
Processing: Xenorhabdus_bovienii_SS-2004
Processing: Leuconostoc_mesenteroides_subsp_mesenteroides_J18
Processing: Pelodictyon_phaeoclathratiforme_BU-1
Processing: Catenulispora_acidiphila_DSM_44928
Processing: Flexibacter_litoralis_DSM_6794
Processing: Ehrlichia_muris_AS145
Processing: Thermincola_potens_JR
Processing: Mycoplasma_putrefaciens_KS1
Processing: Bradyrhizobium_japonicum_USDA_6
Processing: Corallococcus_coralloides_DSM_2259
Processing: Bartonella_tribocorum_CIP_105476
Processing: Acinetobacter_calcoaceticus_PHEA-2
Processing: Thermomonospora_curvata_DSM_43183
Processing: Haliscomenobacter_hydrossis_DSM_1100
Processing: Streptococcus_lutetiensis_033
Processing: Mannheimia_succiniciproducens_MBEL55E
Processing: Candidatus_Zinderia_insecticola_CARI
Processing: Staphylococcus_aureus_subsp_aureus_T0131
Processing: Pelotomaculum_thermopropionicum_SI
Processing: Aminobacterium_colombiense_DSM_12261
Processing: Bacteroides_vulgatus_ATCC_8482
Processing: Chitinophaga_pinensis_DSM_2588
Processing: Enterococcus_mundtii_QU_25
Processing: Calothrix_sp_PCC_6303
Processing: Planctomyces_brasiliensis_DSM_5305
Processing: Marinithermus_hydrothermalis_DSM_14884
Processing: Corynebacterium_glutamicum_ATCC_13032
Processing: Sinorhizobium_medicae_WSM419
Processing: Clostridium_acetobutylicum_DSM_1731
Processing: Acetobacterium_woodii_DSM_1030
Processing: Cellulomonas_fimi_ATCC_484
Processing: Acidaminococcus_fermentans_DSM_20731
Processing: Dickeya_zeae_EC1
Processing: Thermoanaerobacterium_xylanolyticum_LX-11
Processing: Chlorobium_phaeobacteroides_DSM_266
Processing: Desulfocapsa_sulfexigens_DSM_10523
Processing: Burkholderia_rhizoxinica_HKI_454
Processing: Aeromonas_salmonicida_subsp_salmonicida_A449
Processing: Acetohalobium_arabaticum_DSM_5501
Processing: Cyanobium_gracile_PCC_6307
Processing: Cronobacter_turicensis_z3032
Processing: Symbiobacterium_thermophilum_IAM_14863
Processing: Robiginitalea_biformata_HTCC2501
Processing: Pseudomonas_fulva_12-X
Processing: Turneriella_parva_DSM_21527
Processing: Rhizobium_leguminosarum_bv_trifolii_WSM2304
Processing: Staphylococcus_pasteuri_SP1
Processing: Legionella_longbeachae_NSW150
Processing: Desulfococcus_oleovorans_Hxd3
Processing: Pseudomonas_entomophila_L48
Processing: Lactobacillus_casei_subsp_casei_ATCC_393
Processing: Desulfovibrio_magneticus_RS-1
Processing: Candidatus_Kinetoplastibacterium_oncopeltii_TCC290E
Processing: Corynebacterium_maris_DSM_45190
Processing: Streptococcus_equi_subsp_zooepidemicus
Processing: Sphaerochaeta_coccoides_DSM_17374
Processing: Mycoplasma_leachii_PG50
Processing: Deinococcus_peraridilitoris_DSM_19664
Processing: Vibrio_alginolyticus_NBRC_15630_ATCC_17749
Processing: Gramella_forsetii_KT0803
Processing: Burkholderia_xenovorans_LB400
Processing: Elusimicrobium_minutum_Pei191
Processing: Actinobacillus_pleuropneumoniae_serovar_5b_str_L20
Processing: Candidatus_Arthromitus_sp_SFB-mouse-Yit
Processing: Chlamydophila_pneumoniae_CWL029
Processing: Exiguobacterium_sibiricum_255-15
Processing: Streptococcus_sanguinis_SK36
Processing: Mesorhizobium_loti_MAFF303099
Processing: Ferrimonas_balearica_DSM_9799
Processing: Mycoplasma_bovoculi_M165_69
Processing: Arthrobacter_chlorophenolicus_A6
Processing: Granulibacter_bethesdensis_CGDNIH4
Processing: Crinalium_epipsammum_PCC_9333
Processing: Acinetobacter_baumannii_BJAB07104
Processing: Streptomyces_lividans_TK24
Processing: Nautilia_profundicola_AmH
Processing: Corynebacterium_halotolerans_YIM_70093_DSM_44683
Processing: _Clostridium_clariflavum_DSM_19732
Processing: Rickettsia_typhi_str_TH1527
Processing: Kytococcus_sedentarius_DSM_20547
Processing: Borrelia_afzelii_Tom3107
Processing: Oscillibacter_valericigenes_Sjm18-20
Processing: Shewanella_loihica_PV-4
Processing: Candidatus_Azobacteroides_pseudotrichonymphae_genomovar_CFP2
Processing: Thioalkalimicrobium_cyclicum_ALM1
Processing: Brucella_ovis_ATCC_25840
Processing: Methylobacterium_extorquens_AM1
Processing: Candidatus_Endolissoclinum_faulkneri_L2
Processing: Streptococcus_uberis_0140J
Processing: Brucella_melitensis_ATCC_23457
Processing: Dehalococcoides_mccartyi_CG5
Processing: Deinococcus_proteolyticus_MRP
Processing: Fimbriimonas_ginsengisoli_Gsoil_348
Processing: Brachyspira_murdochii_DSM_12563
Processing: Thermus_thermophilus_HB8
Processing: Anaerococcus_prevotii_DSM_20548
Processing: Waddlia_chondrophila_WSU_86-1044
Processing: Maricaulis_maris_MCS10
Processing: _Cellvibrio_gilvus_ATCC_13127
Processing: Streptococcus_infantarius_subsp_infantarius_CJ18
Processing: Myxococcus_fulvus_HW-1
Processing: Terriglobus_saanensis_SP1PR4
Processing: Rickettsia_rhipicephali_str_3-7-female6-CWPP
Processing: Desulfobulbus_propionicus_DSM_2032
Processing: Chlamydophila_felis_Fe_C-56
Processing: Mycobacterium_gilvum_PYR-GCK
Processing: Shewanella_putrefaciens_200
Processing: Paracoccus_aminophilus_JCM_7686
Processing: Variovorax_paradoxus_EPS
Processing: Helicobacter_pylori_F16
Processing: Thioalkalivibrio_nitratireducens_DSM_14787
Processing: Leuconostoc_gelidum_JB7
Processing: Ammonifex_degensii_KC4
Processing: Klebsiella_variicola_At-22
Processing: Bacillus_pseudofirmus_OF4
Processing: Aromatoleum_aromaticum_EbN1
Processing: Synechococcus_elongatus_PCC_7942
Processing: _Clostridium_acidurici_9a
Processing: Nocardia_cyriacigeorgica_GUH-2
Processing: Frankia_alni_ACN14a
Processing: Streptomyces_cattleya_NRRL_8057_DSM_46488
Processing: Ochrobactrum_anthropi_ATCC_49188
Processing: Psychromonas_ingrahamii_37
Processing: Serratia_proteamaculans_568
Processing: Mycobacterium_yongonense_05-1390
Processing: Rhodobacter_sphaeroides_2_4_1
Processing: Pediococcus_claussenii_ATCC_BAA-344
Processing: Xanthomonas_axonopodis_pv_citrumelo_F1
Processing: Enterococcus_hirae_ATCC_9790
Processing: Candidatus_Portiera_aleyrodidarum_MED_Bemisia_tabaci
Processing: Gordonia_bronchialis_DSM_43247
Processing: Bacillus_megaterium_NBRC_15308_ATCC_14581
Processing: Yersinia_aldovae_670-83
Processing: Synechocystis_sp_PCC_6803_substr_PCC-P
Processing: Thioflavicoccus_mobilis_8321
Processing: Borrelia_garinii_SZ
Processing: Shewanella_halifaxensis_HAW-EB4
Processing: Aliivibrio_salmonicida_LFI1238
Processing: Wolbachia_endosymbiont_of_Drosophila_simulans_wHa
Processing: Campylobacter_insulaenigrae_NCTC_12927
Processing: Dehalobacter_restrictus_DSM_9455
Processing: Haemophilus_parasuis_ZJ0906
Processing: Blattabacterium_sp_Panesthia_angustipennis_spadica_str_BPAA
Processing: Tannerella_forsythia_ATCC_43037
Processing: Bartonella_henselae_str_Houston-1
Processing: Rickettsia_peacockii_str_Rustic
Processing: Desulfotalea_psychrophila_LSv54
Processing: Lactobacillus_acidophilus_NCFM
Processing: Desulfotomaculum_carboxydivorans_CO-1-SRB
Processing: Mycobacterium_marinum_M
Processing: Leptospira_interrogans_serovar_Copenhageni_str_Fiocruz_L1-130
Processing: Cellulomonas_flavigena_DSM_20109
