Hi @jwdebelius,
I have filtered my data using phyloseq and then imported the biom table to run ANCOM. When I run the following command:
qiime composition ancom --i-table table-filtered-ancom-abund-comp.qza --m-metadata-file metadata_rockwool.tsv --m-metadata-column Diagnostic --o-visualization ancom-filtered-diagnostic.qzv --verbose
I get the following error:
Traceback (most recent call last):
File "/Users/pablo/opt/anaconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "</Users/pablo/opt/anaconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-480>", line 2, in ancom
File "/Users/pablo/opt/anaconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/Users/pablo/opt/anaconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 452, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/Users/pablo/opt/anaconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_composition/_ancom.py", line 46, in ancom
metadata = metadata.filter_ids(table.index)
File "/Users/pablo/opt/anaconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/metadata/metadata.py", line 1105, in filter_ids
ids_to_keep)
File "/Users/pablo/opt/anaconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/metadata/metadata.py", line 198, in _filter_ids_helper
% (', '.join(repr(e) for e in sorted(missing_ids))))
ValueError: The following IDs are not present in the metadata: '021f9f6d5cea1fb4903d7e3b4db61d33', '0302ece4031dfaf3eac34ddbfc2c7d6f', '04b8b02dd86522f055095c2ef17286ad', '04ecfad5772d2e09a84a0f5ef460536c', '0551bb63d550ae8c8f89dacebda76822', '084f5bc37bfe2e673033d1d4c47d6377', '0a4c8bffc9aac53bd22ac6dd2c468c44', '0ab25b517ef52f4bf414661f7a6d5e9b', '0c579d21280801f02a641e1608606927', '0ddcd311e02f742e2e0e61ce02cf9c29', '10f7d3043212747fec7e8064ab2cd213', '1290e271fbc50c66e2cd8e437d0d4a44', '133862bc5656b433803da453daeb9375', '13e333f11c5a6224f6fea469b509306f', '14ff660452637cf706f1a97b7c9d2c57', '16a7d8ffc6f02f49aeadebb5f9a85829', '18a980ed927822f60eebf93600ee8ff4', '19573493f06e15f074f664ad7505ac52', '1c2b8892a0d7f828d72808cd01cfd199', '1de4896460562cae3be7c9d14bfe84cf', '1e104b993416995498346089f57fd3bf', '1e542d2112237ddb072880742ade6180', '20b3df08cd5fac2be26a2928155bab69', '220795da096a5acfebca378d68cfb00a', '23dd3ddcb8dfc1dc043713b988712ed0', '25c9884cd991eb1695f6a20546b4a231', '2b0fbcfebbfdfd18c3a90d6442985776', '2b77359306bbc33b0cb6452265701700', '2dd9e191a81b91117b77df5eac7e6048', '2ea6405c484061e2f28c03e18175c0ea', '33a198a979ec6f8252b36eb5ae643d5e', '36ecd054f5309a9658926a0926d7ee82', '377ab0ace4b9be30cbefe96d0e4192fe', '37a7a573f969549bb14095707d0a41fd', '3c3861c581adf9b8a8cf01f20fdbaf2c', '3d