All ``feature_ids`` must be present as tip names in ``phylogeny`

lostmouse · May 28, 2020, 2:03pm

Hi,

I am new to Qiime and have only spent a week or so pulling my hair.

I am trying to generate some beta diversity plots relating some 16S gut samples.

I executing the following commands:

qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree_exp1_2_3.qza
--i-table Table_Freq_EXP11_12_13.qza
--p-sampling-depth 1000
--m-metadata-file Metadata_exp11_12_13_Valid.txt
--output-dir core_metrics_results

I get the following error:

/Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/sklearn/metrics/pairwise.py:1735: DataConversionWarning: Data was converted to boolean for metric jaccard
warnings.warn(msg, DataConversionWarning)
/Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:152: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.05259711795033266 and the largest is 7.863737098882202.
RuntimeWarning
/Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:152: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.24217353423261714 and the largest is 8.119482582194188.
RuntimeWarning
Traceback (most recent call last):
File "/Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_diversity/_alpha/_method.py", line 54, in alpha_phylogenetic
tree=phylogeny)
File "/Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/skbio/diversity/_driver.py", line 170, in alpha_diversity
counts, otu_ids, tree, validate, single_sample=False)
File "/Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/skbio/diversity/alpha/_faith_pd.py", line 136, in _setup_faith_pd
_validate_otu_ids_and_tree(counts[0], otu_ids, tree)
File "/Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/skbio/diversity/_util.py", line 104, in _validate_otu_ids_and_tree
" ".join(missing_tip_names)))
skbio.tree._exception.MissingNodeError: All otu_ids must be present as tip names in tree. otu_ids not corresponding to tip names (n=557): 1160 1240 717 72 514 876 825 747 621 822 858 453 851 208 207 383 673 922 84 1237 830 674 1209 366 719 10 73 893 33 1115 601 872 1095 96 182 646 395 1143 1135 1107 1079 1096 452 1219 356 908 549 14 175 1057 52 407 1011 1148 1027 17 577 527 268 1264 956 424 467 1047 415 1072 190 1162 511 1068 1249 1051 382 768 874 1086 1097 217 1164 884 507 103 380 1030 1167 495 174 128 429 1025 252 980 362 712 1262 29 30 655 647 910 1247 186 303 421 767 404 663 282 665 97 623 641 274 107 0 210 74 115 191 644 12 1112 9 28 78 600 40 161 784 901 1033 1141 1099 257 561 1127 585 676 1136 304 92 285 231 944 1191 1175 277 126 917 1120 473 170 502 1253 921 83 1165 70 414 111 713 443 619 1083 995 589 1172 920 493 794 399 155 446 875 288 795 863 195 94 11 62 1125 295 656 812 1198 567 700 1223 134 868 1074 1186 730 731 168 750 279 1016 894 1013 124 476 571 269 89 938 1038 1218 159 45 81 202 1192 223 197 243 1222 651 1111 86 393 392 16 528 587 791 693 862 701 69 697 1202 435 1084 127 188 34 675 997 1133 888 233 1022 401 218 834 213 1138 7 823 235 566 163 575 1019 857 136 440 698 1094 192 664 289 370 953 586 579 643 594 457 524 1085 501 171 1034 125 1056 850 559 529 1109 1217 273 329 433 439 363 318 491 229 374 466 503 965 723 671 912 272 151 932 71 271 183 300 432 899 283 526 66 627 255 1062 605 381 821 149 1031 1169 88 1073 203 164 344 630 961 1174 322 123 313 106 118 172 861 1113 537 121 556 287 576 114 598 616 833 354 755 327 1005 582 215 840 442 918 1076 31 1061 889 1001 530 764 219 438 458 702 517 800 808 1014 778 242 290 680 548 553 679 845 1254 1225 18 509 926 1026 686 999 1193 241 1046 1078 201 705 624 1242 954 892 883 142 572 225 21 205 198 578 909 1075 1029 112 809 291 745 541 46 1236 24 1063 143 311 709 22 607 756 640 369 687 90 211 504 945 376 981 787 947 618 915 426 1155 116 64 15 65 196 765 963 762 375 216 555 240 138 342 769 42 305 706 782 397 1060 412 1118 1035 1119 456 1088 51 849 135 610 817 714 76 385 1117 162 236 614 102 1070 131 262 199 461 890 405 652 583 1166 87 253 666 455 933 653 265 710 148 19 35 990 720 987 725 1250 337 328 275 542 193 120 340 2 154 436 1080 481 1055 986 881 551 428 425 1228 1146 781 82 454 220 683 716 437 1132 609 101 852 886 1221 510 263 336 667 1173 1201 505 1087 93 626 992 450 293 1 1102 1255 608 775 525 129 44 1054 855

