Partitioned analysis with mixed aa and nt data

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Carmen Gibbs

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Mar 4, 2020, 12:49:13 PM3/4/20

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Hi!

I am using IQTree 2.0 with macOS Catalina and fairly new to ML.

I am trying to run a partitioned analysis of bacterial sequence alignments. One is of 16S and the other is of rpoB amino acids. I am using the strategy that I found in the manual (http://www.iqtree.org/doc/Advanced-Tutorial#partitioned-analysis-with-mixed-data) to run the mixed data but I run in to a killed: 9 message.

The partition file that I set up is:

#nexus
begin sets;
charset part1 = Rhizobiales_16S_128.phy: 1-1553;
charset part2 = Rhizobiales_rpoB_aa_95.phy: 1-1551;
charpartition mine = GTR+F+R5:part1, LG+F+R8:part2;
end;

and in the command line I am trying the following (I am in the directory with my files):

(base) Carmens-MacBook-Pro:rpob_aa_ML carmenallen$ /Users/carmenallen/Programs/iqtree-2.0-rc1-MacOSX/bin/iqtree -p Rhizobiales_mix_16s_rpoBaa.nex -nt auto -pre 16S_rpoBaa -mem 0.5

The run seems to start OK but then my computer thinks for awhile and then gives me a Killed:9 error which I think means that it took too much memory. There is one aa sequence that did not pass the chi2 (below) although it looks just fine on the alignment. Not sure if that is a problem. Any suggestions??

Thank you in advance,

Carmen

(base) Carmens-MacBook-Pro:rpob_aa_ML carmenallen$ /Users/carmenallen/Programs/iqtree-2.0-rc1-MacOSX/bin/iqtree -p Rhizobiales_mix_16s_rpoBaa.nex -nt auto -pre 16S_rpoBaa -mem 0.5

IQ-TREE multicore version 2.0-rc1 for Mac OS X 64-bit built Nov 21 2019

Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,

Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host: Carmens-MacBook-Pro.local (AVX2, FMA3, 16 GB RAM)

Command: /Users/carmenallen/Programs/iqtree-2.0-rc1-MacOSX/bin/iqtree -p Rhizobiales_mix_16s_rpoBaa.nex -nt auto -pre 16S_rpoBaa -mem 0.5

Seed: 900334 (Using SPRNG - Scalable Parallel Random Number Generator)

Time: Wed Mar 4 09:35:53 2020

Kernel: AVX+FMA - auto-detect threads (12 CPU cores detected)

Reading partition model file Rhizobiales_mix_16s_rpoBaa.nex ...

Loading 2 partitions...

Reading alignment file Rhizobiales_16S_128.phy ... Phylip format detected

Alignment most likely contains DNA/RNA sequences

WARNING: 1 sites contain only gaps or ambiguous characters.

