I have a design file and i made my shared file from my output from qiime. every time I run the metastat command I get an error of nothing being on my design file. i have remade the design file multiple times and still don’t know the problem.
Hi there - it looks like your group names in the shared file have a hyphen (i.e., “-”) and they have an underscore (i.e., “_”) in your design file. If gettting those to agree doesn’t do the trick, can you post the error message?
Pat
i identified the issue in this but I was trying to run the metastats command but with 5 groups and didn’t work and this is my design file. error is missing shared info for the treatment and skipping comparison.
| group | treatment |
|---|---|
| SF_1 | Wolbachia |
| SF_5 | Wolbachia |
| SF_7 | Wolbachia |
| SF_8 | Wolbachia |
| SF_9 | Wolbachia |
| SF_11 | Wolbachia |
| SF_13 | Wolbachia |
| SF_14 | Wolbachia |
| SF_15 | Wolbachia |
| SF_19 | Wolbachia |
| SF_20 | Wolbachia |
| SF_43 | Wolbachia |
| SF_46 | Wolbachia |
| SF_58 | Wolbachia |
| SF_63 | Wolbachia |
| SF_64 | Wolbachia |
| SF_68 | Wolbachia |
| SF_69 | Wolbachia |
| SF_75 | Wolbachia |
| SF_80 | Wolbachia |
| SF_83 | Wolbachia |
| 1SF15 | Wolbachia |
| 10SF15 | Wolbachia |
| 16SF15 | Wolbachia |
| 21SF15 | Wolbachia |
| 24SF15 | Wolbachia |
| 33SF15 | Wolbachia |
| 50SF15 | Wolbachia |
| 54SF15 | Wolbachia |
| 58SF15 | Wolbachia |
| 63SF15 | Wolbachia |
| 66SF15 | Wolbachia |
| 72SF15 | Wolbachia |
| 80SF15 | Wolbachia |
| 83SF15 | Wolbachia |
| 88SF15 | Wolbachia |
| 107SF15 | Wolbachia |
| 131SF15 | Wolbachia |
| 136SF15 | Wolbachia |
| 169SF15 | Wolbachia |
| 179SF15 | Wolbachia |
| 196SF15 | Wolbachia |
| 201SF15 | Wolbachia |
| 6SF16 | Wolbachia |
| 12SF16 | Wolbachia |
| 22SF16 | Wolbachia |
| 43SF16 | Wolbachia |
| 47SF16 | Wolbachia |
| 48SF16 | Wolbachia |
| 58SF16 | Wolbachia |
| 62SF16 | Wolbachia |
| 76SF16 | Wolbachia |
| 78SF16 | Wolbachia |
| 83SF16 | Wolbachia |
| 131SF16 | Wolbachia |
| 140SF16 | Wolbachia |
| 160SF16 | Wolbachia |
| 173SF16 | Wolbachia |
| 176SF16 | Wolbachia |
| 178SF16 | Wolbachia |
| 193SF16 | Wolbachia |
| 217SF16 | Wolbachia |
| 108SF15 | Cardinium |
| 192SF15 | Cardinium |
| 204SF15 | Cardinium |
| 7SF16 | Cardinium |
| 17SF16 | Cardinium |
| 36SF16 | Cardinium |
| 93SF16 | Cardinium |
| 119SF16 | Cardinium |
| 91SF16 | Cardinium_Spiroplasma |
| 120SF16 | Cardinium_Spiroplasma |
| 141SF16 | Cardinium_Spiroplasma |
| SF_2 | Cardinium_Wolbachia |
| SF_12 | Cardinium_Wolbachia |
| SF_16 | Cardinium_Wolbachia |
| SF_17 | Cardinium_Wolbachia |
| SF_18 | Cardinium_Wolbachia |
| SF_24 | Cardinium_Wolbachia |
| SF_26 | Cardinium_Wolbachia |
| SF_27 | Cardinium_Wolbachia |
| SF_31 | Cardinium_Wolbachia |
| SF_33 | Cardinium_Wolbachia |
| SF_34 | Cardinium_Wolbachia |
| SF_36 | Cardinium_Wolbachia |
| SF_38 | Cardinium_Wolbachia |
| SF_57 | Cardinium_Wolbachia |
| SF_59 | Cardinium_Wolbachia |
| SF_61 | Cardinium_Wolbachia |
| SF_62 | Cardinium_Wolbachia |
| SF_76 | Cardinium_Wolbachia |
| SF_77 | Cardinium_Wolbachia |
| SF_78 | Cardinium_Wolbachia |
| SF_82 | Cardinium_Wolbachia |
| 61SF15 | Cardinium_Wolbachia |
| 74SF15 | Cardinium_Wolbachia |
| 105SF15 | Cardinium_Wolbachia |
| 152SF15 | Cardinium_Wolbachia |
| 189SF15 | Cardinium_Wolbachia |
| 44SF16 | Cardinium_Wolbachia |
| 96SF16 | Cardinium_Wolbachia |
| 110SF16 | Cardinium_Wolbachia |
| 115SF16 | Cardinium_Wolbachia |
| 146SF16 | Cardinium_Wolbachia |
| 228SF16 | Cardinium_Wolbachia |
| SF_3 | Spiroplasma_Wolbachia |
| SF_4 | Spiroplasma_Wolbachia |
| SF_6 | Spiroplasma_Wolbachia |
| SF_10 | Spiroplasma_Wolbachia |
| SF_21 | Spiroplasma_Wolbachia |