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "</Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-386>", line 2, in core_metrics_phylogenetic
File "/Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 484, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_diversity/_core_metrics.py", line 57, in core_metrics_phylogenetic
metric='faith_pd')
File "</Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-477>", line 2, in alpha_phylogenetic
File "/Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/Users/xxx/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_diversity/_alpha/_method.py", line 58, in alpha_phylogenetic
raise skbio.tree.MissingNodeError(message)
skbio.tree._exception.MissingNodeError: All feature_ids must be present as tip names in phylogeny. feature_ids not corresponding to tip names (n=557): 1160 1240 717 72 514 876 825 747 621 822 858 453 851 208 207 383 673 922 84 1237 830 674 1209 366 719 10 73 893 33 1115 601 872 1095 96 182 646 395 1143 1135 1107 1079 1096 452 1219 356 908 549 14 175 1057 52 407 1011 1148 1027 17 577 527 268 1264 956 424 467 1047 415 1072 190 1162 511 1068 1249 1051 382 768 874 1086 1097 217 1164 884 507 103 380 1030 1167 495 174 128 429 1025 252 980 362 712 1262 29 30 655 647 910 1247 186 303 421 767 404 663 282 665 97 623 641 274 107 0 210 74 115 191 644 12 1112 9 28 78 600 40 161 784 901 1033 1141 1099 257 561 1127 585 676 1136 304 92 285 231 944 1191 1175 277 126 917 1120 473 170 502 1253 921 83 1165 70 414 111 713 443 619 1083 995 589 1172 920 493 794 399 155 446 875 288 795 863 195 94 11 62 1125 295 656 812 1198 567 700 1223 134 868 1074 1186 730 731 168 750 279 1016 894 1013 124 476 571 269 89 938 1038 1218 159 45 81 202 1192 223 197 243 1222 651 1111 86 393 392 16 528 587 791 693 862 701 69 697 1202 435 1084 127 188 34 675 997 1133 888 233 1022 401 218 834 213 1138 7 823 235 566 163 575 1019 857 136 440 698 1094 192 664 289 370 953 586 579 643 594 457 524 1085 501 171 1034 125 1056 850 559 529 1109 1217 273 329 433 439 363 318 491 229 374 466 503 965 723 671 912 272 151 932 71 271 183 300 432 899 283 526 66 627 255 1062 605 381 821 149 1031 1169 88 1073 203 164 344 630 961 1174 322 123 313 106 118 172 861 1113 537 121 556 287 576 114 598 616 833 354 755 327 1005 582 215 840 442 918 1076 31 1061 889 1001 530 764 219 438 458 702 517 800 808 1014 778 242 290 680 548 553 679 845 1254 1225 18 509 926 1026 686 999 1193 241 1046 1078 201 705 624 1242 954 892 883 142 572 225 21 205 198 578 909 1075 1029 112 809 291 745 541 46 1236 24 1063 143 311 709 22 607 756 640 369 687 90 211 504 945 376 981 787 947 618 915 426 1155 116 64 15 65 196 765 963 762 375 216 555 240 138 342 769 42 305 706 782 397 1060 412 1118 1035 1119 456 1088 51 849 135 610 817 714 76 385 1117 162 236 614 102 1070 131 262 199 461 890 405 652 583 1166 87 253 666 455 933 653 265 710 148 19 35 990 720 987 725 1250 337 328 275 542 193 120 340 2 154 436 1080 481 1055 986 881 551 428 425 1228 1146 781 82 454 220 683 716 437 1132 609 101 852 886 1221 510 263 336 667 1173 1201 505 1087 93 626 992 450 293 1 1102 1255 608 775 525 129 44 1054 855

I would note that I have imported a number of partially processed files to get to this point. Qiime seemed satisfied with my imported files:

a .biom table with my OTU frequencies per sample formatted to match the metadata. (BIOMV210Format)
A fasta file of unaligned sequences converted to an .fna file formatted to match the biom table data, especially the #OTU_ID column consists of otus labelled by number only from 0 to 1265
values are delineated by tabs in all the precursor files.
The only thing off here I can think of is that the fasta file includes the representative sequence which is not included in the biom table. I used the format of the sequences.fna / sequences.qza example.
a metadata file was formatted against the qiime sample-metadata.tsv format, except a txt.

I have painstakingly removed all the "_" which I thought was the problem before.

These commands were executed before the error commands successfully:

qiime tools import
--input-path collapsed_ref_OTUs_97_pct_rep_seqs_Silva_v108_untrimmed2.fna
--output-path RepSeq_Exp1_2_3.qza
--type 'FeatureData[Sequence]'

biom convert -i Table_Match_Metadata_countsMatrix_collapsed_ref_OTUs_97_pct_rep_seqs_Silva_v108_untrimmed22.txt -o EXP11_12_13.biom --to-hdf5 --table-type="OTU table" --process-obs-metadata taxonomy

qiime tools import
--input-path EXP11_12_13.biom
--type 'FeatureTable[Frequency]'
--input-format BIOMV210Format
--output-path Table_Freq_EXP11_12_13.qza

qiime feature-table summarize
--i-table Table_Freq_EXP11_12_13.qza
--o-visualization FreqTable_exp1_2_3.qzv
--m-sample-metadata-file Metadata_exp11_12_13_Valid.txt
qiime feature-table tabulate-seqs
--i-data RepSeq_Exp1_2_3.qza
--o-visualization seq_exp1_2_3.qzv

qiime phylogeny align-to-tree-mafft-fasttree
--i-sequences RepSeq_Exp1_2_3.qza
--o-alignment aligned-rep-seqs_exp1_2_3.qza
--o-masked-alignment masked-aligned-rep-seqs_exp1_2_3.qza
--o-tree unrooted-tree_exp1_2_3.qza
--o-rooted-tree rooted-tree_exp1_2_3.qza

runnning qiime2-2020.2

Huge thanks to anyone who can tell me where my wrong turn is. At this point I'm thinking I need to start with the sequencer raw outputs.

Thanks!

jwdebelius · May 28, 2020, 2:52pm

Hi @lostmouse ,

Welcome to the :qiime2: forum.

The error says that the name of the tips in the tree and the name of the features in your table don't line up. Which probably means that the names of the sequences you imported for maftt alignment didn't match the names in your table.

How did you build your feature table? Where do the rep set come from?

Best,
Justine

lostmouse · May 29, 2020, 1:53pm

Hi Justin,
The feature table had already been constructed as had the fasta file with the rep set. I converted them both. The data by appearance lines up when I view it, but I did have to make some changes in order to get qiime to accept the file. The fasta file was not recognized as a DNA fasta file until I executed some edits on the original file with unix commands.
.fna sequence data: first 4 lines