Alignment has 128 sequences with 1553 columns, 809 distinct patterns

502 parsimony-informative, 201 singleton sites, 850 constant sites

Gap/Ambiguity Composition p-value

1 Acetobacter_aceti 4.70% passed 46.11%

2 Endobacter_medicaginis 3.93% passed 52.99%

3 Rhodovastum_atsumiense 4.19% passed 17.14%

4 Aurantimonas_coralicida 9.85% passed 99.63%

5 Fulvimarina_pelagi 7.15% passed 91.96%

6 Bartonella_bacilliformis 5.28% passed 75.86%

7 Brucella_melitensis 9.08% passed 99.64%

8 Ochrobactrum_anthropi 10.62% passed 98.06%

9 Daeguia_caeni 7.21% passed 85.48%

10 Mycoplana_dimorpha 7.86% passed 93.18%

11 Sinorhizobium_fredii 7.47% passed 97.94%

12 Ensifer_adhaerens 8.18% passed 98.64%

13 Ciceribacter_lividus 10.37% passed 99.27%

14 Rhizobium_giardinii 4.89% passed 93.61%

15 Shinella_zoogloeoides 9.53% passed 94.43%

16 Shinella_granuli 8.89% passed 93.22%

17 Agrobacterium_tumefaciens 5.22% passed 85.07%

18 Neorhizobium_galegae 6.18% passed 95.18%

19 Pseudorhizobium_pelagicum 4.19% passed 97.68%

20 Chelativorans_multitrophicus 8.89% passed 90.46%

21 Mesorhizobium_loti 7.47% passed 99.80%

22 Aminobacter_aminovorans 5.34% passed 99.44%

23 Carbophilus_carboxidus 4.89% passed 99.55%

24 Phyllobacterium_myrsinacearum 9.79% passed 99.68%

25 Pseudaminobacter_salicylatoxidans 6.05% passed 98.43%

26 Corticibacterium_populi 7.60% passed 93.95%

27 Tianweitania_sediminis 6.83% passed 96.85%

28 Aquamicrobium_defluvii 8.37% passed 99.51%

29 Oricola_cellulosilytica 6.31% passed 99.59%

30 Pseudohoeflea_suaedae 6.70% passed 96.45%

31 Roseitalea_porphyridii 8.63% passed 99.35%

32 Rhizobium_undicola 7.86% passed 95.81%

33 Rhizobium_leguminosarum 8.37% passed 96.59%

34 Falsochrobactrum_ovis 6.12% passed 38.73%

35 Paenochrobactrum_gallinarii 13.39% passed 58.63%

36 Pseudochrobactrum_asaccharolyticum 6.25% passed 37.10%

37 Nitratireductor_aquibiodomus 6.25% passed 99.59%

38 Hoeflea_marina 4.89% passed 99.57%

39 Lentilitoribacter_donghaensis 7.08% passed 68.37%

40 Pseudahrensia_aquimaris 7.21% passed 70.62%

41 Amorphus_coralli 7.41% passed 89.36%

42 Afifella_marina 10.50% passed 91.26%

43 Butyratibacter_algicola 3.99% passed 84.54%

44 Lutibaculum_baratangense 6.31% passed 54.37%

45 Tepidamorphus_gemmatus 10.43% passed 37.93%

46 Rhodobium_orientis 9.34% passed 95.77%

47 Cucumibacter_marinus 12.56% passed 89.34%

48 Pelagibacterium_halotolerans 9.34% passed 67.29%

49 Arsenicitalea_aurantiaca 7.41% passed 100.00%

50 Methyloterrigena_soli 8.56% passed 91.79%

51 Paradevosia_shaoguanensis 9.40% passed 90.90%

52 Youhaiella_tibetensis 6.83% passed 84.10%

53 Devosia_riboflavina 8.44% passed 81.84%

54 Prosthecomicrobium_sp 7.73% passed 60.06%

55 Pseudoxanthobacter_soli 7.53% passed 98.31%

56 Chthonobacter_albigriseus 9.59% passed 70.73%

57 Oharaeibacter_diazotrophicus 9.34% passed 48.85%

58 Pleomorphomonas_oryzae 7.60% passed 92.12%

59 Pleomorphomonas_koreensis 8.76% passed 99.59%

60 Pleomorphomonas_diazotrophica 7.15% passed 96.57%

61 Angulomicrobium_tetraedrale 9.40% passed 96.57%

62 Starkeya_novella 9.47% passed 86.11%

63 Ancylobacter_aquaticus 8.56% passed 98.36%

64 Methylorhabdus_multivorans 13.91% passed 73.30%

65 Aquabacter_spiritensis 5.09% passed 97.27%

66 Xanthobacter_autotrophicus 9.08% passed 89.97%