008a07a63e01193561eb4f27931678', '42000cb927e3155d3af5b15b0df14149', '43f8d1ced946461f54ea0b5b7001d5d6', '44349931377434a54bb432488ce41d8f', '44a96c286137bd1ef96e5a0811fd1033', '49a250849d64ca63b354b4b3281030d0', '4aebcc69b46614d3365683ba49d95dc1', '4e1f22b1dd5a8a42b8c61212342004e5', '4ef19fc863b7ff2cd97e5007547ddf7a', '4fed591b948101b5cdecaa91af4dde8b', '50275cde92eb0f51a7e19f361b869f48', '502fe0d91a4a63700820def15640e03e', '50ecca04e76cff8f632e6a69ef1add10', '5116c9fcb49e815e7bbccd35da2a5edc', '539d88c2d414548df829f33f937de8c7', '558799b297c6419c59fc5bc008ff9353', '56aedcf6ae4ccd4e92f4a6e6429fe7be', '573091d7ddd85f9c5f14a7e53d2ba0bf', '57fa2e5d2e2e046de926685af878fdd5', '581d47e597c62716475aaf024802ee58', '58b326519fbd0acb1a99c0926a104de6', '59ffa9945b1b25873c52ab906e9d4f2d', '5afec052157f7768bf459883f118a638', '5c2392591fbe650b20394fc09e9ca90c', '5e6494ce2ce4dff7e1dcbe60b1144bbc', '5f8db894a571d35c9d2fa4f8df8581f9', '60c24e14ac67927ee85a38e54d24a54e', '60d6aebce485be862de282eb2497989d', '6112d362565c5797eb555106a550d353', '6173b09cb82fab430423bf0d6bfd65a5', '6326363cc12189a386d6c9e5c711038d', '6356351ad36d913e8f7951adb0edd88e', '64d9b39739febe82181f29f7a63569b2', '685a02dea108c4edf364bb4e4b9006c7', '68c56896f754db932a51a88ebad5bc6a', '690e2d312e3f83ab4ef9893d8c5eb3ab', '695ca004c600fa100dd3a195e045eaac', '6a42f6b31b1958a4fd7c015ad7affbf4', '6d8af7f219f9fee5bebdca626bac50c4', '6ef30ad70950c7994898405da4aa1f2a', '6f35231a57c7a34013f732680c201284', '702af9e944edfd5a1a7f0dce0d566376', '70869d0feda2b000386a1851bdfcaffe', '71c85d9364bd003b2dbecd3275898630', '7433f49009bcca4a3ca6cfc7db672d08', '766462642f96a8afb24bb8056266c422', '77fb97381b583af41aec56a89b31e21c', '78a5149ffb21d2c6268bb3053f086d03', '7c9260cb39c10fef45b09ad77d5adb8f', '7df792d3bb049b81ba1bafc2049c38e6', '7e46d2d718bdf66a05368a43c52da32e', '7ead17a076e7b7b419bf50abe7eee3f4', '834408b5dea275ad6ac778a97c1414cb', '8403b6dbf52ec50c0a7b83ee636cd6e9', '860b11244363460108e1a96df96599a1', '8735f92a7f18db944bc862777fbd3222', '8a3a2d75c466b3a04af23532bb6fa6da', '8c46ebd0a248fe82636f79086d5499fd', '8ce12e88f6b59bb09494567f0d678092', '8d354b3efd44bcb690ba13412f9101a0', '8d4a33d6038a914f39e40abf0d001f06', '8e083a59abb06a47f9e349d9a45740c6', '8edc60b1393f150c44ab8546c368b6a9', '8f90932836eec8eb89164f265ebd63f5', '90790e2535c96a11d93bc0ddbc31d7b7', '92bdbee428f33594adb9ba31bab30815', '93d6a9f2d4768702315d61f6559584d9', '943a9f0fef606ac9c31536907d1e8150', '945184b6386c192c0066e0a98a154780', '95409f0f627d9bbbad895d1fd1fbb228', '95a7e70fb332ba3cda224b5fa86471f2', '99533e942a2fc83f5e47d8f9d5d69927', '9bc71d8512f20485209528c79522f3f2', '9fc55fff41bec4e5233a254867fa8829', 