Processing: Solibacillus_silvestris_StLB046
Processing: Edwardsiella_ictaluri_93-146
Processing: Nitrosomonas_europaea_ATCC_19718
Processing: Glaciecola_nitratireducens_FR1064
Processing: Corynebacterium_variabile_DSM_44702
Processing: Mycobacterium_rhodesiae_NBB3
Processing: Basilea_psittacipulmonis_DSM_24701
Processing: Borrelia_duttonii_Ly
Processing: Alkaliphilus_metalliredigens_QYMF
Processing: Roseibacterium_elongatum_DSM_19469
Processing: Prochlorococcus_marinus_str_MIT_9313
Processing: Streptomyces_scabiei_87_22
Processing: Alicyclobacillus_acidocaldarius_subsp_acidocaldarius_DSM_446
Processing: Amycolatopsis_mediterranei_S699
Processing: Burkholderia_ambifaria_AMMD
Processing: Nocardia_nova_SH22a
Processing: Kutzneria_albida_DSM_43870
Processing: Saccharophagus_degradans_2-40
Processing: Pandoraea_pnomenusa_3kgm
Processing: Candidatus_Desulforudis_audaxviator_MP104C
Processing: Arcobacter_butzleri_7h1h
Processing: Methylobacterium_radiotolerans_JCM_2831
Processing: Gallibacterium_anatis_UMN179
Processing: Pseudomonas_mendocina_NK-01
Processing: Mycobacterium_ulcerans_Agy99
Processing: Streptomyces_fulvissimus_DSM_40593
Processing: Listeria_ivanovii_subsp_ivanovii
Processing: Cardinium_endosymbiont_cEper1_of_Encarsia_pergandiella
Processing: Bacillus_methanolicus_MGA3
Processing: Flavobacterium_psychrophilum_JIP02_86
Processing: Neisseria_gonorrhoeae_FA_1090
Processing: Butyrivibrio_proteoclasticus_B316
Processing: Ruegeria_pomeroyi_DSS-3
Processing: Yersinia_enterocolitica_subsp_palearctica_105_5R_r
Processing: Thioalkalivibrio_sulfidiphilus_HL-EbGr7
Processing: Thermoanaerobacter_mathranii_subsp_mathranii_str_A3
Processing: Methylocella_silvestris_BL2
Processing: Mycoplasma_haemofelis_str_Langford_1
Processing: _Bacillus_selenitireducens_MLS10
Processing: Cupriavidus_metallidurans_CH34
Processing: Sulfobacillus_acidophilus_DSM_10332
Processing: Nitrosomonas_eutropha_C91
Processing: Kineococcus_radiotolerans_SRS30216_ATCC_BAA-149
Processing: Desulfosporosinus_orientis_DSM_765
Processing: Sulfuritalea_hydrogenivorans_sk43H
Processing: Truepera_radiovictrix_DSM_17093
Processing: Streptomyces_collinus_Tu_365
Processing: Chlorobium_phaeovibrioides_DSM_265
Processing: Hahella_chejuensis_KCTC_2396
Processing: Burkholderia_glumae_BGR1
Processing: Enterobacter_lignolyticus_SCF1
Processing: Xanthomonas_campestris_pv_vesicatoria_str_85-10
Processing: Bacillus_subtilis_PY79
Processing: Clostridium_botulinum_202F
Processing: Xanthomonas_axonopodis_pv_citri_str_306
Processing: Streptococcus_gallolyticus_UCN34
Processing: Rickettsia_slovaca_str_D-CWPP
Processing: Mycobacterium_liflandii_128FXT
Processing: Kosakonia_sacchari_SP1
Processing: Bacillus_weihenstephanensis_KBAB4
Processing: Muricauda_ruestringensis_DSM_13258
Processing: Verrucomicrobium_spinosum_DSM_4136_JCM_18804
Processing: Desulfovibrio_desulfuricans_subsp_desulfuricans_str_ATCC_27774
Processing: Dickeya_dadantii_3937
Processing: Microbacterium_testaceum_StLB037
Processing: Mesorhizobium_opportunistum_WSM2075
Processing: Geobacter_lovleyi_SZ
Processing: Sulfurospirillum_multivorans_DSM_12446
Processing: Thermus_scotoductus_SA-01
Processing: Prevotella_ruminicola_23
Processing: Salinispora_arenicola_CNS-205
Processing: Propionibacterium_avidum_44067
Processing: Thermosediminibacter_oceani_DSM_16646
Processing: Lactobacillus_delbrueckii_subsp_bulgaricus_2038
Processing: Flexistipes_sinusarabici_DSM_4947
Processing: Mycobacterium_chubuense_NBB4
Processing: Mycoplasma_ovis_str_Michigan
Processing: Bradyrhizobium_diazoefficiens_USDA_110
Processing: Acidovorax_citrulli_AAC00-1
Processing: Arcanobacterium_haemolyticum_DSM_20595
Processing: Bifidobacterium_longum_DJO10A
Processing: Fluviicola_taffensis_DSM_16823
Processing: Rhizobium_gallicum_bv_gallicum_R602
Processing: Pseudoxanthomonas_spadix_BD-a59
Processing: Lactobacillus_sakei_subsp_sakei_23K
Processing: Proteus_mirabilis_BB2000
Processing: Gemmatimonas_aurantiaca_T-27
Processing: Shewanella_baltica_OS117
Processing: Lactobacillus_buchneri_NRRL_B-30929
Processing: Paludibacter_propionicigenes_WB4
Processing: Sodalis_glossinidius_str_morsitans
Processing: Thermoanaerobacter_pseudethanolicus_ATCC_33223
Processing: Chroococcidiopsis_thermalis_PCC_7203
Processing: Pseudomonas_protegens_Pf-5
Processing: Parabacteroides_distasonis_ATCC_8503
Processing: Staphylococcus_saprophyticus_subsp_saprophyticus_ATCC_15305
Processing: Bacillus_clausii_KSM-K16
Processing: Streptomyces_griseus_subsp_griseus_NBRC_13350
Processing: Serratia_fonticola_RB-25
Processing: Vibrio_furnissii_NCTC_11218
Processing: Candidatus_Ishikawaella_capsulata_Mpkobe
Processing: Xanthomonas_oryzae_pv_oryzae_PXO99A
Processing: Geobacter_sulfurreducens_KN400
Processing: Listonella_anguillarum_M3
Processing: Herbaspirillum_seropedicae_SmR1
Processing: Solitalea_canadensis_DSM_3403
Processing: Hafnia_alvei_FB1
Processing: Candidatus_Pelagibacter_ubique_HTCC1062
Processing: Erythrobacter_litoralis_HTCC2594
Processing: Staphylococcus_haemolyticus_JCSC1435
Processing: Deinococcus_maricopensis_DSM_21211
Processing: Thermobifida_fusca_YX
Processing: Salinispora_tropica_CNB-440
Processing: Allochromatium_vinosum_DSM_180
Processing: Chlamydia_psittaci_MN
Processing: Melissococcus_plutonius_DAT561
Processing: Agrobacterium_fabrum_str_C58
Processing: Rahnella_aquatilis_HX2
Processing: Deferribacter_desulfuricans_SSM1
Processing: Campylobacter_coli_RM1875
Processing: Pectobacterium_carotovorum_subsp_odoriferum
Processing: Psychrobacter_arcticus_273-4
Processing: Burkholderia_pseudomallei_BPC006
Processing: Bacillus_halodurans_C-125
Processing: Shigella_boydii_Sb227
Processing: Bacteroides_helcogenes_P_36-108
Processing: Rickettsia_japonica_YH
Processing: Thermodesulfovibrio_yellowstonii_DSM_11347
Processing: Sorangium_cellulosum_So_ce56
Processing: Amycolatopsis_orientalis_HCCB10007
Processing: Bartonella_australis_Aust_NH1
Processing: Rickettsia_parkeri_str_Portsmouth
Processing: Geobacter_daltonii_FRC-32
Processing: Thermotoga_maritima_MSB8
Processing: Ralstonia_eutropha_H16
Processing: Peptoclostridium_difficile_BI1
Processing: Sanguibacter_keddieii_DSM_10542
Processing: Cellulophaga_lytica_DSM_7489
Processing: Candidatus_Kinetoplastibacterium_desouzaii_TCC079E
Processing: Petrotoga_mobilis_SJ95
Processing: Thermosipho_melanesiensis_BI429
Processing: Anaerobaculum_mobile_DSM_13181
Processing: Acaryochloris_marina_MBIC11017
Processing: Cellulophaga_algicola_DSM_14237
Processing: Intrasporangium_calvum_DSM_43043
Processing: Phycisphaera_mikurensis_NBRC_102666
Processing: Baumannia_cicadellinicola_str_Hc_Homalodisca_coagulata
Processing: Sinorhizobium_meliloti_AK83
Processing: Marinobacter_hydrocarbonoclasticus_ATCC_49840
Processing: Alcanivorax_borkumensis_SK2
Processing: Oceanithermus_profundus_DSM_14977
Processing: Mycobacterium_indicus_pranii_MTCC_9506
Processing: Bradyrhizobium_oligotrophicum_S58