67 Azorhizobium_caulinodans 5.47% passed 97.86%

68 Blastochloris_viridis 5.54% passed 58.55%

69 Hansschlegelia_plantiphila 10.24% passed 99.83%

70 Methylopila_capsulata 9.92% passed 93.40%

71 Albibacter_methylovorans 4.96% passed 97.17%

72 Rhodoblastus_acidophilus 4.89% passed 81.07%

73 Methylocapsa_acidiphila 8.89% passed 96.34%

74 Methylocella_palustris 10.30% passed 99.97%

75 Methylorosula_polaris 9.01% passed 80.04%

76 Methyloferula_stellata 9.34% passed 88.94%

77 Methylocapsa_palsarum 9.53% passed 93.47%

78 Beijerinckia_indica 4.70% passed 72.67%

79 Methylocella_silvestris 9.27% passed 98.38%

80 Methylocystis_parvus 9.34% passed 94.67%

81 Methylocystis_echinoides 9.40% passed 94.08%

82 Methylosinus_sporium 9.34% passed 99.45%

83 Methylosinus_trichosporium 9.21% passed 93.89%

84 Methylocystis_heyeri 8.24% passed 98.54%

85 Bosea_thiooxidans 5.67% passed 99.28%

86 Lichenihabitans_psoromatis 9.01% passed 99.44%

87 Rhodoplanes_roseus 6.44% passed 60.43%

88 Afipia_felis 8.56% passed 86.94%

89 Oligotropha_carboxidovorans 4.89% passed 97.86%

90 Rhodopseudomonas_palustris 9.08% passed 98.77%

91 Nitrobacter_winogradskyi 4.06% passed 96.80%

92 Bradyrhizobium_japonicum 4.64% passed 98.72%

93 Seliberia_stellata 6.83% passed 91.68%

94 Blastobacter_denitrificans 7.08% passed 98.71%

95 Tardiphaga_robiniae 7.34% passed 81.14%

96 Variibacter_gotjawalensis 9.40% passed 96.79%

97 Psychroglaciecola_arctica 12.88% passed 89.15%

98 Enterovirga_rhinocerotis 5.22% passed 95.48%

99 Methylobacterium_organophilum 7.73% passed 81.43%

100 Methylobacterium_extorquens 7.60% passed 70.70%

101 Uncultured_Methylobacterium 58.15% passed 79.13%

102 Microvirga_subterranea 4.96% passed 82.26%

103 Pseudolabrys_taiwanensis 10.75% passed 76.65%

104 Dichotomicrobium_thermohalophilum 5.41% passed 77.18%

105 Rhodoligotrophos_appendicifer 5.86% passed 58.94%

106 Anderseniella_baltica 9.47% passed 57.79%

107 Ancalomicrobium_adetum 9.47% passed 90.46%

108 Polyprosthecobacterium_yinchuanense 10.11% passed 70.87%

109 Cohaesibacter_gelatinilyticus 11.53% passed 55.72%

110 Mabikibacter_ruber 15.07% passed 96.37%

111 Parvibaculum_lavamentivorans 6.57% passed 98.43%

112 Liberibacter_crescens 4.57% passed 52.07%

113 Kaistia_adipata 9.14% passed 98.77%

114 Labrys_monachus 7.21% passed 93.87%

115 Lichenibacterium_ramalinae 8.44% passed 71.75%

116 Lichenibacterium_minor 8.69% passed 70.30%

117 Uncultured_Rhizobiales 58.02% passed 79.40%

118 Rhodomicrobium_vannielii 5.34% passed 95.00%

119 Meganema_perideroedes 10.95% passed 93.99%

120 Filomicrobium_fusiforme 9.21% passed 97.11%

121 Hyphomicrobium_denitrificans 7.02% passed 88.78%

122 Pedomicrobium_ferrugineum 9.98% passed 93.93%

123 Maritalea_myrionectae 12.94% passed 65.22%

124 Tepidicaulis_marinus 10.11% passed 97.30%

125 Salinarimonas_rosea 9.08% passed 52.48%

126 Thalassocola_ureilytica 7.08% passed 94.55%

127 Terasakiella_pusilla 7.98% passed 26.12%

128 Roseospirillum_parvum 15.84% passed 63.21%

WARNING: 2 sequences contain more than 50% gaps/ambiguity

**** TOTAL 8.79% 0 sequences failed composition chi2 test (p-value<5%; df=3)

Reading alignment file Rhizobiales_rpoB_aa_95.phy ... Phylip format detected

Alignment most likely contains protein sequences

WARNING: 66 sites contain only gaps or ambiguous characters.