0 EU136690.1.2033 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;Bacteroides salyersiae
GTTTGATCCTGGCTCAGGATGAACGCTAGCTACAGGCTTAACACATGCAAGTCGAGGGGCATCAGGGTGTAGCAATACACCGCTGGCGACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCCTTTACTCGGGGATAGCCTTTCGAAAGAAAGATTAATACCCGATGGTATAACATGACCTCCTGGTTTTGTTATTAAAGAATTTCGGTAGAGGATGGGGATGCGTTCCATTAGGCAGTTGGCGGGGTAACGGCCCACCAAACCTTCGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAAACTCCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTAGCGTGAAGGATGACCGCCCTATGGGTTATAAACTTCTTTTATATGGGAATAAAGGGTGCCACGTGTGGCATTTTGTATGTACCATATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACATGTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGCGTGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACCGATGCTCGAAAGTGTGGGTATCAAACAGGATTAGATACCCTGGTAGTCCACACAGTAAACGATGAATACTCGCTGTTTGCGATATACAGTAAGCGGCCAAGCGAAAGCATTAAGTATTCCACCTGGGGAGTACGCCGGCAACGGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGAGGAACATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCCGGGCTTAAATTGCAAATGAATATGCCGGAAACGGCATAGCCGCAAGGCATTTGTGAAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTATCTTCAGTTACTAACAGGTTATGCTGAGGACTCTGGAGAGACTGCCGTCGTAAGATGTGAGGAAGGTGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCTACACACGTGTTACAATGGGGGGTACAGAAGGCCGCTACACAGCGATGTGATGCCAATCCCTAAAGCCCCTCTCAGTTCGGATCGAAGTCTGCAACCCGACTTCGTGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCAAGCCATGGGAGCCGGGGGTACCTGAAGTACGTAACCGCAAGGAGCGTCCTAGGGTAAAACTGGTGACTGGGGCTAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGAACACCTCCTTTCTGGAGCGATGCCGTAAAGGGCGTCCATTTCCGGTTCTGAATGTACTACTGGTACTTGTTTATTTATAGCATATAGAATCGACCGTCTATATTATATTATAGAATAGAGATAAACAAGAAGAAAGAAGAAGCCGAGCCGCATGGCGAGGTTGAACTAGTCCTATAGCTCAGTTGGTTAGAGCGCTACACTGATAATGTAAAGGTCGGCAGTTCAACTCTGCCTGGGACTACTTCCGCAAGTCGACGCCTGGTGGATTGCGAGCCTGAAATTACACTTTCAACTCTCAACTTCCAACTTTCAACTTGTACGAAGGGGGATTAGCTCAGCTGGCTAAAGCATCTGCCTTGCACGCAAAGGGTCAACGGTTCGAATCCGTTATTCTCCACTCCGCTTCGGATTGCCGGTTGTCAAAGGACGACTGACAGTTTAGGGCAAACGATCTTTGACATGATGTACAAAAAGTAAATTTTAGTAAAGAGCTAAAAGTATATATCAAACCGTAGTGTTTCGATTTTGGAT
1 M69264.499.2294 Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium;Clostridium perfringens
GTCACTAAGGACGGGCAACAAAAAAAGACAATAAGTTGAAAGAAAACAACTTAAAAAGTTTTTTAAAAAAAGTGTTGACAAAGTTCGAAGGTGATGATAAAATAAAGAAGTCGCTTGAGGGCGACAATGAAATGGTCTTTGAAAATTAAACAGAAGATATTAACATAAACCAGCAATTCTTTTATAAGTAATATGAGTATAGATTAAACTTTTAAATTGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAGCGATGAAGTTTCCTTCGGGAAACGGATTAGCGGCGGGACGGGTGAGTAACACGTGGGTAACCTGCCTCATAGAGTGGAATAGCCTTCCGAAAGGAAGATTAATACCTCATAATGTTGAAAGATGGCATCATCATTCAACCAAAGGAGCAATCCGCTATGAGATGGACCCGCGGCGCATTAGCTAGTTGGTGGGGTAACGGCCTACCAAGGCGACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTCTTTGGGGAAGATAATGACGGTACCCAAGGAGGAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCGAGCGTTATCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGATGATTAAGTGGGATGTGAAATACCCGGGCTCAACTTGGGTGCTGCATTCCAAACTGGTTATCTAGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGACTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAATACTAGGTGTGGGGGTTTCAACACCTCCGTGCCGCCGCTAACGCATTAAGTATTCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGTAGCGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCTACACTTGACATCCCTTGCATTACTCTTAATCGAGGAAATCCTTCGGGGACAAGGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCGTTAGTTACTACCATTAAGTTGAGGACTCTAGCGAGACTGCCTGGGTTAACCAGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTGTAGGGCTACACACGTGCTACAATGGCTGGTACAGAGAGATGCAATACCGCGAGGTGGAGCCAAACTTAAAAACCAGTCTCAGTTCGGATTGTAGGCTGAAACTCGCCTACATGAAGCTGGAGTTACTAGTAATCGCGAATCAGAATGTCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGAGAGTTGGCAATACCCGAAGTCCGTGAGCTAACCGCAAGGAGGCAGCGGCCGAAGTAGGGTCAGCGATTGGGGTGAAGTCGTAACAAGGTAGCCGTAGGAGAACCTGCGGCTGGATCACCTCCTTTCTAAGGAATACATCTTAGGACAACTAAGATGACAATGAATTCTGGATAATATCTCTGTTTAATTTTGAGAGA

Here is the data table text which I have tried converting to both biom v1 and v2 format files (first 4 lines):

#OTU ID Sample.1.Hu.I1 Sample.10.G1.I1.Chex Sample.11.G1.I2.Chex Sample.12.HuCI.Gavage.1.2.Chex Sample.13.G1I.Gavage.Chex Sample.14.2ndG3.Exp11.Gavage.Chex Sample.15.HuCI.Gavage.3.4.Chex Sample.16.HuC.M1.Gavage.Chex Sample.17.HuCM2.Gavage.Chex Sample.18.HuCM3.Gavage.Chex Sample.19.HuCM4.Gavage.CheSample.2.Hu.I2 Sample.20.HuCM5.Gavage.Chex Sample.21.HuC.I3 Sample.22.HuC.I4 Sample.23.HuCM1A Sample.24.HuCM1B Sample.25.HuCM2A Sample.26.HuCM2B Sample.27.HuCM3A Sample.28.HuCM3B Sample.29.HuCM4A Sample.3.G1.I1 Sample.30.HuCM4B Sample.31.HuCM5A Sample.32.HuCM5B Sample.33.2ndG3.Exp13 Sample.34.PBS.Exp13 Sample.35.HuCI.619.Chex Sample.36.HuCI.620.Chex Sample.37.HuCI.621.Chex Sample.38.HuCI.622.Chex Sample.39.HuCI.623.Chex Sample.4.G1.I2 Sample.40.HuCI.624.Chex Sample.41.HuCI.625.Chex Sample.42.HuCI.626.Chex Sample.43.HuCI.627.Chex Sample.44.HuCI.628.Chex Sample.45.HuCI.629.Chex Sample.46.HuCI.630.Chex Sample.47.HuCI.631.Chex Sample.48.HuCI.632.Chex Sample.49.HuCI.633.Chex Sample.5.HuC.Fresh Sample.50.HuCI.634.Chex Sample.51.2ndG3.Exp12.13.Gavage Sample.52.HuC.Fresh Sample.53.HuC.Fresh Sample.54.1.10.DilutionGavage Sample.55.1.33.DilutionGavage Sample.56.1.66.DilutionGavage Sample.57.1.100.DilutionGavage Sample.58.1.1000.DilutionGavage Sample.59.1.0.NoDilution Sample.6.2ndG3.Exp11 Sample.60.1.0.G1.Isolates Sample.61.1.10.Dilution Sample.62.1.10.G1.Isolates Sample.63.1.33.Dilution Sample.64.1.33.G1.Isolates Sample.65.1.66.Dilution Sample.66.1.66.G1.IsolatesSample.67.1.100.Dilution Sample.68.1.100.G1.Isolates Sample.69.1.1000.Dilution Sample.7.PBS.Exp11 Sample.70.1.1000.G1.Isolates Sample.71.PBS.Exp1Sample.72.PBS.G1.Isolates Sample.73.PBS.Exp13.d0 Sample.74.HM5A.d0 Sample.75.HM4A.d0 Sample.76.PBS.Exp13.wk3 Sample.77.HM5A.wk3 Sample.78.HM4A.wk3 Sample.79.HM3A.wk3 Sample.8.Hu.I1.Chex Sample.80.HM2A.wk3 Sample.81.HM1A.wk3 Sample.82.HuI3.wk3 Sample.9.Hu.I2.Chex Rep.Seq.Taxonomy
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;Bacteroides salyersiae
1 319 1 41 7429 0 3 3762 6714 6540 6803 15217 305 7998 112 333 3252 363 897 2457 96254 1313 2 80 10357 294 0 1 2 0 0 1 0 1 1 9 67 23117 19089 18851 14670 18 0 20793 1 20161 0 1 2 1 3 1 0 6 0 0 0 0 1 0 0 80 338 338 153 107 134 115 208 Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium;Clostridium perfringens
2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;mitochondria;uncultured bacterium