Processing: Bordetella_avium_197N
Processing: Mycoplasma_flocculare_ATCC_27399
Processing: Actinobacillus_succinogenes_130Z
Processing: Onion_yellows_phytoplasma_OY-M
Processing: Pseudomonas_balearica_DSM_6083
Processing: Erwinia_billingiae_Eb661
Processing: Lactobacillus_plantarum_ZJ316
Processing: Corynebacterium_aurimucosum_ATCC_700975
Processing: Rickettsia_prowazekii_str_GvV257
Processing: Octadecabacter_antarcticus_307
Processing: Streptococcus_dysgalactiae_subsp_equisimilis_167
Processing: Streptococcus_salivarius_JIM8777
Processing: Streptococcus_parauberis_NCFD_2020
Processing: Hippea_maritima_DSM_10411
Processing: Erwinia_amylovora_LA636
Processing: Pantoea_vagans_C9-1
Processing: Brucella_microti_CCM_4915
Processing: Chlorobium_tepidum_TLS
Processing: Corynebacterium_casei_LMG_S-19264
Processing: Brevundimonas_subvibrioides_ATCC_15264
Processing: Ehrlichia_chaffeensis_str_West_Paces
Processing: Bifidobacterium_breve_689b
Processing: Erwinia_tasmaniensis_Et1_99
Processing: Shewanella_amazonensis_SB2B
Processing: Marinobacter_adhaerens_HP15
Processing: Streptobacillus_moniliformis_DSM_12112
Processing: Providencia_stuartii_MRSN_2154
Processing: Jonesia_denitrificans_DSM_20603
Processing: Helicobacter_acinonychis_str_Sheeba
Processing: Spirosoma_linguale_DSM_74
Processing: Helicobacter_mustelae_12198
Processing: Ethanoligenens_harbinense_YUAN-3
Processing: Geobacillus_thermoleovorans_CCB_US3_UF5
Processing: Desulfosporosinus_acidiphilus_SJ4
Processing: Leifsonia_xyli_subsp_cynodontis_DSM_46306
Processing: Candidatus_Blochmannia_pennsylvanicus_str_BPEN
Processing: Candidatus_Hepatoplasma_crinochetorum_Av
Processing: Clostridium_novyi_NT
Processing: Akkermansia_muciniphila_ATCC_BAA-835
Processing: Mycobacterium_tuberculosis_str_Beijing_NITR203
Processing: Wolbachia_endosymbiont_wPip_Mol_of_Culex_molestus
Processing: Simiduia_agarivorans_SA1_DSM_21679
Processing: Lactococcus_lactis_subsp_cremoris_UC509_9
Processing: Thermus_oshimai_JL-2
Processing: Xylanimonas_cellulosilytica_DSM_15894
Processing: Lactobacillus_helveticus_H10
Processing: Stanieria_cyanosphaera_PCC_7437
Processing: Desulfitobacterium_hafniense_DCB-2
Processing: Granulicella_tundricola_MP5ACTX9
Processing: Carboxydothermus_hydrogenoformans_Z-2901
Processing: Desulfurella_acetivorans_A63
Processing: Nitratifractor_salsuginis_DSM_16511
Processing: Wigglesworthia_glossinidia_endosymbiont_of_Glossina_brevipalpis
Processing: Streptococcus_pyogenes_NZ131
Processing: Corynebacterium_humireducens_NBRC_106098_DSM_45392
Processing: Kosmotoga_olearia_TBF_19_5_1
Processing: Paenibacillus_polymyxa_CR1
Processing: Simkania_negevensis_Z
Processing: Borrelia_bissettii_DN127
Processing: Taylorella_equigenitalis_MCE9
Processing: Thermoanaerobacter_italicus_Ab9
Processing: Aeromonas_hydrophila_AL09-71
Processing: Slackia_heliotrinireducens_DSM_20476
Processing: Neisseria_lactamica_020-06
Processing: Thermotoga_hypogea_NBRC_106472
Processing: Sinorhizobium_fredii_NGR234
Processing: Mycobacterium_avium_subsp_avium_2285_R
Processing: Francisella_noatunensis_subsp_orientalis_str_Toba_04
Processing: Heliobacterium_modesticaldum_Ice1
Processing: Sulfurimonas_denitrificans_DSM_1251
Processing: Rickettsia_felis_URRWXCal2
Processing: Ralstonia_pickettii_12J
Processing: Cytophaga_hutchinsonii_ATCC_33406
Processing: Candidatus_Sodalis_pierantonius_str_SOPE
Processing: Psychrobacter_cryohalolentis_K5
Processing: Spiroplasma_chrysopicola_DF-1
Processing: Chlamydophila_abortus_S26_3
Processing: Salinibacter_ruber_DSM_13855
Processing: Campylobacter_concisus_13826
Processing: Flavobacterium_indicum_GPTSA100-9_DSM_17447
Processing: Wolbachia_endosymbiont_strain_TRS_of_Brugia_malayi
Processing: Anoxybacillus_flavithermus_WK1
Processing: Salmonella_enterica_subsp_enterica_serovar_Heidelberg_str_CFSAN002069
Processing: Halothermothrix_orenii_H_168
Processing: Desulfotomaculum_acetoxidans_DSM_771
Processing: Streptococcus_suis_6407
Processing: Thiomonas_intermedia_K12
Processing: Candidatus_Puniceispirillum_marinum_IMCC1322
Processing: Bordetella_holmesii_44057
Processing: Candidatus_Atelocyanobacterium_thalassa_isolate_ALOHA
Processing: Hydrogenobacter_thermophilus_TK-6
Processing: Candidatus_Amoebophilus_asiaticus_5a2
Processing: Paracoccus_denitrificans_PD1222
Processing: Acidithiobacillus_caldus_ATCC_51756
Processing: Mycobacterium_leprae_Br4923
Processing: Shimwellia_blattae_DSM_4481_NBRC_105725
Processing: Desulfotomaculum_reducens_MI-1
Processing: Streptococcus_intermedius_JTH08
Processing: Sphingobium_chlorophenolicum_L-1
Processing: Streptococcus_parasanguinis_ATCC_15912
Processing: Brucella_abortus_S19
Processing: Paenibacillus_terrae_HPL-003
Processing: Clostridium_tetani_E88
Processing: Burkholderia_cenocepacia_HI2424
Processing: Burkholderia_vietnamiensis_G4
Processing: Spirochaeta_smaragdinae_DSM_11293
Processing: Bacteroides_fragilis_638R
Processing: Eubacterium_rectale_ATCC_33656
Processing: Haemophilus_ducreyi_35000HP
Processing: Borrelia_recurrentis_A1
Processing: Treponema_succinifaciens_DSM_2489
Processing: Lactobacillus_reuteri_SD2112
Processing: Nitrosococcus_halophilus_Nc_4
Processing: Helicobacter_hepaticus_ATCC_51449
Processing: Mahella_australiensis_50-1_BON
Processing: Actinoplanes_friuliensis_DSM_7358
Processing: Odoribacter_splanchnicus_DSM_20712
Processing: Spiroplasma_syrphidicola_EA-1
Processing: Streptococcus_mitis_B6
Processing: Rickettsia_heilongjiangensis_054
Processing: Dictyoglomus_turgidum_DSM_6724
Processing: Syntrophobacter_fumaroxidans_MPOB
Processing: Campylobacter_fetus_subsp_venerealis_cfvi03_293
Processing: Sphingopyxis_alaskensis_RB2256
Processing: Shewanella_woodyi_ATCC_51908
Processing: Lactobacillus_brevis_ATCC_367
Processing: Thermoanaerobacterium_thermosaccharolyticum_M0795
Processing: Kyrpidia_tusciae_DSM_2912
Processing: Candidatus_Blochmannia_vafer_str_BVAF
Processing: Achromobacter_xylosoxidans_A8
Processing: Ilyobacter_polytropus_DSM_2926
Processing: Methylomonas_methanica_MC09
Processing: _Eubacterium_eligens_ATCC_27750
Processing: Corynebacterium_doosanense_CAU_212_DSM_45436
Processing: Alicycliphilus_denitrificans_BC
Processing: Tolumonas_auensis_DSM_9187
Processing: Laribacter_hongkongensis_HLHK9
Processing: Streptococcus_mutans_NN2025
Processing: Prevotella_dentalis_DSM_3688
Processing: Snodgrassella_alvi_wkB2
Processing: Nocardia_brasiliensis_ATCC_700358
Processing: Methylococcus_capsulatus_str_Bath
Processing: Sphingobium_japonicum_UT26S
Processing: Shewanella_frigidimarina_NCIMB_400
Processing: Renibacterium_salmoninarum_ATCC_33209
Processing: Coraliomargarita_akajimensis_DSM_45221
Processing: Comamonas_testosteroni_TK102
Processing: Flavobacterium_columnare_ATCC_49512
Processing: Streptococcus_iniae_SF1
Processing: Streptomyces_avermitilis_MA-4680_NBRC_14893
Processing: Aeromonas_veronii_B565
Processing: Fervidobacterium_nodosum_Rt17-B1
