Hi qimme team,
I'm tying to calculate food diversity in diet intake data using a tree I build with the US FNDDS food database. I'm using qimme2-2019.10 conda environment.
My command of calculating alpha diversity with phylogenetics:
qiime diversity alpha-phylogenetic
--i-table all_patients_food_counts_table_w_maindescrip_featurename.qza
--i-phylogeny ../source/output_food_tree_datatree.qza
--p-metric faith_pd
--o-alpha-diversity faith_pd_vector.qza
I have the newick tree built using the R data.tree package and then convert to qza format using commad:
qiime tools import
--input-path output_food_tree_datatree.newick
--output-path output_food_tree_datatree.qza
--type 'Phylogeny[Rooted]'
There are only 483 tips in the qza format, but I have 498 tips in the newick format.
Also, I have a feature table with 495 features, all of them exist in the 498, so there are 12 features missing in the qza tree format and that is causing the problem:
All feature_ids must be present as tip names in phylogeny. feature_ids not corresponding to tip names (n=483): Pudding__ready_to_eat__low_calorie__containing_artificial_sweetener__chocolate Vegetable_soup__home_recipe Beef_stew_with_potatoes_and_vegetables_including_carrots__broccoli__and_or_dark_green_leafy__tomato_based_sauce Fruit_cocktail__cooked_or_canned__in_light_syrup Water__bottled__flavored__Glaceau_Vitamin_Water_ Milk__lactose_free__fat_free__skim_ Muffin__English Graham_crackers Italian_dressing__made_with_vinegar_and_oil Potato__roasted__from_fresh__peel_eaten__made_with_oil Gravy__mushroom Brussels_sprouts__cooked__from_fresh__fat_not_added_in_cooking Turkey_sandwich__with_spread Spinach__raw Hot_chocolate___Cocoa__made_with_no_sugar_added_dry_mix_and_water Grapes__raw__NS_as_to_type Tilapia__baked_or_broiled__made_with_oil Cream__heavy Sugar_substitute__sucralose__powder Pork_chop__broiled_or_baked__lean_and_fat_eaten Cookie__animal Ripe_plantain_fritters__Puerto_Rican_style Peppers__green__cooked__made_with_oil Soft_drink__fruit_flavored__diet__caffeine_free Tortilla__flour Spinach__cooked__from_fresh__made_with_oil Milk__lactose_free__whole Pasta_with_tomato_based_sauce__home_recipe Cereal__Kelloggs_Corn_Flakes_ Chocolate__sweet_or_dark Meat_loaf_made_with_beef Ice_pop Tea__hot__leaf__green Cabbage__Chinese__cooked__fat_not_added_in_cooking Orange__raw Pumpkin__cooked__from_canned__made_with_oil Chicken_or_turkey_pot_pie Oatmeal__instant__plain__made_with_water__fat_not_added_in_cooking Cereal__Post_Shredded_Wheat_ Ham__prepackaged_or_deli__luncheon_meat Pudding__ready_to_eat__tapioca Romaine_lettuce__raw Teriyaki_sauce Turkey_or_chicken_sausage Waffle__NFS Tea__hot__leaf__black Pasta_with_tomato_based_sauce_and_meat__home_recipe Cantaloupe__raw Quesadilla_with_vegetables_and_chicken Cereal__Kelloggs_Low_Fat_Granola_with_Raisins_ Stuffed_pepper__with_rice_and_meat Cake__pound__with_icing_or_filling Nachos_with_cheese Mixed_nuts__with_peanuts__salted Tomato_soup__cream_of__prepared_with_milk Cheese__Provolone Noodles__cooked Roll__white__hamburger_bun Barley_soup__home_recipe__canned__or_ready_to_serve Muffin__fruit Chicken_sandwich__with_spread Potato__scalloped__from_fresh Turkey_or_chicken_burger__plain__on_white_bun Cheese__Gruyere Milk_shake__home_recipe__flavors_other_than_chocolate Broccoli__cooked__from_fresh__with_cheese_sauce Flounder__baked_or_broiled__made_with_oil Soybean_curd_cheese Potato__baked__peel_eaten Mixed_vegetables__cooked__NS_as_to_form__made_with_oil