Here is the Metadata txt file (first 4):

SampleID	BarcodeSequence	LinkerPrimerSequence	ReverseBarcode	ReversePrimer	fwd	rev	Description
Sample.1.Hu.I1	CGACAA	AGAGTTTGATCCTGGCTCAG	AAGC	ATTACCGCGGCTGCTGG	PE1-F9	PE2-R1	MoBio Pre challenge 4 weeks
Sample.2.Hu.I2	CGACAA	AGAGTTTGATCCTGGCTCAG	TACC	ATTACCGCGGCTGCTGG	PE1-F9	PE2-R2	MoBio Pre challenge 4 weeks
Sample.3.G1.I1	CGACAA	AGAGTTTGATCCTGGCTCAG	CTAC	ATTACCGCGGCTGCTGG	PE1-F9	PE2-R3	MoBio Pre challenge 4 weeks

If this isn't the problem the OTU table was edited from:

OTU_ID Sample.1.HuI1 Sample.10.G1I1 Sample.11.G1I2 Sample.12.HuI_Gavage Sample.13.G1I_Gavage Sample.14.2_deg.G3_Gavage_Exp_11 Sample.15.HuCI_Gavage Sample.16.HuCM1_Gavage Sample.17.HuCM2_Gavage Sample.18.HuCM3_Gavage Sample.19.HuCM4_Gavage Sample.2.HuI2 Sample.20.HuCM5_Gavage Sample.21.HuCI3 Sample.22.HuCI4 Sample.23.HuCM1A Sample.24.HuCM1B Sample.25.HuCM2A Sample.26.HuCM2B Sample.27.HuCM3A Sample.28.HuCM3B Sample.29.HuCM4A Sample.3.G1I1 Sample.30.HuCM4B Sample.31.HuCM5A Sample.32.HuCM5B Sample.33.2_deg_G3_Exp_13 Sample.34.PBS_Exp_13 Sample.35.HuCI_619 Sample.36.HuCI_620 Sample.37.HuCI_621 Sample.38.HuCI_622 Sample.39.HuCI_623 Sample.4.G1I2 Sample.40.HuCI_624 Sample.41.HuCI_625 Sample.42.HuCI_626 Sample.43.HuCI_627 Sample.44.HuCI_628 Sample.45.HuCI_629 Sample.46.HuCI_630 Sample.47.HuCI_631 Sample.48.HuCI_632 Sample.49.HuCI_633 Sample.5.HuC_Fresh Sample.50.HuCI_634 Sample.51.2_deg_G3_Gavage_Exp_12_13 Sample.52.HuC_Fresh Sample.53.HuC_Fresh Sample.54.1_10_Dilution Sample.55.1_33_Dilution Sample.56.1_66_Dilution Sample.57.1_100_Dilution Sample.58.1_1000_Dilution Sample.59.1_0_No_Dilution Sample.6.2_deg_G3_Exp_11 Sample.60.1_0_G1_Isolates Sample.61.1_10_Dilution Sample.62.1_10_G1_Isolates Sample.63.1_33_Dilution Sample.64.1_33_G1_Isolates Sample.65.1_66_Dilution Sample.66.1_66_G1_Isolates Sample.67.1_100_Dilution Sample.68.1_100_G1_Isolates Sample.69.1_1000_Dilution Sample.7.PBS_Exp_11 Sample.70.1_1000_G1_Isolates Sample.71.PBS Sample.72.PBS_G1_Isolates Sample.73.PBS_d0 Sample.74.HM5A_d0 Sample.75.HM4A_d0 Sample.76.PBS_wk3 Sample.77.HM5A_wk3 Sample.78.HM4A_wk3 Sample.79.HM3A_wk3 Sample.8.HuI1 Sample.80.HM2A_wk3 Sample.81.HM1A_wk3 Sample.82.HuI3_wk3 Sample.9.HuI2 Rep_Seq_Accession Rep_Seq_Taxonomy
0 0 0 0 0 0 0 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 0 0 0 0 0 0 EU136690.1.2033 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;Bacteroides salyersiae
1 319 1 41 7429 0 3 3762 6714 6540 6803 15217 305 7998 112 333 3252 363 897 2457 966 254 1313 2 80 10357 294 0 67 23117 19089 18851 14670 18 0 20793 1 20161 0 1 2 1 80 338 338 153 107 134 115 208 M69264.499.2294 Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium;Clostridium perfringens

Maybe there is something I am doing here that is mismatching? I think time wise it may make more sense to start with the original MiSeq raw reads, or some precursor file. The files I am working with were all prepared by a bioinformatics professional exterior to our immediate lab.

Best,
James

jwdebelius · May 29, 2020, 3:18pm

Hi @lostmouse,

I think you need to re-format your table so your Rep_Seq_Accession is your first column, and rename that #OTU_ID and that you want to use only that value as your identifier in your fasta file.

Best,
Justine

lostmouse · May 29, 2020, 6:09pm

That is not a bad idea!

lostmouse · May 29, 2020, 9:00pm

I got the same error essentially.