Processing: Aquifex_aeolicus_VF5
Processing: Chlamydia_pecorum_P787
Processing: Syntrophobotulus_glycolicus_DSM_8271
Processing: Mycobacterium_kansasii_ATCC_12478
Processing: Clostridium_lentocellum_DSM_5427
Processing: Micromonospora_aurantiaca_ATCC_27029
Processing: Lysinibacillus_sphaericus_C3-41
Processing: Thermovibrio_ammonificans_HB-1
Processing: Treponema_denticola_ATCC_35405
Processing: Blattabacterium_sp_Cryptocercus_punctulatus_str_Cpu
Processing: Thioalkalimicrobium_aerophilum_AL3
Processing: Thermacetogenium_phaeum_DSM_12270
Processing: Oligotropha_carboxidovorans_OM4
Processing: Mycoplasma_synoviae_53
Processing: Syntrophus_aciditrophicus_SB
Processing: Novosphingobium_aromaticivorans_DSM_12444
Processing: Pirellula_staleyi_DSM_6068
Processing: Porphyromonas_asaccharolytica_DSM_20707
Processing: Corynebacterium_resistens_DSM_45100
Processing: Advenella_mimigardefordensis_DPN7
Processing: Myxococcus_stipitatus_DSM_14675
Processing: Planktomarina_temperata_RCA23
Processing: Rhodospirillum_rubrum_F11
Processing: Rhodococcus_equi_103S
Processing: Prevotella_melaninogenica_ATCC_25845
Processing: Micrococcus_luteus_NCTC_2665
Processing: Streptococcus_constellatus_subsp_pharyngis_C232
Processing: Filifactor_alocis_ATCC_35896
Processing: Gluconobacter_oxydans_DSM_3504
Processing: Candidatus_Sulcia_muelleri_PSPU
Processing: Campylobacter_hominis_ATCC_BAA-381
Processing: Taylorella_asinigenitalis_MCE3
Processing: Streptococcus_pasteurianus_ATCC_43144
Processing: Enterococcus_faecium_NRRL_B-2354
Processing: Helicobacter_felis_ATCC_49179
Processing: Halobacteroides_halobius_DSM_5150
Processing: Campylobacter_jejuni_subsp_jejuni_M1
Processing: Aeromonas_media_WS
Processing: Rickettsia_bellii_RML369-C
Processing: Klebsiella_oxytoca_E718
Processing: Meiothermus_silvanus_DSM_9946
Processing: Lactobacillus_johnsonii_DPC_6026
Processing: Candidatus_Liberibacter_asiaticus_str_Ishi-1
Processing: Staphylococcus_carnosus_subsp_carnosus_TM300
Processing: Verminephrobacter_eiseniae_EF01-2
Processing: Dechlorosoma_suillum_PS
Processing: Pediococcus_pentosaceus_ATCC_25745
Processing: Lactobacillus_kefiranofaciens_ZW3
Processing: Rhodoferax_ferrireducens_T118
Processing: Coxiella_burnetii_Dugway_5J108-111
Processing: Pseudomonas_monteilii_SB3101
Processing: Borrelia_parkeri_HR1
Processing: Kangiella_koreensis_DSM_16069
Processing: Brachybacterium_faecium_DSM_4810
Processing: Planctomyces_limnophilus_DSM_3776
Processing: Blattabacterium_sp_Mastotermes_darwiniensis_str_MADAR
Processing: Pseudomonas_cichorii_JBC1
Processing: Mycoplasma_pneumoniae_309
Processing: Sulfurospirillum_barnesii_SES-3
Processing: Thalassolituus_oleivorans_MIL-1
Processing: Streptococcus_oralis_Uo5
Processing: Amycolicicoccus_subflavus_DQS3-9A1
Processing: Carnobacterium_maltaromaticum_LMA28
Processing: Thermomicrobium_roseum_DSM_5159
Processing: Chlamydia_avium_10DC88
Processing: Trichodesmium_erythraeum_IMS101
Processing: Magnetospirillum_magneticum_AMB-1
Processing: Calditerrivibrio_nitroreducens_DSM_19672
Processing: Geodermatophilus_obscurus_DSM_43160
Processing: Acholeplasma_laidlawii_PG-8A
Processing: Thermaerobacter_marianensis_DSM_12885
Processing: Myxococcus_xanthus_DK_1622
Processing: Shewanella_violacea_DSS12
Processing: Deinococcus_gobiensis_I-0
Processing: Bartonella_bacilliformis_KC583
Processing: Arthrobacter_aurescens_TC1
Processing: Magnetococcus_marinus_MC-1
Processing: Pectobacterium_atrosepticum_SCRI1043
Processing: Oenococcus_kitaharae_DSM_17330
Processing: Rhodospirillum_centenum_SW
Processing: Streptomyces_albus_J1074
Processing: Sphaerochaeta_globosa_str_Buddy
Processing: Desulfatibacillum_alkenivorans_AK-01
Processing: Xanthomonas_campestris_pv_raphani_756C
Processing: Corynebacterium_jeikeium_K411
Processing: Vibrio_fischeri_ES114
Processing: Acetobacter_pasteurianus_IFO_3283-12
Processing: Mycobacterium_intracellulare_1956
Processing: Lachnoclostridium_phytofermentans_ISDg
Processing: Azorhizobium_caulinodans_ORS_571
Processing: Neorickettsia_helminthoeca_str_Oregon
Processing: Pseudoalteromonas_atlantica_T6c
Processing: Adlercreutzia_equolifaciens_DSM_19450
Processing: Bdellovibrio_exovorus_JSS
Processing: Shewanella_pealeana_ATCC_700345
Processing: Chlorobium_limicola_DSM_245
Processing: Strawberry_lethal_yellows_phytoplasma_CPA_str_NZSb11
Processing: Asticcacaulis_excentricus_CB_48
Processing: Thiobacillus_denitrificans_ATCC_25259
Processing: Methylotenera_mobilis_JLW8
Processing: Rhodococcus_erythropolis_PR4
Processing: Idiomarina_loihiensis_GSL_199
Processing: Lactobacillus_salivarius_CECT_5713
Processing: Haliangium_ochraceum_DSM_14365
Processing: Desulfurivibrio_alkaliphilus_AHT2
Processing: Rubrivivax_gelatinosus_IL144
Processing: Sulfurimonas_autotrophica_DSM_16294
Processing: Fervidobacterium_pennivorans_DSM_9078
Processing: Nitrobacter_winogradskyi_Nb-255
Processing: Thioalkalivibrio_thiocyanoxidans_ARh_4
Processing: Shigella_dysenteriae_Sd197
Processing: Stenotrophomonas_maltophilia_R551-3
Processing: Campylobacter_peloridis_LMG_23910
Processing: Nonlabens_dokdonensis_DSW-6
Processing: Roseburia_hominis_A2-183
Processing: Spiroplasma_culicicola_AES-1
Processing: Citrobacter_freundii_CFNIH1
Processing: Bordetella_parapertussis_Bpp5
Processing: Burkholderia_thailandensis_2002721723
Processing: Ureaplasma_parvum_serovar_3_str_ATCC_700970
Processing: Pelobacter_propionicus_DSM_2379
Processing: Barnesiella_viscericola_DSM_18177
Processing: Thermanaerovibrio_acidaminovorans_DSM_6589
Processing: Bacillus_bombysepticus_str_Wang
Processing: Acidithiobacillus_ferrivorans_SS3
Processing: Selenomonas_sputigena_ATCC_35185
Processing: Granulicella_mallensis_MP5ACTX8
Processing: Nitrosospira_multiformis_ATCC_25196
Processing: Conexibacter_woesei_DSM_14684
Processing: Candidatus_Cloacimonas_acidaminovorans_str_Evry
Processing: Selenomonas_ruminantium_subsp_lactilytica_TAM6421
Processing: Clostridium_saccharoperbutylacetonicum_N1-4_HMT
Processing: Atopobium_parvulum_DSM_20469
Processing: Acidothermus_cellulolyticus_11B
Processing: Halanaerobium_praevalens_DSM_2228
Processing: Opitutus_terrae_PB90-1
Processing: Phenylobacterium_zucineum_HLK1
Processing: Yersinia_pseudotuberculosis_YPIII
Processing: Pectobacterium_wasabiae_WPP163
Processing: Thermoanaerobacterium_saccharolyticum_JW_SL-YS485
Processing: Azotobacter_vinelandii_CA6
Processing: Amphibacillus_xylanus_NBRC_15112
Processing: Clostridiales_genomosp_BVAB3_str_UPII9-5
Processing: Citrobacter_rodentium_ICC168
Processing: Xylella_fastidiosa_subsp_fastidiosa_GB514
Processing: Bacillus_atrophaeus_1942
Processing: Stackebrandtia_nassauensis_DSM_44728
Processing: Kocuria_rhizophila_DC2201
Processing: _Clostridium_saccharolyticum_WM1
Processing: Chlamydia_trachomatis_L3_404_LN
Processing: Chlorobium_chlorochromatii_CaD3
Processing: Geobacillus_thermodenitrificans_NG80-2
Processing: Treponema_pallidum_subsp_pallidum_str_Sea_81-4
