mothur

Get.groups erro

I used get.groups after make.contigs to have subset analysis in version 1.44.3. However, the no. of reads in the the pick.groups (only 318947) is not the same as the no. indicated in the get.groups command (7450314). Any possible reasons ?

mothur > get.groups(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups,accnos=soil.accnosgroups)
Selected 7450314 sequences from your fasta file.
Selected 7450314 sequences from your group file.

Output File names:
stability.trim.contigs.pick.fasta
stability.contigs.pick.groups

mothur > count.groups(group=stability.contigs.pick.groups) 1 contains 3594.
10 contains 3637.
11 contains 3522.
12 contains 3652.
13 contains 3736.
14 contains 3657.
15 contains 3662.
16 contains 3357.
17 contains 3426.
18 contains 3520.
19 contains 3493.
2 contains 3734.
20 contains 3694.
21 contains 3641.
22 contains 3617.
23 contains 3538.
24 contains 3715.
25 contains 136.
26 contains 3551.
27 contains 3638.
28 contains 3636.
29 contains 3639.
3 contains 3476.
30 contains 3496.
31 contains 3742.
32 contains 3564.
33 contains 3520.
34 contains 3465.
35 contains 3678.
36 contains 3731.
37 contains 3571.
38 contains 3690.
39 contains 3594.
4 contains 3602.
40 contains 3765.
41 contains 3573.
42 contains 3679.
43 contains 3575.
44 contains 3637.
45 contains 3705.
46 contains 3618.
47 contains 3443.
48 contains 3428.
49 contains 3528.
5 contains 3549.
50 contains 3589.
51 contains 3697.
52 contains 3631.
53 contains 3582.
54 contains 3620.
55 contains 3509.
56 contains 3612.
57 contains 3535.
58 contains 3441.
59 contains 3650.
6 contains 3552.
60 contains 3132.
61 contains 3557.
62 contains 3616.
63 contains 3576.
64 contains 3330.
65 contains 3670.
66 contains 2712.
67 contains 3532.
68 contains 3500.
69 contains 3599.
7 contains 3490.
70 contains 3635.
71 contains 3660.
72 contains 3583.
73 contains 3587.
74 contains 3569.
75 contains 3613.
76 contains 3562.
77 contains 3569.
78 contains 3535.
79 contains 3651.
8 contains 3552.
80 contains 3670.
81 contains 3627.
82 contains 3639.
83 contains 3658.
84 contains 3717.
85 contains 3685.
86 contains 3708.
87 contains 3689.
88 contains 3678.
89 contains 3559.
9 contains 3524.
90 contains 3721.

Size of smallest group: 136.

Total seqs: 318947.

Output File Names:
stability.contigs.count.summary

The groups after make.contigs
mothur > count.groups(group=stability.contigs.groups)

1 contains 84000.

10 contains 83844.

100 contains 84000.

101 contains 83737.

102 contains 84000.

103 contains 83620.

104 contains 84000.

105 contains 84000.

106 contains 83924.

107 contains 84000.

108 contains 84000.

109 contains 84000.

11 contains 83924.

110 contains 83856.

111 contains 84000.

112 contains 84000.

113 contains 84000.

114 contains 83634.

115 contains 83895.

116 contains 84000.

117 contains 83906.

118 contains 83847.

119 contains 84000.

12 contains 84000.

120 contains 84000.

121 contains 83996.

122 contains 83836.

123 contains 83904.

124 contains 83992.

125 contains 83562.

126 contains 84000.

127 contains 84000.

128 contains 84000.

129 contains 83926.

13 contains 84000.

130 contains 83982.

131 contains 84000.

132 contains 83685.

133 contains 70001.

134 contains 84000.

135 contains 83867.

136 contains 84000.

137 contains 84000.

138 contains 84000.

139 contains 84000.

14 contains 83619.

140 contains 83811.

141 contains 83955.

142 contains 83643.

143 contains 83967.

144 contains 83956.

145 contains 84000.

146 contains 84000.