Plugin error from diversity:

All feature_ids must be present as tip names in phylogeny. feature_ids not corresponding to tip names (n=555): EU456972.1.1394 EF099267.1.1398 FJ880681.1.1492 EU344650.1.1369 FJ679707.1.1457 GQ493778.1.1370 EU457149.1.1397 HM817960.1.1353 FJ685482.1.1392 GQ897252.1.1492 GQ897130.1.1493 EU503886.1.1397 M61903.1.1530 HM840818.1.1347 FM872953.1.1482 EU457921.1.1400 EU454375.1.1404 EU474224.1.1395 HM812324.1.1364 GQ451192.1.1488 GQ897449.1.1490 FM873896.1.1501 JF241909.1.1369 EF405056.1.1496 EF097738.1.1401 DQ809181.1.1397 DQ808574.1.1375 EU511534.1.1394 EF604624.1.1508 JF188128.1.1332 FJ685443.1.1390 EU456334.1.1382 EU505041.1.1377 GQ898470.1.1506 JF163215.1.1332 HM844961.1.1353 EU504370.1.1386 EU507215.1.1395 FJ189568.1.1449 GQ011110.1.1358 GQ492535.1.1351 FJ880662.1.1493 HM317292.1.1352 HM845124.1.1357 AB298748.1.1365 HM845007.1.1355 GQ898705.1.1490 EU510229.1.1415 EF096693.1.1383 EF097871.1.1376 EU509517.1.1393 EF404064.1.1476 HQ216289.1.1244 DQ777935.1.1493 FN563338.1.1452 DQ793433.1.1408 AB606333.1.1493 EF096279.1.1401 EF406724.1.1497 JF229305.1.1317 JF237691.1.1353 EU510563.1.1392 HM124063.1.1490 EU773881.1.1364 EF603177.1.1474 EU509521.1.1388 EF098335.1.1408 AF371829.1.1421 GQ897986.1.1510 X75908.1.1388 EU773890.1.1371 EU455701.1.1401 JF178661.1.1352 HM829348.1.1353 EU455707.1.1389 EU775796.1.1353 JF177963.1.1342 JF234019.1.1368 EU775706.1.1375 EU459172.1.1378 EU778931.1.1400 DQ809292.1.1383 EF602979.1.1482 JF206641.1.1346 EU790971.1.1496 DQ809794.1.1373 EF603861.1.1491 EU455091.1.1392 GU321101.1.1528 GQ492499.1.1357 EU505093.1.1405 GQ493546.1.1366 GQ897948.1.1489 EU454999.1.1392 EU459282.1.1372 EU457659.1.1396 DQ795841.1.1381 GQ448577.1.1294 HM837785.1.1356 EU510342.1.1420 GQ493569.1.1357 EU774678.1.1378 GQ898422.1.1492 EF096652.1.1403 EU778584.1.1376 EU469620.1.1405 GQ896712.1.1521 EU509490.1.1390 HQ716476.1.1449 HM124074.1.1469 DQ797604.1.1374 JF240740.1.1354 M59107.1.1511 EU622676.1.1496 EU505561.1.1408 DQ824449.1.1394 EF099977.1.1381 EU450939.1.1395 EU505574.1.1392 EF098154.1.1313 GQ897283.1.1492 JF052873.1.1355 GU455323.1.1490 GQ898349.1.1488 DQ804411.1.1397 JF161585.1.1330 EF099393.1.1390 EF097056.1.1397 EU457712.1.1408 EU509459.1.1405 EU778974.1.1385 FJ367126.1.1352 GU304171.1.1498 EU455602.1.1395 EU774128.1.1378 GQ897382.1.1488 FM872889.1.1475 DQ800248.1.1398 JF239113.1.1360 DQ797658.1.1393 HM824844.1.1353 EF603800.1.1486 EU452471.1.1389 GQ898390.1.1518 FJ503221.1.1378 EU510149.1.1401 FJ363833.1.1357 EU455663.1.1397 ABQR01000074.99.1621 FM873958.1.1463 GQ493722.1.1366 HM841500.1.1354 EU775644.1.1361 EF099798.1.1396 EF402506.1.1494 DQ805636.1.1390 EU451895.1.1402 EF099620.1.1401 GQ897266.1.1493 EU509452.1.1391 EF098212.1.1399 JF161690.1.1336 GQ896847.1.1487 JF204728.1.1347 EU474417.1.1312 JF241278.1.1380 GQ897319.1.1489 EU456344.1.1394 JF142175.1.1350 GQ477907.1.1519 AB606316.1.1496 EU510309.1.1403 EF099229.1.1392 EU511192.1.1394 DQ793718.1.1395 EU765955.1.1345 GQ897174.1.1458 EF098192.1.1353 AM162306.1.1496 FJ505595.1.1388 GQ448965.1.1384 EU504380.1.1377 DQ795340.1.1389 EU508990.1.1391 FJ880682.1.1491 FJ880925.1.1490 EU455192.1.1405 EU454521.1.1391 EU507860.1.1381 EF098973.1.1393 AB600999.1.1490 EU452543.1.1402 EU778902.1.1270 EU511065.1.1410 FJ364566.1.1365 HM287124.1.1354 AB626951.1.1499 EU504186.1.1398 EU451381.1.1394 EU881319.1.1481 JF237653.1.1356 GQ897209.1.1487 FJ366005.1.1355 DQ905281.1.1486 EU510634.1.1381 EF099207.1.1391 EU504105.1.1404 GQ897023.1.1480 EF403240.1.1474 EU511801.1.1404 EU451140.1.1406 EU455130.1.1398 EU775717.1.1361 EU765919.1.1353 HM828395.1.1353 EU509936.1.1393 FJ679782.1.1473 HQ703912.1.1457 EU505639.1.1398 EU509971.1.1375 EF603948.1.1479 EU457943.1.1404 EF096140.1.1394 JF223124.1.1284 EU455556.1.1402 HM839084.1.1352 EU507473.1.1384 DQ795356.1.1397 GQ897982.1.1472 JF164745.1.1264 EU505258.1.1394 EU451961.1.1397 JF124473.1.1355 X73437.1.1498 EU510699.1.1401 JF211111.1.1353 FJ881355.1.1479 EF096107.1.1403 EF406549.1.1479 GQ493333.1.1374 AM157418.1.1575 HQ400141.1.1493 EU775984.1.1375 FJ368647.1.1359 JF162239.1.1352 FJ716002.1.1493 FJ879403.1.1494 FN563298.1.1428 GQ898843.1.1499 HM255371.1.1345 EU452170.1.1394 JF233248.1.1359 GQ492824.1.1379 GQ159246.1.1476 EF603423.1.1484 Y18174.1.1479 FR733682.1.1494 FJ504462.1.1377 FJ509217.1.1371 GQ175474.1.1451 EU777763.1.1358 HM124257.1.1495 DQ904727.1.1491 DQ798997.1.1369 EU455030.1.1390 EU457772.1.1395 EU505414.1.1393 HM846625.1.1354 EU006347.1.1493 FJ368968.1.1365 JF163921.1.1351 DQ806037.1.1412 FJ367796.1.1360 