Fruit_juice_drink Doughnut__cake_type Yogurt__Greek__low_fat_milk__plain Cereal__Kelloggs_Rice_Krispies_ Cheese__provolone__reduced_fat Ravioli__meat_filled__no_sauce Orange__mandarin__canned_or_frozen__drained Swedish_meatballs_with_cream_or_white_sauce Cookie__gluten_free Banana__raw French_or_Catalina_dressing Chicken_breast__baked__broiled__or_roasted_with_marinade__skin_eaten__from_raw Squash__winter_type__soup__home_recipe__canned__or_ready_to_serve Chicken_fillet__breaded__fried__sandwich_with_lettuce__tomato_and_spread Hamburger__1_medium_patty__plain__on_white_bun Gravy__poultry__home_recipe Stuffed_pepper__with_rice__meatless Tortilla_chips__flavored Chicken__wings__with_other_sauces_or_seasoning__from_fast_food___restaurant Blueberries__frozen__unsweetened Beef_and_vegetables_including_carrots__broccoli__and_or_dark_green_leafy__no_potatoes__soy_based_sauce Fruit_smoothie__with_whole_fruit_and_dairy Sea_bass__baked_or_broiled__fat_added_in_cooking Rice__white__cooked__fat_added_in_cooking__made_with_oil Salsa__red__homemade Nutritional_powder_mix__Muscle_Milk_ Carrots__cooked__from_fresh__fat_not_added_in_cooking Crepe__plain Prune_juice__100_ Soft_drink__ginger_ale__diet Cereal__Post_Honeycomb_ Vegetable_noodle_soup__canned__prepared_with_water__or_ready_to_serve Soft_drink__fruit_flavored__caffeine_free Rice__cooked__NFS Beef__broth__bouillon__or_consomme Shrimp__baked_or_broiled__made_with_oil Strudel__apple Cod__baked_or_broiled__made_with_oil Corned_beef__cooked__lean_and_fat_eaten Pepperoni__NFS Rice__brown__cooked__fat_added_in_cooking__made_with_oil Pretzels__soft__ready_to_eat__salted__no_butter Tomato_and_vegetable_juice__100___low_sodium Crackers__cheese__Cheez_It_ Coconut_milk Honeydew_melon__raw Cake_or_cupcake__yellow__with_icing_or_filling Honey_mustard_dressing Meat_loaf_made_with_chicken_or_turkey Potato__mashed__from_fast_food__with_gravy Soft_drink__ginger_ale Mayonnaise__regular Paella_with_seafood Soft_drink__cola__diet Soy_sauce Matzo_ball_soup Peach__cooked_or_canned__drained_solids Yogurt_parfait__low_fat__with_fruit Cookie__brownie__without_icing Potato_soup__prepared_with_water Nutritional_drink_or_shake__ready_to_drink__sugar_free__Glucerna_ Pancakes__plain Coffee__brewed__decaffeinated Cereal__Kelloggs_Low_Fat_Granola_ Quesadilla__just_cheese__meatless Gravy__beef_or_meat Pancakes__gluten_free Tomatoes__NS_as_to_form__broiled Guacamole__NFS Spaghetti_sauce Clam_chowder__Manhattan Crackers__wheat Soy_milk__light__chocolate Cereal__raisin_bran Reeses_Peanut_Butter_Cup Cabbage_salad_or_coleslaw__made_with_creamy_dressing Nutritional_drink_or_shake__ready_to_drink__Ensure_Plus_ Chicken_breast__grilled_without_sauce__skin_not_eaten Egg_white_omelet__scrambled__or_fried__made_without_fat Beef_steak__broiled_or_baked__lean_and_fat_eaten Popcorn__microwave__plain Cookie__almond Cauliflower__cooked__from_fresh__fat_not_added_in_cooking Duck_sauce Cake_or_cupcake__white__with_icing_or_filling Meat_loaf_made_with_beef__with_tomato_based_sauce Minestrone_soup__home_recipe Chocolate_milk__ready_to_drink__fat_free Cookie__marshmallow__with_rice_cereal__no_bake French_toast__plain Grape_juice__100_ Coffee__brewed Lasagna_with_meat Cookie__chocolate_sandwich Cookie__molasses Pad_Thai_with_seafood Cake_or_cupcake__chocolate__devils_food_or_fudge__with_icing_or_filling Sugar_substitute__saccharin__powder Tortilla_chips__nacho_cheese_flavor__Doritos_ Spaghetti_sauce_with_meat Tea__hot__leaf__black__decaffeinated