'a1a6090285725afd6024202a80bc47ed', 'a1d06f9ab908c1ca186f7a58357d8226', 'a26da340960942d894b28559f2430838', 'a33fcf3f1ae5cb63ec00dc2cf90e3c77', 'a4870cb22cb2f6ad880433b42d281866', 'a52ca5460d3b1b0d79e89747bcb5bd52', 'a5b90aeb2ab3b1da1ad0e3f7ab8dd3e4', 'a5e4fa1c4fdfceff6877d2ba21ae0b91', 'a9164d01308501b576afa06256a15b0f', 'aa5631f5d83e474773bbec18a4dc887d', 'ad145b5c8b7c9b7ffb1c647fa0da640d', 'ad16b779f2ec6d8afc200de7c5d2f39a', 'aed191bac0b1c3264208a084af848bed', 'aee83626bf99f96165a5c90cc9511595', 'af1eff0471fc6384606db4ad3c718bf4', 'af9f74d482cf671395fabba3dbc91081', 'afc9946b7c28e2e6500fd5f3e51c8f64', 'b34f7ad7d579d045804c113656f63eff', 'b68bc26bac6a234304e60debcf0badc8', 'b6d16645619f084c15f25f496ee50de0', 'b7f5af401f678ffbe9f7299cfa59e3bf', 'b8575d0fb2096a10b007fce89b0ee322', 'b9508e3cafc10a7910b7ad3cbd9c6c12', 'bc480af024be641e79b2536924725672', 'bcc6da5f621cbdfc1f0c9becbac6cdff', 'bd2ad00d586fbb853586dae6812f7b24', 'bd8ebcd25d5d8b78e2a417f0e855be85', 'bdf8a26094624622d68509a87fa75ba7', 'bec6480df9edec378680faa3af2b14fd', 'bf321c05d79f766c0099afb9ecc42f52', 'bfa2c70b068441a79415949856e6e9d9', 'c053c6bfc7a32d897d3dcb5ff0205190', 'c17b9f556b16dd11584378735ea5fe9d', 'c330ad54b5bc5de082da3c5bca80f16e', 'c37e7e03a26fbfce94680b5fe323d0d7', 'c59336b98498412a3a7b20ab3b1791f9', 'c757ad670c5d796cb866c941c62c4e33', 'c83102b352f538b7031b8ab74c4858c9', 'ca1fe70202213a0522f8b97c6d8b1720', 'cac706621d99e7ad647bda595c8360d2', 'cae956edaaa912def15b50e07101ce73', 'ccfb97768be91fb0df9201b46d4aa94e', 'cf3381318906e1e08f58bca905636dc0', 'd0523e63a384821e91e3db756b874650', 'd08d880f3e419559708da8cca5085c09', 'd114fb4c335125128be28401522dd41a', 'd1c2ac4bb95711b1e5f88052ee02ab55', 'd30ec6a7ed3f2a53b1ef1e93a14b8cb3', 'd68820236056c00e2edf7e6271924578', 'd6a526b572996ed919a3e009473bc860', 'd6aa1d235fa5e66393c7cd0e437ba917', 'd829bee4984f82ffc2453212157caf96', 'dac2cd571e9978b6b55c699782b22c87', 'dae7a3a5a57d7015f0125db58af1eb88', 'db42eb257100c547793051ee942fba0d', 'ddfd49f939f92958b1ec816741055348', 'ded222c7ca605c57684c8c8d62861f19', 'e000f235b3286e140999e9989244d7e0', 'e024fec14b521ebf12c9b6ec926eaf9f', 'e1c7d97fe13e9127d225d76a1feb8c78', 'e1d18a4a63fc8ff4f5933d3516b83ffb', 'e3051e337fce58aae842ec6b02d4c7c7', 'e38cdc0771494753c7c0e451a0fef477', 'e5c19d7800b18015f3a917fc015fc42f', 'e80c1d38713975f023a894256a50f771', 'eaedbc36ab419c72fe12c3ab0b7aa58a', 'eb0c1770f8003ef04e74ce5daed81b65', 'ed1310b15b2c3828eb68f9c0213d8dce', 'ede15fb563222a59b54464ff3857badb', 'eef66829d5fc7df94d378640e68cdaa8', 'ef55590f4d699f5fdf77bdee6d72d9cf', 'ef85237f10fdf52a8677fa1c9ce82312', 