Processing: Brucella_canis_HSK_A52141
Processing: Niastella_koreensis_GR20-10
Processing: Thiomicrospira_crunogena_XCL-2
Processing: Sulfuricurvum_kujiense_DSM_16994
Processing: Xanthomonas_albilineans_GPE_PC73
Processing: Mycoplasma_penetrans_HF-2
Processing: Candidatus_Liberibacter_solanacearum_CLso-ZC1
Processing: Clostridium_cellulovorans_743B
Processing: Eubacterium_acidaminophilum_DSM_3953
Processing: Pseudoalteromonas_haloplanktis_TAC125
Processing: Komagataeibacter_medellinensis_NBRC_3288
Processing: Mycoplasma_gallisepticum_str_F
Processing: Caldicellulosiruptor_saccharolyticus_DSM_8903
Processing: Pseudomonas_fluorescens_F113
Processing: Ignavibacterium_album_JCM_16511
Processing: Thermodesulfobacterium_commune_DSM_2178
Processing: Acidovorax_ebreus_TPSY
Processing: Oceanobacillus_iheyensis_HTE831
Processing: Syntrophomonas_wolfei_subsp_wolfei_str_Goettingen_G311
Processing: Candidatus_Tremblaya_phenacola_PAVE
Processing: Staphylococcus_pseudintermedius_ED99
Processing: Segniliparus_rotundus_DSM_44985
Processing: Fibrobacter_succinogenes_subsp_succinogenes_S85
Processing: Mycoplasma_californicum_HAZ160_1
Processing: Halobacillus_halophilus_DSM_2266
Processing: Mannheimia_haemolytica_USDA-ARS-USMARC-185
Processing: Corynebacterium_terpenotabidum_Y-11
Processing: Trueperella_pyogenes_TP8
Processing: Edwardsiella_tarda_FL6-60
Processing: Caldicellulosiruptor_obsidiansis_OB47
Processing: Ralstonia_eutropha_JMP134
Processing: Pedobacter_saltans_DSM_12145
Processing: Acidobacterium_capsulatum_ATCC_51196
Processing: Melioribacter_roseus_P3M-2
Processing: Exiguobacterium_antarcticum_B7
Processing: Desulfovibrio_africanus_str_Walvis_Bay
Processing: Marivirga_tractuosa_DSM_4126
Processing: Shigella_sonnei_53G
Processing: Dechloromonas_aromatica_RCB
Processing: Stigmatella_aurantiaca_DW4_3-1
Processing: Campylobacter_volucris_LMG_24379
Processing: Mycoplasma_hominis_ATCC_23114
Processing: Agrobacterium_radiobacter_K84
Processing: Listeria_monocytogenes_serotype_4b_str_CLIP_80459
Processing: Caldicellulosiruptor_kronotskyensis_2002
Processing: Saprospira_grandis_str_Lewin
Processing: Prevotella_denticola_F0289
Processing: Cryptobacterium_curtum_DSM_15641
Processing: Clostridium_kluyveri_NBRC_12016
Processing: Brucella_pinnipedialis_B2_94
Processing: Streptococcus_gordonii_str_Challis_substr_CH1
Processing: Edwardsiella_piscicida_C07-087
Processing: Arthrobacter_phenanthrenivorans_Sphe3
Processing: Desulfarculus_baarsii_DSM_2075
Processing: Desulfovibrio_alaskensis_G20
Processing: Cyanobacterium_stanieri_PCC_7202
Processing: Desulfovibrio_aespoeensis_Aspo-2
Processing: Ehrlichia_canis_str_Jake
Processing: Brachyspira_intermedia_PWS_A
Processing: Bdellovibrio_bacteriovorus_W
Processing: Lactobacillus_ruminis_ATCC_27782
Processing: Mycobacterium_bovis_BCG_str_Pasteur_1173P2
Processing: Colwellia_psychrerythraea_34H
Processing: Methylibium_petroleiphilum_PM1
Processing: Acidovorax_avenae_subsp_avenae_ATCC_19860
Processing: Methylobacillus_flagellatus_KT
Processing: Spirochaeta_africana_DSM_8902
Processing: Bacillus_amyloliquefaciens_SQR9
Processing: Eubacterium_limosum_KIST612
Processing: Actinoplanes_missouriensis_431
Processing: Burkholderia_phenoliruptrix_BR3459a
Processing: Mycoplasma_capricolum_subsp_capricolum_ATCC_27343
Processing: Methylobacterium_populi_BJ001
Processing: Treponema_caldaria_DSM_7334
Processing: Clostridium_beijerinckii_ATCC_35702
Processing: Thermotoga_petrophila_RKU-1
Processing: Phaeobacter_inhibens_DSM_17395
Processing: Thermotoga_naphthophila_RKU-10
Processing: Bifidobacterium_animalis_subsp_lactis_ATCC_27673
Processing: Thermotoga_lettingae_TMO
Processing: Thermodesulfobacterium_geofontis_OPF15
Processing: Corynebacterium_vitaeruminis_DSM_20294
Processing: Pseudomonas_syringae_pv_phaseolicola_1448A
Processing: Sideroxydans_lithotrophicus_ES-1
Processing: Leuconostoc_citreum_KM20
Processing: Oscillatoria_nigro-viridis_PCC_7112
Processing: Serratia_marcescens_subsp_marcescens_Db11
Processing: Leptospira_biflexa_serovar_Patoc_strain_Patoc_1_Paris
Processing: Lactobacillus_gasseri_ATCC_33323_JCM_1131
Processing: Bifidobacterium_pseudolongum_PV8-2
Processing: Methylobacterium_oryzae_CBMB20
Processing: Clostridium_baratii_str_Sullivan
Processing: Thermotoga_neapolitana_DSM_4359
Processing: Rhodothermus_marinus_DSM_4252
Processing: Thermoanaerobacter_brockii_subsp_finnii_Ako-1
Processing: Thiocystis_violascens_DSM_198
Processing: Serratia_plymuthica_RVH1
Processing: Buchnera_aphidicola_str_G002_Myzus_persicae
Processing: Salmonella_bongori_NCTC_12419
Processing: Thermotoga_profunda_AZM34c06
Processing: Anaerolinea_thermophila_UNI-1
Processing: Advenella_kashmirensis_WT001
Processing: Candidatus_Accumulibacter_phosphatis_clade_IIA_str_UW-1
Processing: Deinococcus_deserti_VCD115
Processing: Oenococcus_oeni_PSU-1
Processing: Nocardiopsis_dassonvillei_subsp_dassonvillei_DSM_43111
Processing: Natranaerobius_thermophilus_JW_NM-WN-LF
Processing: Nitrobacter_hamburgensis_X14
Processing: Corynebacterium_pseudotuberculosis_FRC41
Processing: Riemerella_anatipestifer_RA-GD
Processing: Yersinia_pestis_biovar_Microtus_str_91001
Processing: Alistipes_finegoldii_DSM_17242
Processing: Porphyromonas_gingivalis_TDC60
Processing: Caulobacter_segnis_ATCC_21756
Processing: Listeria_welshimeri_serovar_6b_str_SLCC5334
Processing: Sphingomonas_sanxanigenens_DSM_19645_NX02
Processing: Streptomyces_violaceusniger_Tu_4113
Processing: Actinosynnema_mirum_DSM_43827
Processing: Burkholderia_mallei_ATCC_23344
Processing: Vibrio_campbellii_ATCC_BAA-1116
Processing: Borrelia_turicatae_91E135
Processing: Corynebacterium_falsenii_DSM_44353
Processing: Francisella_cf_tularensis_subsp_novicida_3523
Processing: Parachlamydia_acanthamoebae_UV-7
Processing: Staphylococcus_epidermidis_RP62A
Processing: Rickettsia_akari_str_Hartford
Processing: Clostridium_pasteurianum_DSM_525_ATCC_6013
Processing: Mycoplasma_suis_KI3806
Processing: Mycoplasma_fermentans_JER
Processing: Lactobacillus_fermentum_F-6
Processing: Azotobacter_chroococcum_NCIMB_8003
Processing: Pseudomonas_mosselii_SJ10
Processing: Yersinia_frederiksenii_Y225
Processing: Legionella_oakridgensis_ATCC_33761_DSM_21215
Processing: Mycoplasma_mobile_163K
Processing: Marinitoga_piezophila_KA3
Processing: Neisseria_meningitidis_LNP21362
Processing: Desulfitobacterium_dichloroeliminans_LMG_P-21439
Processing: Pseudonocardia_dioxanivorans_CB1190
Processing: Leptospirillum_ferrooxidans_C2-3
Processing: Thermodesulfobium_narugense_DSM_14796
Processing: Desulfurispirillum_indicum_S5
Processing: Pseudomonas_brassicacearum_subsp_brassicacearum_NFM421
Processing: Mycobacterium_canettii_CIPT_140010059
Processing: Actinobacillus_suis_ATCC_33415
Processing: Bacillus_cellulosilyticus_DSM_2522
Processing: Bifidobacterium_asteroides_PRL2011
Processing: Saccharomonospora_viridis_DSM_43017
Processing: uncultured_Termite_group_1_bacterium_phylotype_Rs-D17
