Error: "No valid OG groups or families"

[sjfleck]

I've already run BadiRate a couple times without issue.

My collaborators generated a more accurate .tre file for me to use, so I'm starting a new run. This tree has 5 fewer species, so I made sure to remove those species columns from the tsv file. I also made sure that the species names were all exactly the same. When I try to run BadiRate now, I get an error: No valid OG groups or families

Do you know why I'm getting this error? I can provide my files if it helps. Thanks in advance

[fgvieira]

Can you paste here the first 10 lines of your family size file and the tree your are using?

[sjfleck]

.tsv file: Orthogroup Cyrtophyllum_caudatum_GEN43 Cyrtophyllum_caudatum_GEN44 Cyrtophyllum_fragrans_GEN30 Cyrtophyllum_fragrans_GEN31 Cyrtophyllum_wallichianum_GEN41 Cyrtophyllum_wallichianum_GEN42 Fagraea_AYAMARU_GEN23 Fagraea_MatCincang_GEN3 Fagraea_NEWGUINEA_GEN22 Fagraea_NEWGUINEA_GEN24 Fagraea_NEWGUINEA_GEN25 Fagraea_auriculata_GEN2 Fagraea_berteroana_GEN13 Fagraea_borneensis_GEN37 Fagraea_cambagei_GEN15 Fagraea_cf_ceilanica_GEN5 Fagraea_crassifolia_GEN4 Fagraea_fagraeacea_GEN14 Fagraea_ridleyi_BRUNEI_GEN6 Fagraea_ridleyi_GEN21 Fagraea_woodiana_GEN33 Limahlania_crenulata_GEN1 Picrophloeus_GunungBotak_GEN34 Picrophloeus_GunungBotak_GEN35 Picrophloeus_belukar_GEN38 Picrophloeus_javanensis_GEN12 Picrophloeus_rugulosus_GEN11 Utania_austromalayensis_GEN10 Utania_cuspidata_SABAH_GEN16 Utania_cuspidata_SABAH_GEN39 Utania_cuspidata_SARAWAK_GEN40 Utania_nervosa_GEN8 Utania_racemosa_NEWGUINEA_GEN19 Utania_racemosa_PENMSIA_GEN9 Utania_sp_GEN17 Utania_sp_GEN18 Utania_spicata_GEN7 Utania_stenophylla_GEN29 Utania_volubilis_v_microcalyx_GEN36 OG0000007 31 38 39 48 41 46 30 36 28 34 28 49 30 66 23 59 53 24 49 51 35 41 24 32 36 38 34 52 44 42 53 48 38 49 49 51 45 40 40 OG0000009 47 46 47 43 51 54 18 26 30 28 30 32 23 38 24 24 28 40 31 26 29 28 35 38 44 40 32 57 50 54 45 41 37 52 47 53 38 44 45 OG0000010 25 31 35 34 39 40 32 17 35 39 36 30 31 28 43 28 29 38 41 44 29 46 40 38 57 36 43 50 39 38 42 39 43 46 46 37 46 42 36 OG0000008 43 44 42 44 45 39 23 19 30 29 25 29 29 34 42 27 27 27 28 28 17 37 42 41 43 44 49 34 53 38 40 45 37 44 34 38 46 45 46 OG0000012 36 32 40 42 37 36 14 21 16 15 12 22 14 19 15 26 22 17 27 28 26 35 51 54 68 66 40 45 52 53 50 41 46 52 39 42 51 46 49 OG0000013 9 9 5 9 9 7 66 95 59 46 2 121 58 135 2 97 104 2 154 146 102 8 6 6 12 5 8 5 13 11 11 7 1 6 12 14 9 8 12 OG0000011 54 41 41 48 51 60 2 42 6 9 2 54 2 32 12 56 65 7 47 42 53 135 94 96 97 75 18 13 15 14 16 12 8 14 10 17 7 12 10 OG0000014 25 26 37 34 26 20 13 54 9 22 18 24 17 32 21 56 67 30 44 34 26 19 16 19 30 22 13 69 47 52 52 49 36 50 60 67 49 40 52 OG0000016 28 26 27 31 32 30 13 46 11 12 4 39 11 32 7 77 58 5 78 80 92 17 23 20 17 22 26 45 45 48 33 39 31 38 36 40 35 33 42

.tre file:

NEXUS

begin taxa; dimensions ntax=39; taxlabels Cyrtophyllum_caudatum_GEN43 Cyrtophyllum_caudatum_GEN44 Cyrtophyllum_fragrans_GEN30 Cyrtophyllum_fragrans_GEN31 Cyrtophyllum_wallichianum_GEN41 Cyrtophyllum_wallichianum_GEN42