Alignment has 95 sequences with 1551 columns, 902 distinct patterns

684 parsimony-informative, 170 singleton sites, 697 constant sites

Gap/Ambiguity Composition p-value

1 Acetobacter_aceti 10.38% passed 98.74%

2 Rhodovastum_atsumiense 10.32% passed 52.87%

3 Roseospirillum_parvum 10.44% passed 97.65%

4 Terasakiella_pusilla 10.70% passed 99.60%

5 Aurantimonas_coralicida 10.44% passed 99.86%

6 Fulvimarina_pelagi 11.03% passed 98.92%

7 Brucella_melitensis 11.22% passed 100.00%

8 Ochrobactrum_anthropi 11.22% passed 100.00%

9 Falsochrobactrum_ovis 11.22% passed 99.99%

10 Pseudochrobactrum_asaccharolyticum 11.15% passed 99.98%

11 Phyllobacterium_myrsinacearum 10.77% passed 100.00%

12 Mesorhizobium_loti 11.15% passed 100.00%

13 Aminobacter_aminovorans 11.22% passed 99.94%

14 Aquamicrobium_defluvii 11.15% passed 100.00%

15 Pseudaminobacter_salicylatoxidans 11.09% passed 100.00%

16 Nitratireductor_aquibiodomus 11.09% passed 99.97%

17 Mabikibacter_ruber 10.32% passed 100.00%

18 Shinella_zoogloeoides 11.09% passed 99.99%

19 Shinella_granuli 11.09% passed 100.00%

20 Mycoplana_dimorpha 11.09% passed 100.00%

21 Sinorhizobium_fredii 11.03% passed 100.00%

22 Ensifer_adhaerens 11.09% passed 100.00%

23 Rhizobium_giardinii 11.09% passed 100.00%

24 Agrobacterium_tumefaciens 11.15% passed 99.03%

25 Ciceribacter_lividus 11.15% passed 99.05%

26 Rhizobium_undicola 11.09% passed 99.25%

27 Neorhizobium_galegae 11.15% passed 99.73%

28 Pseudorhizobium_pelagicum 10.64% passed 99.38%

29 Rhizobium_leguminosarum 11.09% passed 99.98%

30 Hoeflea_marina 11.03% passed 99.58%

31 Pseudohoeflea_suaedae 11.03% passed 100.00%

32 Oricola_cellulosilytica 10.96% passed 99.97%

33 Roseitalea_porphyridii 11.03% passed 100.00%

34 Bartonella_bacilliformis 10.83% passed 99.42%

35 Rhodoblastus_acidophilus 11.22% passed 100.00%

36 Methylocapsa_acidiphila 11.28% passed 100.00%

37 Methylocapsa_palsarum 11.28% passed 100.00%

38 Methylocella_silvestris 11.28% passed 100.00%

39 Beijerinckia_indica 10.57% passed 99.99%

40 Methyloferula_stellata 11.09% passed 99.98%

41 Lichenihabitans_psoromatis 11.61% passed 99.98%

42 Lichenibacterium_ramalinae 11.15% passed 99.51%

43 Lichenibacterium_minor 11.15% passed 99.73%

44 Methylocystis_parvus 9.74% passed 99.78%

45 Methylocystis_heyeri 11.03% passed 99.83%

46 Methylosinus_trichosporium 10.83% passed 99.99%

47 Methylosinus_sporium 10.90% passed 99.85%

48 Afipia_felis 11.15% passed 99.97%

49 Oligotropha_carboxidovorans 11.22% passed 99.99%

50 Rhodopseudomonas_palustris 11.41% passed 99.99%

51 Bradyrhizobium_japonicum 11.54% passed 99.97%

52 Nitrobacter_winogradskyi 11.03% passed 100.00%

53 Tardiphaga_robiniae 11.61% passed 99.92%

54 Pseudolabrys_taiwanensis 11.54% passed 99.94%

55 Rhodoplanes_roseus 11.48% passed 99.95%

56 Variibacter_gotjawalensis 11.54% passed 99.90%

57 Aquabacter_spiritensis 11.28% passed 100.00%

58 Azorhizobium_caulinodans 11.28% passed 100.00%

59 Xanthobacter_autotrophicus 12.44% passed 99.99%

60 Ancylobacter_aquaticus 11.28% passed 100.00%

61 Starkeya_novella 11.28% passed 100.00%

62 Blastochloris_viridis 11.28% passed 99.48%