| SF_22 | Spiroplasma_Wolbachia |
| SF_23 | Spiroplasma_Wolbachia |
| SF_25 | Spiroplasma_Wolbachia |
| SF_28 | Spiroplasma_Wolbachia |
| SF_30 | Spiroplasma_Wolbachia |
| SF_32 | Spiroplasma_Wolbachia |
| SF_35 | Spiroplasma_Wolbachia |
| SF_37 | Spiroplasma_Wolbachia |
| SF_39 | Spiroplasma_Wolbachia |
| SF_40 | Spiroplasma_Wolbachia |
| SF_41 | Spiroplasma_Wolbachia |
| SF_42 | Spiroplasma_Wolbachia |
| SF_45 | Spiroplasma_Wolbachia |
| SF_47 | Spiroplasma_Wolbachia |
| SF_51 | Spiroplasma_Wolbachia |
| SF_52 | Spiroplasma_Wolbachia |
| SF_53 | Spiroplasma_Wolbachia |
| SF_55 | Spiroplasma_Wolbachia |
| SF_56 | Spiroplasma_Wolbachia |
| SF_60 | Spiroplasma_Wolbachia |
| SF_65 | Spiroplasma_Wolbachia |
| SF_66 | Spiroplasma_Wolbachia |
| SF_67 | Spiroplasma_Wolbachia |
| SF_70 | Spiroplasma_Wolbachia |
| SF_71 | Spiroplasma_Wolbachia |
| SF_74 | Spiroplasma_Wolbachia |
| SF_81 | Spiroplasma_Wolbachia |
| SF_84 | Spiroplasma_Wolbachia |
| 12SF15 | Spiroplasma_Wolbachia |
| 15SF15 | Spiroplasma_Wolbachia |
| 18SF15 | Spiroplasma_Wolbachia |
| 26SF15 | Spiroplasma_Wolbachia |
| 35SF15 | Spiroplasma_Wolbachia |
| 38SF15 | Spiroplasma_Wolbachia |
| 41SF15 | Spiroplasma_Wolbachia |
| 42SF15 | Spiroplasma_Wolbachia |
| 45SF15 | Spiroplasma_Wolbachia |
| 46SF15 | Spiroplasma_Wolbachia |
| 47SF15 | Spiroplasma_Wolbachia |
| 48SF15 | Spiroplasma_Wolbachia |
| 55SF15 | Spiroplasma_Wolbachia |
| 60SF15 | Spiroplasma_Wolbachia |
| 68SF15 | Spiroplasma_Wolbachia |
| 87SF15 | Spiroplasma_Wolbachia |
| 90SF15 | Spiroplasma_Wolbachia |
| 155SF15 | Spiroplasma_Wolbachia |
| 165SF15 | Spiroplasma_Wolbachia |
| 167SF15 | Spiroplasma_Wolbachia |
| 29SF16 | Spiroplasma_Wolbachia |
| 70SF16 | Spiroplasma_Wolbachia |
| 74SF16 | Spiroplasma_Wolbachia |
| 100SF16 | Spiroplasma_Wolbachia |
| 104SF16 | Spiroplasma_Wolbachia |
| 113SF16 | Spiroplasma_Wolbachia |
| 123SF16 | Spiroplasma_Wolbachia |
| 127SF16 | Spiroplasma_Wolbachia |
| 137SF16 | Spiroplasma_Wolbachia |
| 139SF16 | Spiroplasma_Wolbachia |
| 148SF16 | Spiroplasma_Wolbachia |
| 151SF16 | Spiroplasma_Wolbachia |
| 156SF16 | Spiroplasma_Wolbachia |
| 174SF16 | Spiroplasma_Wolbachia |
| 180SF16 | Spiroplasma_Wolbachia |
| 183SF16 | Spiroplasma_Wolbachia |
| 188SF16 | Spiroplasma_Wolbachia |
| 218SF16 | Spiroplasma_Wolbachia |
| 221SF16 | Spiroplasma_Wolbachia |
| SF_44 | Cardinium_Spiroplasma_Wolbachia |
| SF_48 | Cardinium_Spiroplasma_Wolbachia |
| SF_50 | Cardinium_Spiroplasma_Wolbachia |
| SF_54 | Cardinium_Spiroplasma_Wolbachia |
| SF_72 | Cardinium_Spiroplasma_Wolbachia |
| 187SF15 | Cardinium_Spiroplasma_Wolbachia |
| 25SF16 | Cardinium_Spiroplasma_Wolbachia |
| 55SF16 | Cardinium_Spiroplasma_Wolbachia |
| 92SF16 | Cardinium_Spiroplasma_Wolbachia |
Hi - can you post the text of the error message?
shared info for Wolbachia and the rest of the groups, skipping comparison
The get.groups command may be helpful in figuring out what is missing. It can be run with a shared and design file, and you can select the treatments.
mothur > get.groups(shared=yourSharedFile, design=yourDesignFile, sets=Wolbachia)
The command above will select all the groups in your shared and design file that belong to the Wolbachia treatment.
but there are groups without wolbachia
The original error from mothur indicates you have groups present in your design file that are not present in your shared file. This is likely a simple mistake or typo. Using the get.groups command may help you spot the issue. If you are unable to find the missing groups, you can send your shared and design file to mothur.bugs@gmail.com and I will take a look.