ERROR: Tree has different number of taxa!

lah...@gmail.com

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Apr 26, 2019, 3:31:30 PM4/26/19

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Hi,

I'm running into the error in the subject line when trying to run non-parametric bootstraps. The command I am running is listed below and the dataset consists of 8 partitions (7 DNA and 1 morphological). I am using IQ-TREE 1.6.10.

iqtree -spp platy_all_morphmolecular_partitions.nex -b 100 -alrt 1000 -lbp 1000 -abayes -bspec GENESITE -nt 8

Please let me know where to send relevant log files.

Thank you,

Zach

Minh Bui

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May 3, 2019, 4:16:03 AM5/3/19

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Hi Zach, Please send the log file to my personal email.

Did it happen at the very end of the run?

Thanks,

Minh

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Minh Bui

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Jun 3, 2019, 8:01:43 AM6/3/19

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Hi Zach,

This is because the GENESITE resampling caused three bootstrap trees to have fewer taxa:

minh@Minhs-MacBook-Pro:~/projects/bugs/laheyzj/iqtree_failed_run$ for i in {1..100}; do echo -n $i; head -n$i platy_all_morphmolecular_partitions.nex.boottrees |tail -n1 | grep '(' -o |wc -l; done

1     165

2     165

3     165

4     165

5     165

6     165

7     165

8     165

9     165

10     165

11     165

12     165

13     165

14     161

15     165

16     165

17     165

18     165

19     165

20     165

21     165

22     165

23     165

24     165

25     165

26     165

27     165

28     165

29     165

30     165

31     165

32     165

33     165

34     165

35     165

36     165

37     165

38     165

39     165

40     165

41     165

42     165

43     165

44     165

45     165

46     165

47     165

48     165

49     165

50     165

51     165

52     165

53     165

54     165

55     165

56     165

57     165

58     165

59     165

60     165

61     165

62     165

63     165

64     165

65     165

66     165

67     165

68     165

69     165

70     165

71     165

72     165

73     165

74     165

75     150

76     165

77     165

78     165

79     165

80     165

81     165

82     165

83     165

84     165

85     165

86     165

87     165

88     165

89     165

90     165

91     165

92     165

93     165

94     165

95     165

96     165

97     161

98     165

99     165

100     165

As you can see above, trees 14, 75 and 97 has fewer brackets than other trees. Therefore, a consensus tree can’t be constructed and IQ-TREE reported this error message at the end of the run when computing consensus tree.

Unfortunately this problem can’t be resolved. You have to manually removed these trees and then build a consensus tree with -con option. See for example http://www.iqtree.org/doc/Frequently-Asked-Questions#how-do-i-save-time-for-standard-bootstrap for how to use that option.