147 contains 84000.

148 contains 83766.

149 contains 83763.

15 contains 83703.

150 contains 83987.

151 contains 84000.

152 contains 84000.

153 contains 83745.

154 contains 84000.

155 contains 83887.

156 contains 84000.

157 contains 83717.

158 contains 84000.

16 contains 83691.

160 contains 84000.

161 contains 83928.

162 contains 84000.

163 contains 83727.

164 contains 84000.

165 contains 84000.

166 contains 83970.

167 contains 83868.

168 contains 84000.

169 contains 84000.

17 contains 84000.

170 contains 83811.

171 contains 84000.

172 contains 84000.

173 contains 83899.

174 contains 83957.

175 contains 84000.

176 contains 78892.

177 contains 84000.

178 contains 83994.

179 contains 84000.

18 contains 84000.

180 contains 84000.

19 contains 84000.

2 contains 83860.

20 contains 83968.

21 contains 83812.

22 contains 84000.

23 contains 84000.

24 contains 83989.

25 contains 84000.

26 contains 83958.

27 contains 83564.

28 contains 83957.

29 contains 83750.

3 contains 83886.

30 contains 83594.

31 contains 84000.

32 contains 83867.

33 contains 83953.

34 contains 83822.

35 contains 84000.

36 contains 83903.

37 contains 83942.

38 contains 83731.

39 contains 84000.

4 contains 83740.

40 contains 84000.

41 contains 84000.

42 contains 84000.

43 contains 84000.

44 contains 84000.

45 contains 84000.

46 contains 84000.

47 contains 83843.

48 contains 83739.

49 contains 83927.

5 contains 83958.

50 contains 84000.

51 contains 83792.

52 contains 83992.

53 contains 83858.

54 contains 83920.

55 contains 83850.

56 contains 84000.

57 contains 84000.

58 contains 84000.

59 contains 83918.

6 contains 83920.

60 contains 72007.

61 contains 83971.

62 contains 84000.

63 contains 83959.

64 contains 78655.

65 contains 83974.

66 contains 65563.

67 contains 84000.

68 contains 84000.

69 contains 84000.

7 contains 83717.

70 contains 83710.

71 contains 84000.

72 contains 84000.

73 contains 84000.

74 contains 84000.

75 contains 83733.

76 contains 84000.

77 contains 83714.

78 contains 83851.

79 contains 83989.

8 contains 83935.

80 contains 84000.

81 contains 84000.

82 contains 84000.

83 contains 83614.

84 contains 83939.

85 contains 83948.

86 contains 83984.

87 contains 84000.

88 contains 84000.

89 contains 83745.

9 contains 84000.

90 contains 84000.

91 contains 84000.

92 contains 84000.

93 contains 83771.

94 contains 83906.

95 contains 83892.

96 contains 83870.

97 contains 83694.

98 contains 83768.

99 contains 84000.

Size of smallest group: 65563.

Total seqs: 14967116.

Thanks,

Hui

I’m not sure what the problem is - is this related to your other post?

Hei, Pat,

It is different post with another dataset. There are two subset in the groups (soil and plant). The total seq. after make.contigs was 14967116, in which soil had 7450314 seq. i used the get.groups command selecting 7450314 seq. but when runing count.groups, only 318947 seqs. was listed in the samples. i could not figure out the possible reasons.

mothur > get.groups(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups,accnos=soil.accnosgroups)
Selected 7450314 sequences from your fasta file.
Selected 7450314 sequences from your group file.

mothur > count.groups(group=stability.contigs.pick.groups)
1 contains 3594.
10 contains 3637.
11 contains 3522.


Total seqs: 318947.

Output File Names:
stability.contigs.count.summary

the count.groups after make.contigs
he groups after make.contigs
mothur > count.groups(group=stability.contigs.groups)

1 contains 84000.
10 contains 83844.
11 contains 83924.


Total seqs: 14967116.

thanks,

hui

Could you send your logfile and input files to mothur.bugs@gmail.com?