Tomato_catsup Cookie__fig_bar Tomato_soup__prepared_with_water__or_ready_to_serve Cereal__General_Mills_Cheerios_ Salmon__baked_or_broiled__made_with_oil Cheese__Ricotta Tomatoes__red__dried Sour_cream Potato_chips__barbecue_flavored Bread__white Olive_oil Butter__NFS Beef_sausage Cookie__vanilla_wafer Milk__whole Pasta_with_cream_sauce__home_recipe Wrap_sandwich__filled_with_meat__poultry__or_fish__vegetables__and_cheese Cheese__NFS Cheese__Mozzarella__NFS Mushroom_soup__cream_of__prepared_with_milk Apple__raw Lettuce__salad_with_assorted_vegetables_including_tomatoes_and_or_carrots__no_dressing Pie__apple__two_crust Water__bottled__unsweetened Bagel__with_raisins Squash__summer__yellow_or_green__cooked__from_fresh__made_with_oil Muffin__carrot Rice__white__cooked__fat_not_added_in_cooking Blue_or_roquefort_cheese_dressing Onions__cooked__from_fresh__made_with_oil Potato__baked__peel_not_eaten Cranberries__dried Cookie__butter_or_sugar Crackers__oyster Lentil_soup__home_recipe__canned__or_ready_to_serve Soybean_curd__breaded__fried Yellow_rice__cooked__fat_added_in_cooking Vegetable_soup__chunky_style Pretzels__hard__NFS Lobster_bisque Cheese__Cheddar Black_bean_soup__home_recipe__canned_or_ready_to_serve Broccoli_soup__prepared_with_milk__home_recipe__canned_or_ready_to_serve Rice_noodles__cooked Coconut__packaged Egg_roll__meatless Cream_of_wheat__instant__made_with_milk__fat_not_added_in_cooking Yogurt__whole_milk__fruit Clam_chowder__New_England__prepared_with_milk Cheese_spread__cream_cheese__regular Cereal__General_Mills_Cheerios_Fruity_ Peanut_butter Pickles__mixed Squash__summer__yellow__raw Potato_salad__German_style Pesto_sauce Potato__french_fries__restaurant Egg_salad__made_with_mayonnaise Steak_and_cheese_submarine_sandwich__with_fried_peppers_and_onions__on_roll Syrup__pancake__reduced_calorie Sugar_substitute__aspartame__powder Beef__roast__roasted__lean_only_eaten Sauerkraut__cooked__fat_not_added_in_cooking Cream__half_and_half Asian_chicken_or_turkey_garden_salad_with_crispy_noodles__chicken_and_or_turkey__lettuce__fruit__nuts__crispy_noodles__no_dressing Yogurt__low_fat_milk__fruit Nutritional_drink_or_shake__ready_to_drink__Ensure_ Cheese__Parmesan__dry_grated Artichoke_salad_in_oil Carbonated_water__unsweetened Bread__rye Pancakes__whole_grain Coffee_cake__crumb_or_quick_bread_type Soup__mostly_noodles Mushrooms__raw Creamy_dressing Crackers__butter__Ritz_ Milk__fat_free__skim_ Tzatziki_dip Tartar_sauce Celery__raw Manicotti__cheese_filled__with_tomato_sauce__meatless Cereal__Quaker_Capn_Crunch_ Kit_Kat Oatmeal__instant__fruit_flavored__fat_not_added_in_cooking Pasta__vegetable__cooked Chocolate_milk__ready_to_drink__whole Potato__mashed__NFS Margarine__stick__salted Onions__mature__raw Split_pea_soup Roll__white__hard Strawberries__raw Milk_chocolate_candy__plain Pudding__rice Rice_pilaf Baked_beans__NFS Ice__fruit Egg_roll__with_beef_and_or_pork Cottage_cheese__farmers Caesar_dressing Egg__whole__fried_with_oil Hummus__plain Lettuce__raw Butter__stick__salted Vegetable_broth__bouillon Beef_steak__braised__lean_and_fat_eaten Watermelon__raw Hard_candy Potato_chowder Barley__fat_added_in_cooking Coffee_creamer__liquid Cheese_dip Wrap_sandwich__filled_with_vegetables Crab_cake Apple_juice__100_ Corn__cooked__NS_as_to_form__NS_as_to_color__made_with_oil Tortilla_chips__plain Applesauce__stewed_apples__unsweetened Mushrooms__cooked__from_fresh__made_with_oil Cake_or_cupcake__carrot__with_icing_or_filling