JF127027.1.1354 EU454004.1.1391 FJ511003.1.1381 EF604619.1.1518 EU456482.1.1379 EU509117.1.1393 EF098985.1.1401 EU778599.1.1375 EU455375.1.1390 GU304431.1.1503 AB606239.1.1494 DQ807609.1.1405 EF408243.1.1494 AB606269.1.1510 EU006341.1.1471 GQ898394.1.1486 EU772909.1.1382 JF162747.1.1332 EU504958.1.1362 EU505646.1.1399 EU511989.1.1380 EF406793.1.1486 EU457084.1.1390 EU534562.1.1390 DQ905591.1.1501 EU456875.1.1393 EU776887.1.1390 EU505058.1.1384 FJ503713.1.1343 EU506537.1.1401 EU457878.1.1392 EU771517.1.1377 EU455136.1.1393 FM873805.1.1485 GQ897417.1.1495 EF401651.1.1485 EU504216.1.1399 EU510736.1.1393 JF162928.1.1356 EU509846.1.1415 EF096766.1.1404 JF231771.1.1370 FJ879272.1.1498 X73440.1.1526 JF180686.1.1348 EF100054.1.1403 EU508236.1.1378 HM459667.1.1598 DQ815472.1.1461 EU451143.1.1396 FJ372297.1.1359 EU456614.1.1395 FJ681199.1.1382 EU503954.1.1388 HM124080.1.1492 EU506210.1.1356 FJ880895.1.1488 HQ716212.1.1452 EU511225.1.1391 EU510501.1.1393 EU511139.1.1394 GQ493752.1.1375 GQ897959.1.1477 AJ308386.1.1462 EF099895.1.1383 HM845462.1.1354 EU474401.1.1390 EU775022.1.1388 AM405127.1.1487 EU452973.1.1406 Y18187.1.1550 EU452573.1.1412 EF404854.1.1491 EU506171.1.1401 EU508111.1.1390 EU136690.1.2033 FJ881243.1.1487 EF406423.1.1471 GQ898126.1.1466 GQ896986.1.1478 EU773887.1.1377 X73451.1.1501 EU452237.1.1403 EU887823.1.1452 AJ715378.1.1489 DQ810119.1.1400 HM124326.1.1493 HM837060.1.1396 EU505619.1.1394 EU510380.1.1404 HM812919.1.1331 FM873875.1.1480 HM844568.1.1352 DQ808599.1.1393 GQ449097.1.1378 EU511005.1.1388 EU939412.1.1505 EU454731.1.1393 EU457743.1.1393 EU450964.1.1384 JF059568.1.1363 GQ159184.1.1472 AY572476.1.1548 EF098415.1.1384 JF504704.1.1498 EU509800.1.1386 JF121622.1.1346 GQ898088.1.1492 EU455958.1.1398 DQ905779.1.1515 GQ493969.1.1362 HM830915.1.1332 M58679.1.1457 FJ879355.1.1484 Y18188.1.1489 EU510538.1.1402 GQ898845.1.1491 EU862559.1.1520 JF241936.1.1367 DQ806205.1.1382 GQ896605.1.1491 HM831798.1.1350 M23732.1.1480 EU778942.1.1391 HM277769.1.1338 EU455974.1.1374 DQ800999.1.1400 EU454523.1.1392 DQ799932.1.1393 EF406417.1.1463 GQ448949.1.1400 DQ804909.1.1390 EU504716.1.1407 HM845702.1.1344 EU506909.1.1400 GQ897714.1.1491 EU508214.1.1391 DQ824068.1.1380 FJ367654.1.1336 EF602805.1.1436 EU773188.1.1362 GQ897002.1.1483 EU450945.1.1390 EU504001.1.1389 HM630157.1.1425 EU775710.1.1376 EU505206.1.1376 FJ880484.1.1489 DQ824505.1.1401 EF096208.1.1399 HM306045.1.1355 EU508100.1.1372 EU460771.1.1421 GQ897925.1.1489 EU508902.1.1403 GQ898687.1.1485 FJ512049.1.1346 HM124306.1.1486 EU505522.1.1387 FJ880298.1.1492 DQ905814.1.1554 HM844611.1.1324 AJ853737.1.1552 EU504140.1.1390 EU460122.1.1346 EF434341.1.1349 JF161763.1.1353 EU776621.1.1349 EU503942.1.1403 DQ905711.1.1583 EU887815.1.1465 EU773775.1.1373 AM697541.1.1481 AY992253.1.1280 EU504059.1.1390 EF402828.1.1485 GQ898776.1.1487 FJ365183.1.1339 EU457286.1.1391 EF098242.1.1417 HM844675.1.1352 GQ491217.1.1331 HM845633.1.1354 EF402716.1.1494 GQ448417.1.1415 EU777650.1.1359 AB606258.1.1495 AB447716.1.1452 EU506958.1.1376 GQ898637.1.1476 DQ801101.1.1393 JF161844.1.1333 FJ369761.1.1380 GQ175368.1.1453 DQ795795.1.1380 HM008264.1.1475 HQ176092.1.1485 EU454185.1.1392 JF057160.1.1343 JF231495.1.1327 EU511941.1.1361 X73447.1.1495 DQ798409.1.1389 FJ680132.1.1403 FJ683644.1.1415 EU775403.1.1392 DQ824242.1.1371 EF404225.1.1485 GU303384.1.1488 EU455337.1.1411 EU508047.1.1391 EU775276.1.1364 EU452598.1.1397 EU453405.1.1396 FJ369766.1.1376 FJ363028.1.1361 EU453170.1.1399 EU474103.1.1387 GQ896714.1.1488 EU510407.1.1394 DQ800982.1.1403 EU505554.1.1397 EU509801.1.1390 EU510916.1.1391 FM874762.1.1470 EU381507.1.1508 AY764158.1.1332 M69264.499.2294 JF504705.1.1535 FJ881266.1.1494 GQ896571.1.1492 FJ365303.1.1354 JF163913.1.1333 EU511884.1.1395 EU506990.1.1396 GQ896923.1.1489 EU507659.1.1390 GQ897728.1.1501 GQ448052.1.1379 EF400909.1.1493 HM123958.1.1494 EU459340.1.1385 AJ408960.1.1496 EU453371.1.1396 EU452565.1.1393 EU504176.1.1390 HM848484.1.1353 DQ905760.1.1529 HM124237.1.1496 AJ400261.1.1495 EU505608.1.1404 DQ805375.1.1389 EU506533.1.1397 EU454472.1.1391 JF161618.1.1360 AF157051.1.1494 DQ825213.1.1366 FJ679376.1.1391 GQ493900.1.1345 EU453071.1.1376 EF401181.1.1491 FJ365323.1.1360 EU457334.1.1397 FJ367867.1.1361 EU452336.1.1306 EU457963.1.1378 EU510378.1.1393 GQ898006.1.1488 HQ183762.1.1466 HQ716165.1.1440 EU455041.1.1392 EU508342.1.1389 EU451106.1.1392 HM844964.1.1355 EF403999.1.1478 JF211895.1.1352 EU503920.1.1395 EF099262.1.1404 EU452660.1.1398 GQ496624.1.1458 EU510986.1.1392 GQ897212.1.1492

