im going through the FMT tutorial and trying to create a taxonomic bar plot of swab samples and stool samples (separately)
i'll include one example in which im trying to generate a bar plot for swab samples
ive already filtered the FeatureTable to include only swab samples
qiime feature-table filter-samples
--i-table table.qza
--m-metadata-file sample-metadata.tsv
--p-where "[sample-type]='swab'"
--o-filtered-table swab-filtered-table.qza
Output
Swab-filtered-table.qza
then filtered the FeatureSequences
qiime feature-table filter-seqs
--i-data rep-seqs.qza
--i-table swab-filtered-table.qza
--o-filtered-data swab-filtered-seqs.qza
Output
Swab-filtered-seqs.qza
i also filtered the original FMT metadata file so it includes only swab samples
i trained a feature classifier to obtain a swab-taxonomy.qza
when i try to generate a taxa bar plot of the swab-filtered samples i get the following error message
qiime taxa barplot
--i-table swab-filtered-table.qza
--i-taxonomy swab-taxonomy.qza
--m-metadata-file swab-metadata.tsv
--o-visualization taxa-bar-plots.qzv
Plugin error from taxa:
Sample IDs found in the table are missing in the metadata: {'11f3f37a.3698.4031.8183.75f6f2c6c04c', 'eb4ece61.6afe.4c88.8a06.d616dab1dd34', 'bd64992d.87cc.464f.9e1b.9c0156ed65d8', '683047f6.fe17.477f.9950.a6190ca34054', 'fe826a14.1ed8.4d19.b14d.2233b960e1bc', '1fe19636.3708.4a87.8e5a.cf10d8530d4e', '595e93ed.e4b3.42b5.91b1.1ad4f31e7134', '90120dc2.ad2e.4916.a660.633ba4b6a7b8', '04ea008a.d444.4833.988c.a2a3f5d4ad23', '59d06f37.995b.40a5.91a8.c825d1a7ca6f', 'cfe0d2d7.c78b.4092.b923.3322b4312c6d', '873473f6.eef2.4718.b5f4.e88757055760', '98c66ce0.1f4c.422c.86e9.3561ea63b612', '40112074.09e5.42b1.b332.17c9b89686e5', '558a13e5.f4a8.47bc.a63e.47d6dffe528b', 'd623471b.5a0c.4291.a780.2ae6532752a9', '98d36350.175c.439b.a534.27de6e5783ad', '593b1c57.09b3.43f2.97b1.7051761e13c9', '7e1f1b3f.4575.458c.9f42.287d03499e25', 'ea89c98c.42eb.484a.aed3.33711e20a6fe', '8cbe736d.b553.450d.af3c.d5ad08863390', 'c1a66804.c565.448a.8371.0c8e386f4969', 'c287751e.0263.4fda.8aa2.3b717855e2ee', 'c61b44a5.ae92.4202.9d0c.b4507197e456', 'e7a2370c.f80c.4703.b2ee.10c65967e05f', 'cfc37a70.9ba6.4d25.b541.4c0ff9d1bfeb', '124dc1db.9029.41c6.afff.b73a692e19b1'}.
i dont understand this because the table.qza has been filtered to include only swab samples and the metadata file itself has also been filtered to include only the swab samples - so why is qiime expecting additional feature IDs to be present in the table which are absent from the metadata? (these feature IDs refers to those features which are not swab related - they are stool samples)
included all files which have been mentioned and needed to generate the taxa bar plot
swab-metadata.tsv (8.2 KB) swab-taxonomy.qza (94.6 KB) swab-filtered-seqs.qza (77.2 KB) swab-filtered-table.qza (46.6 KB)