Dear mothur team,
I am currently using mothur 1.48.0 (and 1.48.3 too, but the issue below remains the same) with Ubuntu 24.04.
I do have a problem with the Lefse analysis, more specifically with the output. A few years ago, with older version of mothur and ubuntu, in the Lefse output there were 5 columns:
OTU LogMaxMean Class LDA pValue
Now in the output, I only have 4 columns with “Class” being missing:
OTU logMaxMean LDA pValue
So as you can imagine, it is a bit annoying because I can identify discriminant OTU but I can not know directly from the output, in which class/ecosystem this OTU is more abundant.
I am running this command :
lefse(shared=data16S.shared, design=data16S.design, lda=3, iters=1000)
and here is the data16S.design file
| group | treatment | |
|---|---|---|
| PAP0001 | Marine | |
| PAP0003 | Marine | |
| PAP0004 | Marine | |
| PAP0005 | Marine | |
| PAP0006 | Marine | |
| PAP0007 | Marine | |
| PAP0008 | Marine | |
| PAP0009 | Marine | |
| PAP0010 | Marine | |
| PAP0011 | Marine | |
| PAP0012 | Marine | |
| PAP0013 | Marine | |
| PAP0014 | Marine | |
| PAP0015 | Mangrove | |
| PAP0016 | Mangrove | |
| PAP0017 | Mangrove | |
| PAP0018 | Mangrove | |
| PAP0019 | Mangrove | |
| PAP0020 | Marine | |
| PAP0021 | Marine | |
| PAP0022 | Marine | |
| PAP0023 | Marine | |
| PAP0024 | Marine | |
| PAP0025 | Urban | |
| PAP0026 | Urban | |
| PAP0027 | Urban | |
| PAP0028 | Mangrove | |
| PAP0029 | Urban | |
| PAP0030 | Urban | |
| PAP0031 | Marine | |
| PAP0032 | Urban | |
| PAP0033 | Urban | |
| PAP0034 | Urban | |
| PAP0035 | Urban | |
| PAP0036 | Urban | |
| PAP0037 | Urban | |
| PAP0038 | Urban | |
| PAP0039 | Urban | |
| PAP0040 | Mangrove | |
| PAP0041 | Urban | |
| PAP0044 | Urban | |
| PAP0045 | Urban | |
| PAP0046 | Urban | |
| PAP0047 | Urban | |
| PAP0048 | Urban | |
| PAP0049 | Urban | |
| PAP0051 | Urban | |
| PAP0052 | Urban | |
| PAP0053 | Urban | |
| PAP0054 | Urban | |
| PAP0055 | Urban | |
| PAP0056 | Marine | |
| PAP0057 | Marine | |
| PAP0058 | Marine | |
| PAP0059 | Marine | |
| PAP0060 | Marine | |
| PAP0061 | Marine | |
| PAP0062 | Marine | |
| PAP0063 | Marine | |
| PAP0064 | Marine | |
| PAP0065 | Marine | |
| PAP0067 | Marine | |
| PAP0068 | Marine | |
| PAP0069 | Marine | |
| PAP0070 | Marine | |
| PAP0071 | Marine | |
| PAP0072 | Marine | |
| PAP0073 | Marine | |
| PAP0074 | Marine | |
| PAP0075 | Marine | |
| PAP0076 | Marine | |
| PAP0077 | Marine | |
| PAP0078 | Marine | |
| PAP0079 | Marine | |
| PAP0080 | Marine | |
| PAP0081 | Marine | |
| PAP0082 | Marine | |
| PAP0083 | Marine | |
| PAP0084 | Marine | |
| PAP0085 | Marine | |
| PAP0086 | Marine | |
| PAP0087 | Mangrove | |
| PAP0088 | Mangrove | |
| PAP0089 | Mangrove | |
| PAP0090 | Mangrove | |
| PAP0091 | Mangrove | |
| PAP0092 | Marine | |
| PAP0093 | Marine | |
| PAP0094 | Marine | |
| PAP0095 | Urban | |
| PAP0096 | Mangrove | |
| PAP0097 | Mangrove | |
| PAP0098 | Urban | |
| PAP0099 | Urban | |
| PAP0100 | Urban | |
| PAP0101 | Urban | |
| PAP0102 | Urban | |
| PAP0103 | Urban | |
| PAP0104 | Urban | |
| PAP0105 | Urban | |
| PAP0106 | Urban | |
| PAP0107 | Urban | |
| PAP0108 | Urban | |
| PAP0109 | Marine | |
| PAP0110 | Urban | |
| PAP0111 | Urban | |
| PAP0112 | Urban | |
| PAP0113 | Urban | |
| PAP0114 | Urban | |
| PAP0115 | Urban | |
| PAP0116 | Urban | |
| PAP0117 | Urban | |
| PAP0118 | Urban | |
| PAP0119 | Urban | |
| PAP0120 | Urban | |
| PAP0121 | Urban | |
| PAP0122 | Urban | |
| PAP0124 | Urban | |
| PAP0125 | Urban | |
| PAP0126 | Urban | |
| PAP0127 | Urban | |
| PAP0128 | Urban | |
| PAP0129 | Urban |
Do you think you could help me here?
Thanks a lot in advance.
Best,