Chicken_or_turkey_and_rice_with_soy_based_sauce Roll__white__soft Vegetarian_burger_or_patty__meatless__no_bun Cereal_or_granola_bar__Kashi_Crunchy_ Gelatin_dessert__dietetic__sweetened_with_low_calorie_sweetener Pear__cooked_or_canned__drained_solids Egg_white_omelet__scrambled__or_fried__made_with_oil Sweet_potato__baked__peel_not_eaten__made_with_oil Potato_chips__plain Plantain_chips Cheese__Muenster Shrimp__coated__fried__from_fast_food___restaurant Yogurt__whole_milk__plain Cereal__General_Mills_Cheerios_Apple_Cinnamon_ Corn_with_peppers__red_or_green__cooked__made_with_oil Chicken_or_turkey_caesar_garden_salad__chicken_and_or_turkey__lettuce__tomato__cheese__no_dressing Soy_milk__chocolate Pad_Thai__meatless Beef_short_ribs__boneless__with_barbecue_sauce__potatoes__vegetable__frozen_meal Fruit_snacks_candy__with_high_vitamin_C Pudding__ready_to_eat__chocolate Popcorn__microwave__low_sodium Red_beans_and_rice Bread_stuffing Pasta__cooked Russian_dressing Beans__string__green__cooked__from_fresh__fat_not_added_in_cooking Chickpeas__canned__drained__fat_not_added_in_cooking Cookie__ladyfinger Cornbread_muffin__stick__round Sugar__white__granulated_or_lump Blueberries__raw Bread__wheat_or_cracked_wheat Granola__homemade Chicken_or_turkey_parmigiana Tomatoes__raw Shepherds_pie_with_beef Cheese_flavored_corn_snacks__Cheetos_ Cream_of_wheat__regular_or_quick__made_with_milk__NS_as_to_fat_added_in_cooking Vegetable_combination__including_carrots__broccoli__and_or_dark_green_leafy__cooked__with_soy_based_sauce Eggplant_parmesan_casserole__regular Pizza__cheese__from_frozen__thin_crust Nutritional_powder_mix__whey_based__NFS Cheese_spread__cream_cheese__light_or_lite Chocolate_milk__ready_to_drink__reduced_fat Caesar_salad__with_romaine__no_dressing Cranberry_juice_blend__100__juice Turkey__light_and_dark_meat__roasted__skin_not_eaten Couscous__plain__cooked Blueberries__cooked_or_canned__in_heavy_syrup Barbecue_sauce Lamb_chop__NS_as_to_cut__cooked__lean_and_fat_eaten Sports_drink__low_calorie__Gatorade_G2_ Light_ice_cream__chocolate Pudding__ready_to_eat__flavors_other_than_chocolate Tea__iced__bottled__black__diet Peas__green__cooked__from_fresh__fat_not_added_in_cooking Grilled_cheese_sandwich__American_cheese__on_white_bread Maple_syrup Green_peppers_and_onions__cooked__made_with_oil Lemon_butter_sauce Cheese__Feta Orange_juice__100____freshly_squeezed Pizza__no_cheese__thin_crust Peppers__red__cooked__made_with_oil Fruit_flavored_smoothie_drink__frozen__no_dairy Sugar__brown Cereal__Kelloggs_Corn_Pops_ Soy_milk Breakfast_tart Roll__white__hot_dog_bun Salsa__red__commercially_prepared Cheese__cottage__low_fat Cookie__oatmeal__with_raisins Italian_Wedding_Soup Olives__black Pork_bacon__NS_as_to_fresh__smoked_or_cured__cooked Nutrition_bar__PowerBar_ Gelatin_dessert Asparagus__cooked__from_fresh__fat_not_added_in_cooking Macaroni_or_noodles_with_cheese Tuna_salad__made_with_mayonnaise Tea__hot__chamomile Milk__reduced_fat__2__ Lo_mein__meatless Chocolate__semi_sweet_morsel Pineapple__raw Sports_drink__Gatorade_G_ Beef__shortribs__cooked__lean_and_fat_eaten Crackers__sandwich__peanut_butter_filled Frankfurter_or_hot_dog__beef Chili_con_carne_with_beans__canned Cobbler__berry Broccoli__cooked__from_fresh__fat_not_added_in_cooking Stuffed_chicken__drumstick_or_breast__Puerto_Rican_style Chicken_tenders_or_strips__breaded__from_other_sources Ravioli__cheese_filled__no_sauce Quinoa__fat_added_in_cooking