'f1527abad1a3f48f330202f7296bd950', 'f15b29f8cd5dc2b290818ad676b17429', 'f250e1a4176d32a07bdd9bf2f573ba50', 'f37fc1dccfeba0004cbeb4f1ad6083c6', 'f4bc4759d52d874f23238c709b060802', 'f505befbe1ca7e2f81e475fa9e2fcc98', 'f62058acb0472858f1dce91dd0552a5c', 'f6d4f12f5952bf76014386202c1f6574', 'f81f78a345c6fbbdce40078aa2e1d44c', 'f94b7bf8ba0c95ada4451d11dd11f702', 'faf373c2d5dcceb7eca0a6492bd13105', 'fc6622c636a5210293fb2873fc4761d9', 'fccd274e718e26b32c71f188d97d9e59', 'fe067c1146518eacd1c5537f5232ed30', 'ffd660f96ba6668b2d8d86fc4e150862'
Plugin error from composition:
The following IDs are not present in the metadata: '021f9f6d5cea1fb4903d7e3b4db61d33', '0302ece4031dfaf3eac34ddbfc2c7d6f', '04b8b02dd86522f055095c2ef17286ad', '04ecfad5772d2e09a84a0f5ef460536c', '0551bb63d550ae8c8f89dacebda76822', '084f5bc37bfe2e673033d1d4c47d6377', '0a4c8bffc9aac53bd22ac6dd2c468c44', '0ab25b517ef52f4bf414661f7a6d5e9b', '0c579d21280801f02a641e1608606927', '0ddcd311e02f742e2e0e61ce02cf9c29', '10f7d3043212747fec7e8064ab2cd213', '1290e271fbc50c66e2cd8e437d0d4a44', '133862bc5656b433803da453daeb9375', '13e333f11c5a6224f6fea469b509306f', '14ff660452637cf706f1a97b7c9d2c57', '16a7d8ffc6f02f49aeadebb5f9a85829', '18a980ed927822f60eebf93600ee8ff4', '19573493f06e15f074f664ad7505ac52', '1c2b8892a0d7f828d72808cd01cfd199', '1de4896460562cae3be7c9d14bfe84cf', '1e104b993416995498346089f57fd3bf', '1e542d2112237ddb072880742ade6180', '20b3df08cd5fac2be26a2928155bab69', '220795da096a5acfebca378d68cfb00a', '23dd3ddcb8dfc1dc043713b988712ed0', '25c9884cd991eb1695f6a20546b4a231', '2b0fbcfebbfdfd18c3a90d6442985776', '2b77359306bbc33b0cb6452265701700', '2dd9e191a81b91117b77df5eac7e6048', '2ea6405c484061e2f28c03e18175c0ea', '33a198a979ec6f8252b36eb5ae643d5e', '36ecd054f5309a9658926a0926d7ee82', '377ab0ace4b9be30cbefe96d0e4192fe', '37a7a573f969549bb14095707d0a41fd', '3c3861c581adf9b8a8cf01f20fdbaf2c', '3d008a07a63e01193561eb4f27931678', '42000cb927e3155d3af5b15b0df14149', '43f8d1ced946461f54ea0b5b7001d5d6', '44349931377434a54bb432488ce41d8f', '44a96c286137bd1ef96e5a0811fd1033', '49a250849d64ca63b354b4b3281030d0', '4aebcc69b46614d3365683ba49d95dc1', '4e1f22b1dd5a8a42b8c61212342004e5', '4ef19fc863b7ff2cd97e5007547ddf7a', '4fed591b948101b5cdecaa91af4dde8b', '50275cde92eb0f51a7e19f361b869f48', '502fe0d91a4a63700820def15640e03e', '50ecca04e76cff8f632e6a69ef1add10', '5116c9fcb49e815e7bbccd35da2a5edc', '539d88c2d414548df829f33f937de8c7', '558799b297c6419c59fc5bc008ff9353', '56aedcf6ae4ccd4e92f4a6e6429fe7be', '573091d7ddd85f9c5f14a7e53d2ba0bf', '57fa2e5d2e2e046de926685af878fdd5', '581d47e597c62716475aaf024802ee58', '58b326519fbd0acb1a99c0926a104de6', '59ffa9945b1b25873c52ab906e9d4f2d', '5afec052157f7768bf459883f118a638', '5c2392591fbe650b20394fc09e9ca90c', '5e6494ce2ce4dff7e1dcbe60b1144bbc', '5f8db894a571d35c9d2fa4f8df8581f9', '60c24e14ac67927ee85a38e54d24a54e', '60d6aebce485be862de282eb2497989d', '6112d362565c5797eb555106a550d353', '6173b09cb82fab430423bf0d6bfd65a5', '6326363cc12189a386d6c9e5c711038d', '6356351ad36d913e8f7951adb0edd88e', '64d9b39739febe82181f29f7a63569b2', '685a02dea108c4edf364bb4e4b9006c7', '68c56896f754db932a51a88ebad5bc6a', '690e2d312e3f83ab4ef9893d8c5eb3ab', '695ca004c600fa100dd3a195e045eaac', '6a42f6b31b1958a4fd7c015ad7affbf4', '6d8af7f219f9fee5bebdca626bac50c4', '6ef30ad70950c7994898405da4aa1f2a', '6f35231a57c7a34013f732680c201284', '702af9e944edfd5a1a7f0dce0d566376', '70869d0feda2b000386a1851bdfcaffe', '71c85d9364bd003b2dbecd3275898630', '7433f49009bcca4a3ca6cfc7db672d08', '766462642f96a8afb24bb8056266c422', '77fb97381b583af41aec56a89b31e21c', '78a5149ffb21d2c6268bb3053f086d03', '7c9260cb39c10fef45b09ad77d5adb8f', '7df792d3bb049b81ba1bafc2049c38e6', '7e46d2d718bdf66a05368a43c52da32e', '7ead17a076e7b7b419bf50abe7eee3f4', '834408b5dea275ad6ac778a97c1414cb', '8403b6dbf52ec50c0a7b83ee636cd6e9', '860b11244363460108e1a96df96599a1', '8735f92a7f18db944bc862777fbd3222', '8a3a2d75c466b3a04af23532bb6fa6da', '8c46ebd0a248fe82636f79086d5499fd', '8ce12e88f6b59bb09494567f0d678092', '8d354b3efd44bcb690ba13412f9101a0', '8d4a33d6038a914f39e40abf0d001f06', '8e083a59abb06a47f9e349d9a45740c6', '8edc60b1393f150c44ab8546c368b6a9', '8f90932836eec8eb89164f265ebd63f5', '90790e2535c96a11d93bc0ddbc31d7b7', '92bdbee428f33594adb9ba31bab30815', '93d6a9f2d4768702315d61f6559584d9', '943a9f0fef606ac9c31536907d1e8150', '945184b6386c192c0066e0a98a154780', '95409f0f627d9bbbad895d1fd1fbb228', '95a7e70fb332ba3cda224b5fa86471f2', '99533e942a2fc83f5e47d8f9d5d69927', '9bc71d8512f20485209528c79522f3f2', '9fc55fff41bec4e5233a254867fa8829', 'a1a6090285725afd6024202a80bc47ed', 'a1d06f9ab908c1ca186f7a58357d8226', 'a26da340960942d894b28559f2430838', 'a33fcf3f1ae5cb63ec00dc2cf90e3c77', 'a4870cb22cb2f6ad880433b42d281866', 'a52ca5460d3b1b0d79e89747bcb5bd52', 'a5b90aeb2ab3b1da1ad0e3f7ab8dd3e4', 'a5e4fa1c4fdfceff6877d2ba21ae0b91', 'a9164d01308501b576afa06256a15b0f', 'aa5631f5d83e474773bbec18a4dc887d', 'ad145b5c8b7c9b7ffb1c647fa0da640d', 'ad16b779f2ec6d8afc200de7c5d2f39a', 'aed191bac0b1c3264208a084af848bed', 'aee83626bf99f96165a5c90cc9511595', 'af1eff0471fc6384606db4ad3c718bf4', 'af9f74d482cf671395fabba3dbc91081', 'afc9946b7c28e2e6500fd5f3e51c8f64', 'b34f7ad7d579d045804c113656f63eff', 'b68bc26bac6a234304e60debcf0badc8', 