Processing: Bacillus_thuringiensis_serovar_galleriae
Processing: Zunongwangia_profunda_SM-A87
Processing: Corynebacterium_marinum_DSM_44953
Processing: Borrelia_miyamotoi_LB-2001
Processing: Bartonella_quintana_RM-11
Processing: Legionella_pneumophila_subsp_pneumophila_str_Philadelphia_1
Processing: Microcystis_aeruginosa_NIES-843
Processing: Acidithiobacillus_ferrooxidans_ATCC_53993
Processing: Deinococcus_geothermalis_DSM_11300
Processing: Corynebacterium_callunae_DSM_20147
Processing: Psychroflexus_torquis_ATCC_700755
Processing: Mycoplasma_cynos_C142
Processing: Shewanella_piezotolerans_WP3
Processing: Shewanella_oneidensis_MR-1
Processing: Thermocrinis_albus_DSM_14484
Processing: Corynebacterium_kroppenstedtii_DSM_44385
Processing: Mesotoga_prima_MesG1_Ag_4_2
Processing: Halorhodospira_halophila_SL1
Processing: Saccharopolyspora_erythraea_NRRL_2338
Processing: Bordetella_pertussis_18323
Processing: Hymenobacter_swuensis_DY53
Processing: Flavobacterium_branchiophilum_FL-15
Processing: Candidatus_Uzinura_diaspidicola_str_ASNER
Processing: Anabaena_variabilis_ATCC_29413
Processing: Clostridium_autoethanogenum_DSM_10061
Processing: Mycobacterium_abscessus_subsp_bolletii_50594
Processing: Ornithobacterium_rhinotracheale_ORT-UMN_88
Processing: Fusobacterium_nucleatum_subsp_nucleatum_ATCC_25586
Processing: Mobiluncus_curtisii_ATCC_43063
Processing: Shewanella_denitrificans_OS217
Processing: Arcobacter_nitrofigilis_DSM_7299
Processing: Corynebacterium_ulcerans_BR-AD22
Processing: Mycoplasma_hyopneumoniae_7448
Processing: Mycoplasma_mycoides_subsp_mycoides
Processing: Novosphingobium_pentaromativorans_US6-1
Processing: Komagataeibacter_xylinus_E25
Processing: Candidatus_Midichloria_mitochondrii_IricVA
Processing: Emticicia_oligotrophica_DSM_17448
Processing: Propionibacterium_acnes_6609
Processing: Campylobacter_curvus_525_92
Processing: Polaromonas_naphthalenivorans_CJ2
Processing: Anaplasma_marginale_str_Florida
Processing: Kitasatospora_setae_KM-6054
Processing: Bartonella_grahamii_as4aup
Processing: Bacillus_toyonensis_BCT-7112
Processing: Lactobacillus_paracasei_subsp_paracasei_JCM_8130
Processing: Desulfotomaculum_kuznetsovii_DSM_6115
Processing: Azospirillum_lipoferum_4B
Processing: Anaeromyxobacter_dehalogenans_2CP-C
Processing: Mannheimia_varigena_USDA-ARS-USMARC-1388
Processing: Coprothermobacter_proteolyticus_DSM_5265
Processing: Ilumatobacter_coccineus_YM16-304
Processing: Gordonia_polyisoprenivorans_VH2
Processing: Vibrio_tasmaniensis_LGP32
Processing: Propionibacterium_propionicum_F0230a
Processing: Candidatus_Ruthia_magnifica_str_Cm_Calyptogena_magnifica
Processing: Pseudomonas_mandelii_JR-1
Processing: Anaplasma_phagocytophilum_str_HZ2
Processing: Leptospirillum_ferriphilum_YSK
Processing: Vibrio_cholerae_MJ-1236
Processing: Caldilinea_aerophila_DSM_14535_NBRC_104270
Processing: Macrococcus_caseolyticus_JCSC5402
Processing: Blattabacterium_sp_Blattella_germanica_str_Bge
Processing: Staphylococcus_lugdunensis_N920143
Processing: Belliella_baltica_DSM_15883
Processing: Roseiflexus_castenholzii_DSM_13941
Processing: Pseudomonas_putida_F1
Processing: Chlamydophila_caviae_GPIC
Processing: Paenibacillus_sabinae_T27
Processing: Haemophilus_influenzae_PittEE
Processing: Sphaerochaeta_pleomorpha_str_Grapes
Processing: Verrucosispora_maris_AB-18-032
Processing: Desulfobacterium_autotrophicum_HRM2
Processing: Nostoc_azollae_0708
Processing: Caldicellulosiruptor_owensensis_OL
Processing: Ureaplasma_urealyticum_serovar_10_str_ATCC_33699
Processing: Frateuria_aurantia_DSM_6220
Processing: Desulfotomaculum_gibsoniae_DSM_7213
Processing: Halomonas_elongata_DSM_2581
Processing: Clostridium_cellulolyticum_H10
Processing: Burkholderia_gladioli_BSR3
Processing: Streptomyces_hygroscopicus_subsp_jinggangensis_5008
Processing: Neisseria_elongata_subsp_glycolytica_ATCC_29315
Processing: Propionibacterium_freudenreichii_subsp_shermanii_CIRM-BIA1
Processing: Bacillus_lehensis_G1
Processing: Finegoldia_magna_ATCC_29328
Processing: Bacteroides_thetaiotaomicron_VPI-5482
Processing: Leptotrichia_buccalis_C-1013-b
Processing: Candidatus_Kinetoplastibacterium_blastocrithidii_TCC012E
Processing: Cellvibrio_japonicus_Ueda107
Processing: Nostoc_punctiforme_PCC_73102
Processing: Pseudomonas_stutzeri_DSM_4166
Processing: Pseudoxanthomonas_suwonensis_11-1
Processing: Ramlibacter_tataouinensis_TTB310
Processing: Candidatus_Carsonella_ruddii_PV
Processing: Pseudomonas_chlororaphis_subsp_aurantiaca
Processing: Ralstonia_solanacearum_GMI1000
Processing: Borrelia_valaisiana_VS116
Processing: Burkholderia_phytofirmans_PsJN
Processing: Thermotoga_thermarum_DSM_5069
Processing: Cronobacter_sakazakii_SP291
Processing: Thermosynechococcus_elongatus_BP-1
Processing: Caldicellulosiruptor_bescii_DSM_6725
Processing: Clostridium_saccharobutylicum_DSM_13864
Processing: Propionibacterium_acidipropionici_ATCC_4875
Processing: Streptococcus_anginosus_C238
Processing: Neorhizobium_galegae_bv_officinalis_bv_officinalis_str_HAMBI_1141
Processing: Ruminiclostridium_thermocellum_DSM_1313
Processing: Lactobacillus_rhamnosus_Lc_705
Processing: Thermotoga_elfii_NBRC_107921
Processing: Wolbachia_endosymbiont_of_Onchocerca_volvulus_str_Cameroon
Processing: Parvularcula_bermudensis_HTCC2503
Processing: Mycoplasma_parvum_str_Indiana
Processing: Candidatus_Kinetoplastibacterium_crithidii_ex_Angomonas_deanei_ATCC_30255
Processing: Thermobispora_bispora_DSM_43833
Processing: Neorickettsia_sennetsu_str_Miyayama
Processing: Teredinibacter_turnerae_T7901
Processing: Borrelia_garinii_PBi
Processing: Methylobacterium_nodulans_ORS_2060
Processing: Clostridium_ljungdahlii_DSM_13528
Processing: Bartonella_clarridgeiae_73
Processing: Rhodococcus_opacus_B4
Processing: Cyclobacterium_marinum_DSM_745
Processing: Starkeya_novella_DSM_506
Processing: Rhodomicrobium_vannielii_ATCC_17100
Processing: Moraxella_catarrhalis_BBH18
Processing: Candidatus_Tremblaya_princeps_PCVAL
Processing: Xanthomonas_axonopodis_Xac29-1
Processing: Tistrella_mobilis_KA081020-065
Processing: Dictyoglomus_thermophilum_H-6-12
Processing: Bacillus_licheniformis_DSM_13_ATCC_14580
Processing: Herpetosiphon_aurantiacus_DSM_785
Processing: Desulfohalobium_retbaense_DSM_5692
Processing: Desulfomicrobium_baculatum_DSM_4028
Processing: Geobacter_bemidjiensis_Bem
Processing: Chloroflexus_aggregans_DSM_9485
Processing: Dinoroseobacter_shibae_DFL_12_DSM_16493
Processing: Nitrosococcus_oceani_ATCC_19707
Processing: Parvibaculum_lavamentivorans_DS-1
Processing: Streptococcus_pseudopneumoniae_IS7493
Processing: Mycobacterium_africanum_GM041182
Processing: Candidatus_Nasuia_deltocephalinicola_str_NAS-ALF
Processing: Streptomyces_bingchenggensis_BCW-1
Processing: Singulisphaera_acidiphila_DSM_18658
Processing: Mycobacterium_smegmatis_JS623
Processing: Caldicellulosiruptor_hydrothermalis_108
Processing: Owenweeksia_hongkongensis_DSM_17368