Here are the first 4 lines from the new formatted files.
Fasta.fna:
(qiime2-2020.2) MacBook-Pro:try5 jamesmartin$ head -n 4 collapsed_ref_OTUs_97_pct_rep_seqs_Silva_v108_untrimmed_REP.fna

EU136690.1.2033 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;Bacteroides salyersiae
GTTTGATCCTGGCTCAGGATGAACGCTAGCTACAGGCTTAACACATGCAAGTCGAGGGGCATCAGGGTGTAGCAATACACCGCTGGCGACCGGCGCACGGGTGAGTAACACGTATCCAACCTGCCCTTTACTCGGGGATAGCCTTTCGAAAGAAAGATTAATACCCGATGGTATAACATGACCTCCTGGTTTTGTTATTAAAGAATTTCGGTAGAGGATGGGGATGCGTTCCATTAGGCAGTTGGCGGGGTAACGGCCCACCAAACCTTCGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAAACTCCTACGGGAGGCAGCAGTGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTAGCGTGAAGGATGACCGCCCTATGGGTTATAAACTTCTTTTATATGGGAATAAAGGGTGCCACGTGTGGCATTTTGTATGTACCATATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACATGTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGCGTGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACCGATGCTCGAAAGTGTGGGTATCAAACAGGATTAGATACCCTGGTAGTCCACACAGTAAACGATGAATACTCGCTGTTTGCGATATACAGTAAGCGGCCAAGCGAAAGCATTAAGTATTCCACCTGGGGAGTACGCCGGCAACGGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGAGGAACATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCCGGGCTTAAATTGCAAATGAATATGCCGGAAACGGCATAGCCGCAAGGCATTTGTGAAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTATCTTCAGTTACTAACAGGTTATGCTGAGGACTCTGGAGAGACTGCCGTCGTAAGATGTGAGGAAGGTGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCTACACACGTGTTACAATGGGGGGTACAGAAGGCCGCTACACAGCGATGTGATGCCAATCCCTAAAGCCCCTCTCAGTTCGGATCGAAGTCTGCAACCCGACTTCGTGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCAAGCCATGGGAGCCGGGGGTACCTGAAGTACGTAACCGCAAGGAGCGTCCTAGGGTAAAACTGGTGACTGGGGCTAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGAACACCTCCTTTCTGGAGCGATGCCGTAAAGGGCGTCCATTTCCGGTTCTGAATGTACTACTGGTACTTGTTTATTTATAGCATATAGAATCGACCGTCTATATTATATTATAGAATAGAGATAAACAAGAAGAAAGAAGAAGCCGAGCCGCATGGCGAGGTTGAACTAGTCCTATAGCTCAGTTGGTTAGAGCGCTACACTGATAATGTAAAGGTCGGCAGTTCAACTCTGCCTGGGACTACTTCCGCAAGTCGACGCCTGGTGGATTGCGAGCCTGAAATTACACTTTCAACTCTCAACTTCCAACTTTCAACTTGTACGAAGGGGGATTAGCTCAGCTGGCTAAAGCATCTGCCTTGCACGCAAAGGGTCAACGGTTCGAATCCGTTATTCTCCACTCCGCTTCGGATTGCCGGTTGTCAAAGGACGACTGACAGTTTAGGGCAAACGATCTTTGACATGATGTACAAAAAGTAAATTTTAGTAAAGAGCTAAAAGTATATATCAAACCGTAGTGTTTCGATTTTGGAT
M69264.499.2294 Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium;Clostridium perfringens
GTCACTAAGGACGGGCAACAAAAAAAGACAATAAGTTGAAAGAAAACAACTTAAAAAGTTTTTTAAAAAAAGTGTTGACAAAGTTCGAAGGTGATGATAAAATAAAGAAGTCGCTTGAGGGCGACAATGAAATGGTCTTTGAAAATTAAACAGAAGATATTAACATAAACCAGCAATTCTTTTATAAGTAATATGAGTATAGATTAAACTTTTAAATTGAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAGCGATGAAGTTTCCTTCGGGAAACGGATTAGCGGCGGGACGGGTGAGTAACACGTGGGTAACCTGCCTCATAGAGTGGAATAGCCTTCCGAAAGGAAGATTAATACCTCATAATGTTGAAAGATGGCATCATCATTCAACCAAAGGAGCAATCCGCTATGAGATGGACCCGCGGCGCATTAGCTAGTTGGTGGGGTAACGGCCTACCAAGGCGACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTCTTTGGGGAAGATAATGACGGTACCCAAGGAGGAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCGAGCGTTATCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGATGATTAAGTGGGATGTGAAATACCCGGGCTCAACTTGGGTGCTGCATTCCAAACTGGTTATCTAGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGACTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAATACTAGGTGTGGGGGTTTCAACACCTCCGTGCCGCCGCTAACGCATTAAGTATTCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGTAGCGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCTACACTTGACATCCCTTGCATTACTCTTAATCGAGGAAATCCTTCGGGGACAAGGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCGTTAGTTACTACCATTAAGTTGAGGACTCTAGCGAGACTGCCTGGGTTAACCAGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTGTAGGGCTACACACGTGCTACAATGGCTGGTACAGAGAGATGCAATACCGCGAGGTGGAGCCAAACTTAAAAACCAGTCTCAGTTCGGATTGTAGGCTGAAACTCGCCTACATGAAGCTGGAGTTACTAGTAATCGCGAATCAGAATGTCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGAGAGTTGGCAATACCCGAAGTCCGTGAGCTAACCGCAAGGAGGCAGCGGCCGAAGTAGGGTCAGCGATTGGGGTGAAGTCGTAACAAGGTAGCCGTAGGAGAACCTGCGGCTGGATCACCTCCTTTCTAAGGAATACATCTTAGGACAACTAAGATGACAATGAATTCTGGATAATATCTCTGTTTAATTTTGAGAGA