Grits__regular_or_quick__made_with_water__fat_not_added_in_cooking Frankfurter_or_hot_dog__beef_and_pork Chicken_breast__baked__coated__skin___coating_eaten Cheese__Swiss Potato__baked__peel_eaten__with_cheese Cookie__chocolate_wafer Tortellini__cheese_filled__no_sauce Cereal__Kashi_Heart_to_Heart_Oat_Flakes_and_Blueberry_Clusters_ Cilantro__raw Yogurt__whole_milk__flavors_other_than_fruit Jelly__sugar_free__all_flavors Topping__butterscotch_or_caramel Cornmeal_mush__NS_as_to_fat_added_in_cooking Cheese__American Turkey__ground Pretzels__hard__plain__lightly_salted Pudding__ready_to_eat__low_calorie__containing_artificial_sweetener__flavors_other_than_chocolate Snowpea__cooked__from_fresh__made_with_butter Muffin__chocolate_chip Chicken_or_turkey_noodle_soup__home_recipe Bread__multigrain Pasta_with_tomato_based_sauce__ready_to_heat Ice_cream__no_sugar_added__flavors_other_than_chocolate Fruit_juice_drink__with_high_vitamin_C Nutritional_drink_or_shake__ready_to_drink__Boost_Plus_ Peanut_butter_and_jelly_sandwich__with_regular_peanut_butter__reduced_sugar_jelly__on_whole_wheat_bread Lemonade__fruit_juice_drink Potato__boiled__from_fresh___peel_eaten__fat_not_added_in_cooking Egg__whole__boiled_or_poached Cookie__chocolate_chip Cookie__shortbread Egg_omelet_or_scrambled_egg__made_with_oil Danish_pastry__plain_or_spice Canola_and_soybean_oil Fruit__NS_as_to_type Chicken_or_turkey_rice_soup__home_recipe Soft_drink__cola Pineapple_juice__100_ Spinach_quiche__meatless Kale__cooked__from_fresh__fat_not_added_in_cooking Dumpling__vegetable Pancakes__with_fruit Ice_cream__no_sugar_added__chocolate Fish_stick__patty_or_nugget_from_fast_food Milk_shake__home_recipe__chocolate Doughnut__chocolate__cake_type__with_chocolate_icing Yogurt__Greek__nonfat_milk__plain Pork_sausage Stuffed_shells__cheese_filled__with_tomato_sauce__meatless Bread__fruit Crackers__NFS Cheese__Mozzarella__whole_milk Jelly__all_flavors Ravioli__NS_as_to_filling__no_sauce Butterscotch_hard_candy Beans__canned__drained__NS_as_to_type__fat_not_added_in_cooking Chicken_or_turkey_broth__bouillon__or_consomme Vegetable_oil__NFS Jam__preserve__all_flavors Almond_milk__sweetened Ice_cream__regular__chocolate Vegetables__NS_as_to_type__cooked__made_with_oil Cereal__Kelloggs_Frosted_Flakes_ Roll__whole_wheat__hamburger_bun Yogurt__Greek__nonfat_milk__fruit Dill_dip__regular Prune__dried__cooked__with_sugar Oatmeal__instant__fruit_flavored__NS_as_to_fat_added_in_cooking Vodka_sauce_with_tomatoes_and_cream Cheese__Cheddar__reduced_fat Crackers__cheese__Goldfish_ Bread__French_or_Vienna TWIX_Caramel_Cookie_Bars Avocado__raw Turkey_bacon__cooked Carrots__raw Cheese__Colby White_beans__dry__cooked__NS_as_to_fat_added_in_cooking Chicken_breast__baked__broiled__or_roasted__skin_eaten__from_raw Carrot_soup__cream_of__prepared_with_milk__home_recipe__canned_or_ready_to_serve Snack_mix__plain__Chex_Mix_ Ice_cream__regular__flavors_other_than_chocolate Fruit_cocktail__cooked_or_canned__NS_as_to_sweetened_or_unsweetened__sweetened__NS_as_to_type_of_sweetener Potato__hash_brown__NFS Tofu_and_vegetables_excluding_carrots__broccoli__and_dark_green_leafy__no_potatoes__with_soy_based_sauce Cheese__Fontina Lemon_juice__100___freshly_squeezed Sorbet__fruit__noncitrus_flavor Bread__Irish_soda Tea__iced__bottled__black Bagel__whole_wheat Cauliflower__cooked__from_fresh__made_with_oil Coconut_water__unsweetened
I've attached my newick tree. Can you help me check what is causing the problem?
Thank you
Angel