63 Prosthecomicrobium_sp 11.22% passed 100.00%

64 Oharaeibacter_diazotrophicus 11.09% passed 99.91%

65 Pleomorphomonas_oryzae 11.15% passed 100.00%

66 Pleomorphomonas_diazotrophica 11.15% passed 100.00%

67 Pleomorphomonas_koreensis 11.15% passed 100.00%

68 Pseudoxanthobacter_soli 10.64% passed 99.90%

69 Amorphus_coralli 11.15% passed 99.99%

70 Kaistia_adipata 11.03% passed 99.99%

71 Bosea_thiooxidans 11.48% passed 100.00%

72 Salinarimonas_rosea 11.48% passed 99.85%

73 Enterovirga_rhinocerotis 11.48% passed 99.99%

74 Methylobacterium_organophilum 11.41% passed 99.86%

75 Methylobacterium_extorquens 11.28% passed 100.00%

76 Microvirga_subterranea 11.28% passed 99.99%

77 Rhodobium_orientis 11.03% passed 99.85%

78 Lutibaculum_baratangense 10.90% passed 99.96%

79 Tepidamorphus_gemmatus 10.90% passed 99.68%

80 Afifella_marina 10.77% passed 100.00%

81 Cohaesibacter_gelatinilyticus 11.03% passed 99.69%

82 Cucumibacter_marinus 10.83% passed 99.96%

83 Maritalea_myrionectae 10.77% passed 99.29%

84 Pelagibacterium_halotolerans 11.03% passed 99.90%

85 Arsenicitalea_aurantiaca 11.03% passed 99.95%

86 Devosia_riboflavina 11.22% passed 100.00%

87 Youhaiella_tibetensis 11.09% passed 99.06%

88 Parvibaculum_lavamentivorans 12.19% passed 99.93%

89 Tepidicaulis_marinus 12.25% passed 99.98%

90 Rhodoligotrophos_appendicifer 12.25% passed 98.44%

91 Liberibacter_crescens 10.96% failed 0.23%

92 Rhodomicrobium_vannielii 10.51% passed 99.31%

93 Dichotomicrobium_thermohalophilum 11.15% passed 99.91%

94 Hyphomicrobium_denitrificans 10.83% passed 99.32%

95 Meganema_perideroedes 11.99% passed 92.37%

**** TOTAL 11.12% 1 sequences failed composition chi2 test (p-value<5%; df=19)

Subset Type Seqs Sites Infor Invar Model Name

1 DNA 128 1553 502 850 GTR+F+R5 part1

2 AA 95 1551 684 697 LG+F+R8 part2

Degree of missing data: 0.129

Info: multi-threading strategy over partitions

Killed: 9

Minh Bui

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Mar 5, 2020, 8:28:32 PM3/5/20

to IQ-TREE, Carmen Gibbs

Hi Carmen,

That’s strange. Does it work without -mem option?

Minh

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David Diaz Escandon

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Mar 6, 2020, 5:03:37 PM3/6/20

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Hi Minh,

It will not work even you go only with -p or -spp (no matter if use a partition file or alignments within a directory), but it works with the older versions of iqtree (1.6), It's only echoing this error in the 2.0 rc1 version, I haven't try rc2.

David

Minh

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David Diaz Escandon

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Mar 10, 2020, 5:32:14 PM3/10/20

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I already tried Rc2 and the bug persist, I tried with the verbose option (-vvv) and the problem seems to be that it get stuck with ambiguous characters because is not recognizing the two partition sets type (DNA, AA), and it's literally showing (I already try different file formats, and ways to call it):

Degree of missing data: 0.129

Info: multi-threading strategy over partitions