Processing: Escherichia_coli_1303
Processing: Geobacter_metallireducens_GS-15
Processing: Bacteriovorax_marinus_SJ
Processing: Streptococcus_pneumoniae_ST556
Processing: Methylacidiphilum_infernorum_V4
Processing: Streptococcus_oligofermentans_AS_1_3089
Processing: Thermovirga_lienii_DSM_17291
Processing: Olsenella_uli_DSM_7084
Processing: Desulfitobacterium_dehalogenans_ATCC_51507
Processing: Caldicellulosiruptor_kristjanssonii_I77R1B
Processing: Bifidobacterium_bifidum_BGN4
Processing: Gluconacetobacter_diazotrophicus_PA1_5
Processing: Aggregatibacter_actinomycetemcomitans_D7S-1
Processing: Mesorhizobium_australicum_WSM2073
Processing: Oscillatoria_acuminata_PCC_6304
Processing: Ruminococcus_albus_7_DSM_20455
Processing: Blattabacterium_sp_Periplaneta_americana_str_BPLAN
Processing: Geobacillus_kaustophilus_HTA426
Processing: Rothia_dentocariosa_ATCC_17931
Processing: Spiroplasma_sabaudiense_Ar-1343
Processing: Anaplasma_centrale_str_Israel
Processing: Pseudomonas_syringae_pv_syringae_B728a
Processing: Isoptericola_variabilis_225
Processing: Rickettsia_rickettsii_str_Hino
Processing: Acidimicrobium_ferrooxidans_DSM_10331
Processing: Rickettsia_montanensis_str_OSU_85-930
Processing: Bifidobacterium_dentium_Bd1
Processing: Collimonas_fungivorans_Ter331
Processing: Brucella_suis_bv_1_str_S2
Processing: Rhodococcus_pyridinivorans_SB3094
Processing: Campylobacter_subantarcticus_LMG_24377
Processing: Desulfobacca_acetoxidans_DSM_11109
Processing: Candidatus_Chloracidobacterium_thermophilum_B
Processing: Elizabethkingia_anophelis_NUHP1
Processing: Coriobacterium_glomerans_PW2
Processing: Brachyspira_pilosicoli_95_1000
Processing: Moorella_thermoacetica_ATCC_39073
Processing: Streptococcus_agalactiae_COH1
Processing: Leptothrix_cholodnii_SP-6
Processing: Tepidanaerobacter_acetatoxydans_Re1
Processing: Weissella_koreensis_KACC_15510
Processing: Shigella_flexneri_Shi06HN006
Processing: Streptococcus_macedonicus_ACA-DC_198
Processing: Brevibacillus_brevis_NBRC_100599
Processing: Francisella_philomiragia_subsp_philomiragia_ATCC_25015
Processing: Dichelobacter_nodosus_VCS1703A
Processing: Sulfuricella_denitrificans_skB26
Processing: Ketogulonicigenium_vulgare_WSH-001
Processing: Hyphomonas_neptunium_ATCC_15444
Processing: Bordetella_bronchiseptica_253
Processing: Candidatus_Solibacter_usitatus_Ellin6076
Processing: Candidatus_Vesicomyosocius_okutanii_HA
Processing: Tsukamurella_paurometabola_DSM_20162
Processing: Bacteroides_salanitronis_DSM_18170
Processing: Pelobacter_carbinolicus_DSM_2380
Processing: Nocardia_farcinica_IFM_10152
Processing: Dyadobacter_fermentans_DSM_18053
In [28]:
# building tree structure
nest = nestly.Nest()
## varying params
nest.add('rep', range(1,11))
nest.add('percIncorp', [10, 25, 50])
## set params
nest.add('np_many', [24], create_dir=False)
nest.add('np_few', [8], create_dir=False)
nest.add('percTaxa', [25], create_dir=False)
nest.add('abs', ['1e10'], create_dir=False)
#nest.add('subsample', [20000], create_dir=False)
nest.add('subsample_mean', [30000], create_dir=False)
nest.add('subsample_scale', [5000], create_dir=False)
nest.add('BD_min', [1.71], create_dir=False)
nest.add('BD_max', [1.75], create_dir=False)
nest.add('padj', [0.1], create_dir=False)
nest.add('log2', [0.25], create_dir=False)
nest.add('topTaxaToPlot', [100], create_dir=False)
## input/output files
nest.add('buildDir', [buildDir], create_dir=False)
nest.add('frag_file', ['ampFrags_kde_dif'], create_dir=False)
nest.add('comm_file', ['comm.txt'], create_dir=False)
nest.add('genome_index', [os.path.join(genomeDir, 'genome_index.txt')], create_dir=False)
nest.add('R_dir', [R_dir], create_dir=False)
# building directory tree
nest.build(buildDir)
In [29]:
bashFile = os.path.join(buildDir, 'SIPSimRun.sh')
In [30]:
%%writefile $bashFile
#!/bin/bash
# symlinking input files
ln -s {buildDir}/{frag_file}.pkl {frag_file}.pkl
# Creating a community file
SIPSim communities \
{genome_index} \
--n_comm 2 \
> comm.txt
# simulating gradient fractions
SIPSim gradient_fractions \
{comm_file} \
> fracs.txt
# making incorp file
SIPSim incorpConfigExample \
--percTaxa {percTaxa} \
--percIncorpUnif {percIncorp} \
> {percTaxa}_{percIncorp}.config
# adding isotope incorporation to BD distribution
SIPSim isotope_incorp \
{frag_file}.pkl \
{percTaxa}_{percIncorp}.config \
--comm {comm_file} \
--np {np_many} \
> {frag_file}_incorp.pkl
# calculating BD shift from isotope incorporation
SIPSim BD_shift \
{frag_file}.pkl \
{frag_file}_incorp.pkl \
--np {np_few} \
> {frag_file}_incorp_BD-shift.txt
# simulating an OTU table
SIPSim OTU_table \
{frag_file}_incorp.pkl \
{comm_file} \
fracs.txt \
--abs {abs} \
--np {np_few} \
> OTU_n2_abs{abs}.txt
# subsampling from the OTU table (simulating sequencing of the DNA pool)
SIPSim OTU_subsample \
--dist normal \
--dist_params loc:{subsample_mean},scale:{subsample_scale} \
OTU_n2_abs{abs}.txt \
> OTU_n2_abs{abs}_sub-norm.txt
# making a wide table
SIPSim OTU_wideLong -w \
OTU_n2_abs{abs}_sub-norm.txt \
> OTU_n2_abs{abs}_sub-norm_w.txt
# making metadata (phyloseq: sample_data)
SIPSim OTU_sampleData \
OTU_n2_abs{abs}_sub-norm.txt \
> OTU_n2_abs{abs}_sub-norm_meta.txt
Overwriting /home/nick/notebook/SIPSim/dev/bac_genome1210/percIncorpUnifRep/SIPSimRun.sh
In [31]:
!chmod 775 $bashFile
In [ ]:
!cd $workDir; \
nestrun -j 1 --template-file $bashFile -d percIncorpUnifRep --log-file log.txt
2015-07-20 15:08:48,853 * INFO * Template: ./SIPSimRun.sh
2015-07-20 15:08:48,856 * INFO * [31732] Started ./SIPSimRun.sh in percIncorpUnifRep/7/50
2015-07-21 08:57:55,407 * INFO * [49778] percIncorpUnifRep/3/10 Finished with 0
2015-07-21 08:57:55,417 * INFO * [55924] Started ./SIPSimRun.sh in percIncorpUnifRep/10/50
2015-07-21 10:34:08,646 * INFO * [55924] percIncorpUnifRep/10/50 Finished with 0
2015-07-21 10:34:08,668 * INFO * [59923] Started ./SIPSimRun.sh in percIncorpUnifRep/10/25
In [36]:
%%writefile $bashFile
#!/bin/bash
#-- R analysis --#
export PATH={R_dir}:$PATH
# plotting taxon abundances
OTU_taxonAbund.r \
OTU_n2_abs{abs}.txt \
-r {topTaxaToPlot} \
-o OTU_n2_abs{abs}
# plotting taxon abundances
OTU_taxonAbund.r \
OTU_n2_abs{abs}_sub-norm.txt \
-r {topTaxaToPlot} \
-o OTU_n2_abs{abs}_subsub-norm
# running DeSeq2 and making confusion matrix on predicting incorporators
## making phyloseq object from OTU table
phyloseq_make.r \
OTU_n2_abs{abs}_sub-norm_w.txt \
-s OTU_n2_abs{abs}_sub-norm_meta.txt \
> OTU_n2_abs{abs}_sub-norm.physeq
## filtering phyloseq object to just taxa/samples of interest
phyloseq_edit.r \
OTU_n2_abs{abs}_sub-norm.physeq \
--BD_min {BD_min} \
--BD_max {BD_max} \
> OTU_n2_abs{abs}_sub-norm_filt.physeq
## making ordination
phyloseq_ordination.r \
OTU_n2_abs{abs}_sub-norm_filt.physeq \
OTU_n2_abs{abs}_sub-norm_bray-NMDS.pdf
## DESeq2
phyloseq_DESeq2.r \
OTU_n2_abs{abs}_sub-norm_filt.physeq \
--log2 {log2} \
--hypo greater \
