Hi! I am trying to import dada2 table (following the tutorial in its website) to qiime2, and nothing works
hope someone could give a better solution.
I firstly converted freq_table.txt (it was seqtab.nochim transposed) to hdf5 biom table format (freq_table.biom).
then with qiime import tools, convert it to an artifact for qiime2 with this command
qiime tools import --input-path freq_table.biom --type "FeatureTable[Frequency]" --output-path freq_table
I did the same with rep_set.nochimeras.OTUs.fasta (
qiime tools import --input-path rep_set.nochimeras.OTUs.fasta --output-path rep_seqs-table --type "FeatureData[Sequence]"
and Generate the tree for phylogenetic diversity analyses.
Then, I try to run the command qiime diversity core-metrics, it gave this error message.
(qiime2) [labsani@labsani-HP-ProBook-470-G1 200-160]$ qiime diversity core-metrics --i-phylogeny rooted-tree.qza --i-table freq_table.qza --p-sampling-depth 55624 --output-dir cm55624
Traceback (most recent call last):
File "/home/labsani/miniconda3/envs/qiime2/bin/qiime", line 6, in <module>
sys.exit(q2cli.__main__.qiime())
File "/home/labsani/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 716, in __call__
return self.main(*args, **kwargs)
File "/home/labsani/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 696, in main
rv = self.invoke(ctx)
File "/home/labsani/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 1060, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/labsani/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 1060, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/labsani/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 889, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/labsani/miniconda3/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 534, in invoke
return callback(*args, **kwargs)
File "/home/labsani/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2cli-0.0.6-py3.5.egg/q2cli/commands.py", line 210, in __call__
File "<decorator-gen-234>", line 2, in core_metrics
File "/home/labsani/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime-2.0.6-py3.5.egg/qiime/core/callable.py", line 227, in callable_wrapper
output_types, provenance)
File "/home/labsani/miniconda3/envs/qiime2/lib/python3.5/site-packages/qiime-2.0.6-py3.5.egg/qiime/core/callable.py", line 328, in _callable_executor_
output_views = callable(**view_args)
File "<string>", line 26, in core_metrics
File "/home/labsani/miniconda3/envs/qiime2/lib/python3.5/site-packages/q2_diversity-0.0.6-py3.5.egg/q2_diversity/_alpha/_method.py", line 44, in alpha_phylogenetic
File "/home/labsani/miniconda3/envs/qiime2/lib/python3.5/site-packages/skbio/diversity/_driver.py", line 170, in alpha_diversity
counts, otu_ids, tree, validate, single_sample=False)
File "/home/labsani/miniconda3/envs/qiime2/lib/python3.5/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 "/home/labsani/miniconda3/envs/qiime2/lib/python3.5/site-packages/skbio/diversity/_util.py", line 106, 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=971): OTU_370 OTU_145 OTU_846 OTU_539 OTU_944 OTU_200 OTU_470 OTU_205 OTU_819 OTU_853 OTU_829 OTU_940 OTU_103 OTU_237 OTU_264 OTU_973 OTU_533 OTU_355 OTU_343 OTU_363 OTU_949 OTU_759 OTU_588 OTU_739 OTU_872 OTU_762 OTU_662 OTU_92 OTU_868 OTU_315 OTU_531 OTU_27 OTU_858 OTU_675 OTU_571 OTU_771 OTU_451 OTU_78 OTU_63 OTU_52 OTU_891 OTU_397 OTU_442 OTU_406 OTU_305 OTU_419 OTU_309 OTU_915 OTU_895 OTU_970 OTU_542 OTU_263 OTU_257 OTU_864 OTU_589 OTU_719 OTU_354 OTU_273 OTU_20 OTU_130 OTU_921 OTU_478 OTU_960 OTU_398 OTU_296 OTU_91 OTU_192 OTU_848 OTU_15 OTU_559 OTU_179 OTU_875 OTU_881 OTU_534 OTU_285 OTU_266 OTU_964 OTU_520 OTU_688 OTU_597 OTU_232 OTU_458 OTU_898 OTU_258 OTU_371 OTU_678 OTU_906 OTU_368 OTU_823 OTU_209 OTU_789 OTU_802 OTU_365 OTU_543 OTU_639 OTU_56 OTU_244 OTU_48 OTU_77 OTU_161 OTU_447 OTU_380 OTU_854 OTU_694 OTU_149 OTU_943 OTU_268 OTU_182 OTU_299 OTU_885 OTU_961 OTU_776 OTU_839 OTU_653 OTU_918 OTU_832 OTU_81 OTU_602 OTU_967 OTU_874 OTU_8 OTU_219 OTU_345 OTU_54 OTU_49 OTU_624 OTU_903 OTU_625 OTU_393 OTU_279 OTU_98 OTU_911 OTU_723 OTU_408 OTU_367 OTU_251 OTU_19 OTU_908 OTU_689 OTU_213 OTU_745 OTU_210 OTU_157 OTU_724 OTU_959 OTU_38 OTU_247 OTU_191 OTU_506 OTU_265 OTU_805 OTU_456 OTU_657 OTU_847 OTU_880 OTU_269 OTU_515 OTU_732 OTU_238 OTU_699 OTU_167 OTU_786 OTU_746 OTU_217 OTU_859 OTU_55 OTU_443 OTU_513 OTU_704 OTU_754 OTU_391 OTU_204 OTU_837 OTU_978 OTU_508 OTU_472 OTU_930 OTU_738 OTU_95 OTU_256 OTU_640 OTU_133 OTU_884 OTU_93 OTU_88 OTU_267 OTU_979 OTU_412 OTU_528 OTU_74 OTU_121 OTU_471 OTU_125 OTU_525 OTU_208 OTU_538 OTU_275 OTU_926 OTU_937 OTU_431 OTU_626 OTU_344 OTU_935 OTU_289 OTU_716 OTU_3 OTU_430 OTU_33 OTU_609 OTU_659 OTU_246 OTU_171 OTU_830 OTU_198 OTU_32 OTU_293 OTU_413 OTU_399 OTU_907 OTU_831 OTU_556 OTU_600 OTU_68 OTU_429 OTU_298 OTU_580 OTU_582 OTU_41 OTU_425 OTU_593 OTU_796 OTU_685 OTU_26 OTU_420 OTU_128 OTU_968 OTU_766 OTU_410 OTU_339 OTU_127 OTU_455 OTU_183 OTU_564 OTU_417 OTU_79 OTU_690 OTU_385 OTU_105 OTU_433 OTU_173 OTU_616 OTU_714 OTU_155 OTU_446 OTU_302 OTU_548 OTU_598 OTU_825 OTU_512 OTU_203 OTU_567 OTU_774 OTU_5 OTU_43 OTU_629 OTU_16 OTU_236 OTU_168 OTU_599 OTU_952 OTU_278 OTU_654 OTU_428 OTU_554 OTU_971 OTU_498 OTU_311 OTU_622 OTU_517 OTU_710 OTU_312 OTU_107 OTU_36 OTU_223 OTU_156 OTU_924 OTU_335 OTU_769 OTU_282 OTU_190 OTU_113 OTU_778 OTU_876 OTU_503 OTU_194 OTU_494 OTU_426 OTU_222 OTU_845 OTU_349 OTU_642 OTU_611 OTU_120 OTU_353 OTU_369 OTU_330 OTU_382 OTU_172 OTU_310 OTU_901 OTU_813 OTU_701 OTU_529 OTU_842 OTU_184 OTU_744 OTU_322 OTU_124 OTU_755 OTU_466 OTU_96 OTU_734 OTU_607 OTU_772 OTU_454 OTU_462 OTU_692 OTU_592 OTU_199 OTU_932 OTU_303 OTU_596 OTU_577 OTU_80 OTU_482 OTU_216 OTU_812 OTU_933 OTU_474 OTU_764 OTU_958 OTU_329 OTU_527 OTU_253 OTU_788 OTU_672 OTU_324 OTU_366 OTU_1 OTU_917 OTU_387 OTU_294 OTU_888 OTU_763 OTU_806 OTU_211 OTU_252 OTU_697 OTU_863 OTU_185 OTU_475 OTU_945 OTU_75 OTU_620 OTU_396 OTU_601 OTU_480 OTU_45 OTU_469 OTU_507 OTU_535 OTU_546 OTU_637 OTU_750 OTU_667 OTU_108 OTU_146 OTU_817 OTU_914 OTU_735 OTU_700 OTU_768 OTU_245 OTU_197 OTU_621 OTU_818 OTU_843 OTU_569 OTU_486 OTU_177 OTU_619 OTU_392 OTU_117 OTU_284 OTU_473 OTU_614 OTU_11 OTU_740 OTU_207 OTU_705 OTU_742 OTU_334 OTU_180 OTU_931 OTU_941 OTU_591 OTU_336 OTU_544 OTU_414 OTU_665 OTU_76 OTU_154 OTU_394 OTU_46 OTU_671 OTU_563 OTU_214 OTU_636 OTU_623 OTU_375 OTU_782 OTU_364 OTU_709 OTU_405 OTU_465 OTU_633 OTU_791 OTU_286 OTU_501 OTU_175 OTU_308 OTU_481 OTU_821 OTU_85 OTU_39 OTU_23 OTU_877 OTU_110 OTU_758 OTU_730 OTU_461 OTU_713 OTU_886 OTU_887 OTU_106 OTU_373 OTU_202 OTU_963 OTU_668 OTU_927 OTU_321 OTU_797 OTU_416 OTU_139 OTU_913 OTU_316 OTU_785 OTU_553 OTU_909 OTU_628 OTU_712 OTU_338 OTU_502 OTU_318 OTU_83 OTU_249 OTU_174 OTU_757 OTU_972 OTU_557 OTU_218 OTU_99 OTU_144 OTU_753 OTU_261 OTU_53 OTU_243 OTU_484 OTU_70 OTU_728 OTU_890 OTU_82 OTU_581 OTU_37 OTU_905 OTU_632 OTU_47 OTU_670 OTU_647 OTU_291 OTU_733 OTU_195 OTU_69 OTU_566 OTU_160 OTU_231 OTU_337 OTU_545 OTU_651 OTU_119 OTU_452 OTU_18 OTU_288 OTU_674 OTU_946 OTU_947 OTU_233 OTU_347 OTU_361 OTU_404 OTU_572 OTU_14 OTU_388 OTU_225 OTU_612 OTU_300 OTU_568 OTU_485 OTU_595 OTU_307 OTU_586 OTU_348 OTU_434 OTU_715 OTU_896 OTU_975 OTU_811 OTU_59 OTU_66 OTU_794 OTU_28 OTU_104 OTU_444 OTU_826 OTU_779 OTU_698 OTU_227 OTU_44 OTU_22 OTU_491 OTU_660 OTU_115 OTU_893 OTU_381 OTU_7 OTU_680 OTU_643 OTU_151 OTU_129 OTU_631 OTU_476 OTU_815 OTU_957 OTU_729 OTU_460 OTU_403 OTU_761 OTU_807 OTU_851 OTU_165 OTU_500 OTU_112 OTU_170 OTU_814 OTU_725 OTU_441 OTU_295 OTU_61 OTU_438 OTU_435 OTU_965 OTU_21 OTU_90 OTU_346 OTU_248 OTU_606 OTU_239 OTU_810 OTU_374 OTU_325 OTU_143 OTU_449 OTU_922 OTU_109 OTU_916 OTU_297 OTU_902 OTU_558 OTU_467 OTU_673 OTU_457 OTU_594 OTU_317 OTU_64 OTU_587 OTU_804 OTU_953 OTU_574 OTU_358 OTU_722 OTU_242 OTU_519 OTU_855 OTU_681 OTU_835 OTU_840 OTU_135 OTU_360 OTU_497 OTU_547 OTU_850 OTU_411 OTU_551 OTU_861 OTU_71 OTU_682 OTU_866 OTU_956 OTU_319 OTU_448 OTU_362 OTU_240 OTU_942 OTU_440 OTU_292 OTU_94 OTU_900 OTU_824 OTU_407 OTU_856 OTU_439 OTU_630 OTU_189 OTU_147 OTU_206 OTU_820 OTU_590 OTU_798 OTU_241 OTU_841 OTU_126 OTU_857 OTU_934 OTU_111 OTU_706 OTU_328 OTU_153 OTU_703 OTU_645 OTU_883 OTU_928 OTU_510 OTU_314 OTU_254 OTU_372 OTU_516 OTU_879 OTU_67 OTU_164 OTU_499 OTU_65 OTU_718 OTU_57 OTU_468 OTU_663 OTU_60 OTU_84 OTU_751 OTU_635 OTU_463 OTU_379 OTU_100 OTU_390 OTU_720 OTU_780 OTU_123 OTU_777 OTU_138 OTU_162 OTU_422 OTU_166 OTU_152 OTU_676 OTU_384 OTU_641 OTU_711 OTU_320 OTU_708 OTU_912 OTU_450 OTU_140 OTU_948 OTU_13 OTU_962 OTU_4 OTU_141 OTU_923 OTU_869 OTU_748 OTU_504 OTU_17 OTU_646 OTU_415 OTU_809 OTU_610 OTU_573 OTU_9 OTU_137 OTU_976 OTU_201 OTU_652 OTU_644 OTU_351 OTU_677 OTU_377 OTU_658 OTU_784 OTU_731 OTU_378 OTU_58 OTU_920 OTU_565 OTU_341 OTU_304 OTU_432 OTU_792 OTU_427 OTU_765 OTU_323 OTU_800 OTU_181 OTU_801 OTU_950 OTU_487 OTU_276 OTU_383 OTU_386 OTU_395 OTU_707 OTU_97 OTU_488 OTU_376 OTU_767 OTU_691 OTU_743 OTU_250 OTU_272 OTU_212 OTU_521 OTU_760 OTU_936 OTU_634 OTU_50 OTU_865 OTU_122 OTU_492 OTU_696 OTU_726 OTU_522 OTU_882 OTU_356 OTU_148 OTU_352 OTU_274 OTU_747 OTU_186 OTU_277 OTU_87 OTU_89 OTU_524 OTU_224 OTU_136 OTU_873 OTU_532 OTU_132 OTU_799 OTU_585 OTU_684 OTU_878 OTU_560 OTU_781 OTU_904 OTU_40 OTU_727 OTU_340 OTU_30 OTU_142 OTU_229 OTU_134 OTU_401 OTU_118 OTU_327 OTU_479 OTU_255 OTU_116 OTU_808 OTU_131 OTU_683 OTU_666 OTU_687 OTU_196 OTU_62 OTU_862 OTU_290 OTU_530 OTU_737 OTU_230 OTU_836 OTU_176 OTU_389 OTU_270 OTU_437 OTU_342 OTU_178 OTU_514 OTU_549 OTU_910 OTU_459 OTU_693 OTU_576 OTU_951 OTU_695 OTU_163 OTU_505 OTU_803 OTU_158 OTU_226 OTU_849 OTU_518 OTU_897 OTU_477 OTU_939 OTU_828 OTU_24 OTU_29 OTU_301 OTU_550 OTU_669 OTU_537 OTU_661 OTU_445 OTU_424 OTU_679 OTU_894 OTU_955 OTU_721 OTU_795 OTU_870 OTU_235 OTU_664 OTU_615 OTU_326 OTU_2 OTU_816 OTU_169 OTU_42 OTU_570 OTU_287 OTU_228 OTU_31 OTU_526 OTU_756 OTU_357 OTU_790 OTU_421 OTU_834 OTU_648 OTU_313 OTU_331 OTU_833 OTU_359 OTU_496 OTU_402 OTU_752 OTU_262 OTU_575 OTU_101 OTU_51 OTU_686 OTU_603 OTU_552 OTU_649 OTU_511 OTU_844 OTU_72 OTU_736 OTU_741 OTU_215 OTU_271 OTU_10 OTU_892 OTU_827 OTU_34 OTU_793 OTU_423 OTU_613 OTU_899 OTU_234 OTU_259 OTU_540 OTU_493 OTU_114 OTU_464 OTU_187 OTU_749 OTU_608 OTU_280 OTU_333 OTU_787 OTU_12 OTU_489 OTU_702 OTU_332 OTU_860 OTU_561 OTU_523 OTU_627 OTU_954 OTU_938 OTU_73 OTU_578 OTU_281 OTU_584 OTU_221 OTU_541 OTU_483 OTU_618 OTU_260 OTU_605 OTU_617 OTU_579 OTU_220 OTU_25 OTU_555 OTU_6 OTU_773 OTU_509 OTU_150 OTU_102 OTU_919 OTU_418 OTU_193 OTU_871 OTU_35 OTU_159 OTU_770 OTU_852 OTU_889 OTU_350 OTU_436 OTU_717 OTU_409 OTU_867 OTU_656 OTU_655 OTU_638 OTU_495 OTU_929 OTU_283 OTU_583 OTU_536 OTU_400 OTU_188 OTU_490 OTU_604 OTU_453 OTU_783 OTU_306 OTU_562 OTU_86 OTU_838
Apparently, both .qza inputs have the semantic type needed. Both the rooted-tree.qza and freq_table.qza have 979 OTUs. I think that the problem was in importing the tables, but not sure.
Any help would much be appreciated!
Thankss!