#OTU ID Sample.1.Hu.I1 Sample.10.G1.I1.Chex Sample.11.G1.I2.Chex Sample.12.HuCI.Gavage.1.2.Chex Sample.13.G1I.Gavage.Chex Sample.14.2ndG3.Exp11.Gavage.Chex Sample.15.HuCI.Gavage.3.4.Chex Sample.16.HuC.M1.Gavage.Chex Sample.17.HuCM2.Gavage.Chex Sample.18.HuCM3.Gavage.Chex Sample.19.HuCM4.Gavage.CheSample.2.Hu.I2 Sample.20.HuCM5.Gavage.Chex Sample.21.HuC.I3 Sample.22.HuC.I4 Sample.23.HuCM1A Sample.24.HuCM1B Sample.25.HuCM2A Sample.26.HuCM2B Sample.27.HuCM3A Sample.28.HuCM3B Sample.29.HuCM4A Sample.3.G1.I1 Sample.30.HuCM4B Sample.31.HuCM5A Sample.32.HuCM5B Sample.33.2ndG3.Exp13 Sample.34.PBS.Exp13 Sample.35.HuCI.619.Chex Sample.36.HuCI.620.Chex Sample.37.HuCI.621.Chex Sample.38.HuCI.622.Chex Sample.39.HuCI.623.Chex Sample.4.G1.I2 Sample.40.HuCI.624.Chex Sample.41.HuCI.625.Chex Sample.42.HuCI.626.Chex Sample.43.HuCI.627.Chex Sample.44.HuCI.628.Chex Sample.45.HuCI.629.Chex Sample.46.HuCI.630.Chex Sample.47.HuCI.631.Chex Sample.48.HuCI.632.Chex Sample.49.HuCI.633.Chex Sample.5.HuC.Fresh Sample.50.HuCI.634.Chex Sample.51.2ndG3.Exp12.13.Gavage Sample.52.HuC.Fresh Sample.53.HuC.Fresh Sample.54.1.10.DilutionGavage Sample.55.1.33.DilutionGavage Sample.56.1.66.DilutionGavage Sample.57.1.100.DilutionGavage Sample.58.1.1000.DilutionGavage Sample.59.1.0.NoDilution Sample.6.2ndG3.Exp11 Sample.60.1.0.G1.Isolates Sample.61.1.10.Dilution Sample.62.1.10.G1.Isolates Sample.63.1.33.Dilution Sample.64.1.33.G1.Isolates Sample.65.1.66.Dilution Sample.66.1.66.G1.IsolatesSample.67.1.100.Dilution Sample.68.1.100.G1.Isolates Sample.69.1.1000.Dilution Sample.7.PBS.Exp11 Sample.70.1.1000.G1.Isolates Sample.71.PBS.Exp1Sample.72.PBS.G1.Isolates Sample.73.PBS.Exp13.d0 Sample.74.HM5A.d0 Sample.75.HM4A.d0 Sample.76.PBS.Exp13.wk3 Sample.77.HM5A.wk3 Sample.78.HM4A.wk3 Sample.79.HM3A.wk3 Sample.8.Hu.I1.Chex Sample.80.HM2A.wk3 Sample.81.HM1A.wk3 Sample.82.HuI3.wk3 Sample.9.Hu.I2.Chex Rep.Seq.Taxonomy
EU136690.1.2033 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 91 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Bacteroides;Bacteroides salyersiae
M69264.499.2294 319 1 41 7429 0 3 3762 6714 6540 6803 15217 305 7998 112 333 3252 363 897 2457 966 254 1313 2 80 10357 294 0 1 2 0 0 1 0 1 1 9 67 23117 19089 18851 14670 18 0 20793 1 20161 0 1 2 1 3 1 0 6 0 0 0 0 1 80 338 338 153 107 134 115 208 Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium;Clostridium perfringens
DQ532133.1.1709 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;mitochondria;uncultured bacterium

Thanks for your input so far,
James

jwdebelius · May 29, 2020, 10:22pm

Hi @lostmouse,

I think you also need to exclude the taxonomy header; Im guessing that's getting read incorrectly.

Can you try running

qiime feature-table tabulate-seqs

on your imported sequences, and then checking what you see in the qzv?

Best,
Justine

lostmouse · May 30, 2020, 2:07am

I've done those visualizations and the sequences seem to be in order. My suspicion is the table, especially since its been formatted. Previously I corrected errors such as newlines being replaced as spaces. I am dumping the taxonomy column from the table data now.

lostmouse · May 30, 2020, 3:08am

I changed the Rep.seq.taxonomy to taxonomy and that didn't help. Also tried deleting the whole column which makes the format invalid. I tried leaving the header blank and that also invalidates the format for .biom. Did I misunderstand your suggestion?

I am going to scrutinize the table to see if something is off in the format.

Thanks,
James

jwdebelius · May 30, 2020, 11:57pm

Hi @lostmouse,

Could attach the summary files for the table and the sequences? You can DM them to me if you're not comfortable posting them.

Best,
Justine

lostmouse · May 31, 2020, 8:45pm

Hey Justine,

Thanks for taking a look at this.FreqTable_exp1_2_3.qzv (424.1 KB) seq_exp1_2_3.qzv (836.5 KB)

jwdebelius · June 1, 2020, 1:30pm

Hi @lostmouse,

Thank you! I wanted to verify the issue isn't at import. It's not! So, yay!

There was a recent thread with a similar issue that might have some solutions

lostmouse · June 4, 2020, 1:25pm

omg it worked! I am grateful, very grateful. But let's see if the next step works!

system · July 5, 2020, 7:25pm

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