> OTU_n2_abs{abs}_sub-norm_DESeq2
## Confusion matrix
DESeq2_confuseMtx.r \
{frag_file}_incorp_BD-shift.txt \
OTU_n2_abs{abs}_sub-norm_DESeq2 \
--padj {padj}
Overwriting /home/nick/notebook/SIPSim/dev/bac_genome1210/percIncorpUnifRep/SIPSimRun.sh
In [37]:
!chmod 775 $bashFile
In [38]:
!cd $workDir; \
nestrun -j 30 --template-file $bashFile -d percIncorpUnifRep --log-file logR.txt
2015-07-23 06:57:24,365 * INFO * Template: ./SIPSimRun.sh
2015-07-23 06:57:24,367 * INFO * [110662] Started ./SIPSimRun.sh in percIncorpUnifRep/7/50
2015-07-23 06:57:24,370 * INFO * [110663] Started ./SIPSimRun.sh in percIncorpUnifRep/7/25
2015-07-23 06:57:24,372 * INFO * [110665] Started ./SIPSimRun.sh in percIncorpUnifRep/7/10
2015-07-23 06:57:24,374 * INFO * [110669] Started ./SIPSimRun.sh in percIncorpUnifRep/9/50
2015-07-23 06:57:24,376 * INFO * [110671] Started ./SIPSimRun.sh in percIncorpUnifRep/9/25
2015-07-23 06:57:24,378 * INFO * [110675] Started ./SIPSimRun.sh in percIncorpUnifRep/9/10
2015-07-23 06:57:24,380 * INFO * [110685] Started ./SIPSimRun.sh in percIncorpUnifRep/8/50
2015-07-23 06:57:24,382 * INFO * [110688] Started ./SIPSimRun.sh in percIncorpUnifRep/8/25
2015-07-23 06:57:24,384 * INFO * [110703] Started ./SIPSimRun.sh in percIncorpUnifRep/8/10
2015-07-23 06:57:24,387 * INFO * [110706] Started ./SIPSimRun.sh in percIncorpUnifRep/3/50
2015-07-23 06:57:24,390 * INFO * [110718] Started ./SIPSimRun.sh in percIncorpUnifRep/3/25
2015-07-23 06:57:24,392 * INFO * [110728] Started ./SIPSimRun.sh in percIncorpUnifRep/3/10
2015-07-23 06:57:24,394 * INFO * [110731] Started ./SIPSimRun.sh in percIncorpUnifRep/10/50
2015-07-23 06:57:24,397 * INFO * [110739] Started ./SIPSimRun.sh in percIncorpUnifRep/10/25
2015-07-23 06:57:24,399 * INFO * [110746] Started ./SIPSimRun.sh in percIncorpUnifRep/10/10
2015-07-23 06:57:24,400 * INFO * [110751] Started ./SIPSimRun.sh in percIncorpUnifRep/2/50
2015-07-23 06:57:24,403 * INFO * [110758] Started ./SIPSimRun.sh in percIncorpUnifRep/2/25
2015-07-23 06:57:24,408 * INFO * [110773] Started ./SIPSimRun.sh in percIncorpUnifRep/2/10
2015-07-23 06:57:24,410 * INFO * [110779] Started ./SIPSimRun.sh in percIncorpUnifRep/1/50
2015-07-23 06:57:24,412 * INFO * [110785] Started ./SIPSimRun.sh in percIncorpUnifRep/1/25
2015-07-23 06:57:24,414 * INFO * [110792] Started ./SIPSimRun.sh in percIncorpUnifRep/1/10
2015-07-23 06:57:24,416 * INFO * [110794] Started ./SIPSimRun.sh in percIncorpUnifRep/4/50
2015-07-23 06:57:24,418 * INFO * [110801] Started ./SIPSimRun.sh in percIncorpUnifRep/4/25
2015-07-23 06:57:24,420 * INFO * [110809] Started ./SIPSimRun.sh in percIncorpUnifRep/4/10
2015-07-23 06:57:24,423 * INFO * [110819] Started ./SIPSimRun.sh in percIncorpUnifRep/5/50
2015-07-23 06:57:24,425 * INFO * [110822] Started ./SIPSimRun.sh in percIncorpUnifRep/5/25
2015-07-23 06:57:24,427 * INFO * [110826] Started ./SIPSimRun.sh in percIncorpUnifRep/5/10
2015-07-23 06:57:24,429 * INFO * [110832] Started ./SIPSimRun.sh in percIncorpUnifRep/6/50
2015-07-23 06:57:24,431 * INFO * [110843] Started ./SIPSimRun.sh in percIncorpUnifRep/6/25
2015-07-23 06:57:24,433 * INFO * [110850] Started ./SIPSimRun.sh in percIncorpUnifRep/6/10
2015-07-23 06:58:51,336 * INFO * [110706] percIncorpUnifRep/3/50 Finished with 0
2015-07-23 06:58:56,075 * INFO * [110669] percIncorpUnifRep/9/50 Finished with 0
2015-07-23 06:58:58,158 * INFO * [110739] percIncorpUnifRep/10/25 Finished with 0
2015-07-23 06:58:59,856 * INFO * [110671] percIncorpUnifRep/9/25 Finished with 0
2015-07-23 06:59:00,350 * INFO * [110850] percIncorpUnifRep/6/10 Finished with 0
2015-07-23 06:59:01,164 * INFO * [110685] percIncorpUnifRep/8/50 Finished with 0
2015-07-23 06:59:01,808 * INFO * [110688] percIncorpUnifRep/8/25 Finished with 0
2015-07-23 06:59:01,961 * INFO * [110746] percIncorpUnifRep/10/10 Finished with 0
2015-07-23 06:59:02,067 * INFO * [110794] percIncorpUnifRep/4/50 Finished with 0
2015-07-23 06:59:02,143 * INFO * [110751] percIncorpUnifRep/2/50 Finished with 0
2015-07-23 06:59:02,265 * INFO * [110718] percIncorpUnifRep/3/25 Finished with 0
2015-07-23 06:59:02,353 * INFO * [110663] percIncorpUnifRep/7/25 Finished with 0
2015-07-23 06:59:02,586 * INFO * [110792] percIncorpUnifRep/1/10 Finished with 0
2015-07-23 06:59:02,838 * INFO * [110703] percIncorpUnifRep/8/10 Finished with 0
2015-07-23 06:59:02,900 * INFO * [110731] percIncorpUnifRep/10/50 Finished with 0
2015-07-23 06:59:03,550 * INFO * [110758] percIncorpUnifRep/2/25 Finished with 0
2015-07-23 06:59:03,982 * INFO * [110801] percIncorpUnifRep/4/25 Finished with 0
2015-07-23 06:59:04,153 * INFO * [110843] percIncorpUnifRep/6/25 Finished with 0
2015-07-23 06:59:04,274 * INFO * [110773] percIncorpUnifRep/2/10 Finished with 0
2015-07-23 06:59:04,419 * INFO * [110675] percIncorpUnifRep/9/10 Finished with 0
2015-07-23 06:59:04,475 * INFO * [110785] percIncorpUnifRep/1/25 Finished with 0
2015-07-23 06:59:04,589 * INFO * [110809] percIncorpUnifRep/4/10 Finished with 0
2015-07-23 06:59:04,676 * INFO * [110832] percIncorpUnifRep/6/50 Finished with 0
2015-07-23 06:59:04,966 * INFO * [110826] percIncorpUnifRep/5/10 Finished with 0
2015-07-23 06:59:05,058 * INFO * [110665] percIncorpUnifRep/7/10 Finished with 0
2015-07-23 06:59:05,625 * INFO * [110662] percIncorpUnifRep/7/50 Finished with 0
2015-07-23 06:59:06,998 * INFO * [110822] percIncorpUnifRep/5/25 Finished with 0
2015-07-23 06:59:07,820 * INFO * [110779] percIncorpUnifRep/1/50 Finished with 0
2015-07-23 06:59:08,269 * INFO * [110819] percIncorpUnifRep/5/50 Finished with 0
2015-07-23 06:59:09,365 * INFO * [110728] percIncorpUnifRep/3/10 Finished with 0
In [39]:
# aggregating confusion matrix data
## table
!cd $workDir; \
nestagg delim \
-d percIncorpUnifRep \
-k percIncorp,rep \
-o ./percIncorpUnifRep/DESeq2-cMtx_table.csv \
DESeq2-cMtx_table.csv
## overall
!cd $workDir; \
nestagg delim \
-d percIncorpUnifRep\
-k percIncorp,rep \
-o ./percIncorpUnifRep/DESeq2-cMtx_overall.csv \
DESeq2-cMtx_overall.csv
## byClass
!cd $workDir; \
nestagg delim \
-d percIncorpUnifRep \
-k percIncorp,rep \
-o ./percIncorpUnifRep/DESeq2-cMtx_byClass.csv \
DESeq2-cMtx_byClass.csv
In [43]:
%%R -i workDir
setwd(workDir)
byClass = read.csv('./percIncorpUnifRep/DESeq2-cMtx_byClass.csv')
byClass %>% head
X byClass rep percIncorp
1 Sensitivity 0.06363636 7 50
2 Specificity 1.00000000 7 50
3 Pos Pred Value 1.00000000 7 50
4 Neg Pred Value 0.66558442 7 50
5 Prevalence 0.34920635 7 50
6 Detection Rate 0.02222222 7 50
In [58]:
%%R -w 500 -h 350
col2keep = c('Balanced Accuracy', 'Sensitivity','Specificity')
byClass.f = byClass %>%
filter(X %in% col2keep) %>%
mutate(percIncorp = as.character(percIncorp))
ggplot(byClass.f, aes(X, byClass, fill=percIncorp)) +
geom_boxplot(position='dodge') +
labs(y='Value') +
theme(
text = element_text(size=16),
axis.title.x = element_blank()
)
In [ ]:
Content source: nick-youngblut/SIPSim
Similar notebooks: