ERROR: Tree taxa and alignment sequence do not match

[rresendepinto]

Hello!
Iqtree is crashing on some of my files with the "ERROR: Tree taxon Apteryx_owenii does not appear in the alignment" even though there is a sequence for that taxon in the alignment file. I noticed that all the taxa for which this happens appear in a note like so: "NOTE: Apteryx_owenii (identical to Apteryx_australis) is ignored but added at the end".
What could be the problem here?
This happens in versions 2.0.3 and 2.1.2.

[leomrtns]

Hello as well!
I would like to mention that I have been affected recently by the same problem, using v2.1.2 (from conda). This happens when I use -t foo.tre, and the output, before exiting looks something like

NOTE: 5 identical sequences (see below) will be ignored for subsequent analysis
NOTE: PAK-S66 (identical to PAK-S25) is ignored but added at the end
NOTE: England/ALDP-C3CA4D/2020 (identical to Japan/IC-0910/2021) is ignored but added at the end
NOTE: Japan/IC-1081/2021 (identical to Japan/IC-0921/2021) is ignored but added at the end
NOTE: Japan/IC-0976/2021 (identical to Japan/IC-0921/2021) is ignored but added at the end
NOTE: Japan/IC-1051/2021 (identical to Japan/IC-1049/2021) is ignored but added at the end
Alignment was printed to 05.b117.aln.uniqueseq.phy

For your convenience alignment with unique sequences printed to 05.b117.aln.uniqueseq.phy

Reading input tree file 05.b117.tre ...
ERROR: Tree taxon England/ALDP-C3CA4D/2020 does not appear in the alignment
ERROR: Tree taxon Japan/IC-1051/2021 does not appear in the alignment
ERROR: Tree taxon Japan/IC-1081/2021 does not appear in the alignment
ERROR: Tree taxon Japan/IC-0976/2021 does not appear in the alignment
ERROR: Tree taxon  does not appear in the alignment
ERROR: Tree taxon  does not appear in the alignment
ERROR: Tree taxon  does not appear in the alignment
ERROR: Tree taxon  does not appear in the alignment
ERROR: Tree taxon  does not appear in the alignment
ERROR: Tree taxa and alignment sequence do not match (see above)

So iqtree is removing them from the alignment and then complaining that they are not there :D

(BTW a workaround is to use the option --keep-ident)

[jbloom]

I had exactly same problem as above, also fixed by using --keep-ident.

[Chjulian]

Any solution to this?
Im using version 2.1.3 and -keep-ident but the error keeps happening (with different datasets).

iqtree2 -s sim.fasta -m GTR+I+G -B 1000 -T AUTO -keep-ident -quiet

ERROR: Alignment sequence [xxxx] does not appear in the tree
ERROR: Alignment sequence [xxxx] does not appear in the tree
ERROR: Tree taxa and alignment sequence do not match (see above)

[Zhanglab-IOZ-admin]

I also encountered the same problem.
I used the command "- keep ident", but still reported the same error.
Then I deleted all the previous output files from iqtree and ran again.
Well done. Solved!!!

[bfauskee]

I get the same error. code: iqtree2 -s cluster8845.fasta -m MFP -T 6 -b 100 --keep-ident -pre cluster8845

I've tried running this about 100 times until it eventually worked, deleting the output files each time. For different loci, I have found that it works sporadically (might fail 5 or 6 times but eventually i get a contree and 100 boottrees).

I wonder if --keep-ident is really doing anything here. seems like i just have to get lucky enough for a run to get through 100 bs reps without getting two identical sequences by chance

[xonq]

sporadically get this error, reappears if I try to resume a run that was initialized with --keep-ident