'b6d16645619f084c15f25f496ee50de0', 'b7f5af401f678ffbe9f7299cfa59e3bf', 'b8575d0fb2096a10b007fce89b0ee322', 'b9508e3cafc10a7910b7ad3cbd9c6c12', 'bc480af024be641e79b2536924725672', 'bcc6da5f621cbdfc1f0c9becbac6cdff', 'bd2ad00d586fbb853586dae6812f7b24', 'bd8ebcd25d5d8b78e2a417f0e855be85', 'bdf8a26094624622d68509a87fa75ba7', 'bec6480df9edec378680faa3af2b14fd', 'bf321c05d79f766c0099afb9ecc42f52', 'bfa2c70b068441a79415949856e6e9d9', 'c053c6bfc7a32d897d3dcb5ff0205190', 'c17b9f556b16dd11584378735ea5fe9d', 'c330ad54b5bc5de082da3c5bca80f16e', 'c37e7e03a26fbfce94680b5fe323d0d7', 'c59336b98498412a3a7b20ab3b1791f9', 'c757ad670c5d796cb866c941c62c4e33', 'c83102b352f538b7031b8ab74c4858c9', 'ca1fe70202213a0522f8b97c6d8b1720', 'cac706621d99e7ad647bda595c8360d2', 'cae956edaaa912def15b50e07101ce73', 'ccfb97768be91fb0df9201b46d4aa94e', 'cf3381318906e1e08f58bca905636dc0', 'd0523e63a384821e91e3db756b874650', 'd08d880f3e419559708da8cca5085c09', 'd114fb4c335125128be28401522dd41a', 'd1c2ac4bb95711b1e5f88052ee02ab55', 'd30ec6a7ed3f2a53b1ef1e93a14b8cb3', 'd68820236056c00e2edf7e6271924578', 'd6a526b572996ed919a3e009473bc860', 'd6aa1d235fa5e66393c7cd0e437ba917', 'd829bee4984f82ffc2453212157caf96', 'dac2cd571e9978b6b55c699782b22c87', 'dae7a3a5a57d7015f0125db58af1eb88', 'db42eb257100c547793051ee942fba0d', 'ddfd49f939f92958b1ec816741055348', 'ded222c7ca605c57684c8c8d62861f19', 'e000f235b3286e140999e9989244d7e0', 'e024fec14b521ebf12c9b6ec926eaf9f', 'e1c7d97fe13e9127d225d76a1feb8c78', 'e1d18a4a63fc8ff4f5933d3516b83ffb', 'e3051e337fce58aae842ec6b02d4c7c7', 'e38cdc0771494753c7c0e451a0fef477', 'e5c19d7800b18015f3a917fc015fc42f', 'e80c1d38713975f023a894256a50f771', 'eaedbc36ab419c72fe12c3ab0b7aa58a', 'eb0c1770f8003ef04e74ce5daed81b65', 'ed1310b15b2c3828eb68f9c0213d8dce', 'ede15fb563222a59b54464ff3857badb', 'eef66829d5fc7df94d378640e68cdaa8', 'ef55590f4d699f5fdf77bdee6d72d9cf', 'ef85237f10fdf52a8677fa1c9ce82312', 'f1527abad1a3f48f330202f7296bd950', 'f15b29f8cd5dc2b290818ad676b17429', 'f250e1a4176d32a07bdd9bf2f573ba50', 'f37fc1dccfeba0004cbeb4f1ad6083c6', 'f4bc4759d52d874f23238c709b060802', 'f505befbe1ca7e2f81e475fa9e2fcc98', 'f62058acb0472858f1dce91dd0552a5c', 'f6d4f12f5952bf76014386202c1f6574', 'f81f78a345c6fbbdce40078aa2e1d44c', 'f94b7bf8ba0c95ada4451d11dd11f702', 'faf373c2d5dcceb7eca0a6492bd13105', 'fc6622c636a5210293fb2873fc4761d9', 'fccd274e718e26b32c71f188d97d9e59', 'fe067c1146518eacd1c5537f5232ed30', 'ffd660f96ba6668b2d8d86fc4e150862'
See above for debug info.
Most probably the error has something to do with the filtering but I am not sure how to fix it. Could you please help me out here?
Thank you!
Cheers,
Pablo