Taxon name error

[iqtree]

Taxon name error

[thomaskf]

Dear Zhenzhi Han,
The issue of ERROR: Alignment sequence xxx does not appear in the tree" has been fixed in version 2.2.0.2 (https://github.com/iqtree/iqtree2/releases/tag/v2.2.0.2). Thank you!
Thomas

[bqminh]

This could be a bug in v2.1.2. Can you pls check if it works in v2.1.0? https://github.com/iqtree/iqtree2/releases/tag/v2.1.0 <https://github.com/iqtree/iqtree2/releases/tag/v2.1.0> Thanks Minh

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On 6 Nov 2020, at 4:40 pm, Zhenzhi ***@***.***> wrote: Dear Bui Quang Minh: I am meeting a error report from IQTREE2 (IQ-TREE multicore version 2.1.2 COVID-edition for Linux 64-bit built Oct 22 2020). Here is the partial detailed reports from that. ---------> Rate parameters: A-C: 2.09932 A-G: 3.94693 A-T: 1.47380 C-G: 1.38623 C-T: 5.05624 G-T: 1 Base frequencies: A: 0.280 C: 0.189 G: 0.208 T: 0.323 Site proportion and rates: (0.085,0.021) (0.048,0.194) (0.028,0.194) (0.042,0.199) (0.076,0.4 Parameters optimization took 99 rounds (1005.335 sec) Computing ML distances based on estimated model parameters... Computing ML distances took 0.072589 sec (of wall-clock time) 1.404860 sec(of CPU time) Computing RapidNJ tree took 0.012983 sec (of wall-clock time) 0.263654 sec (of CPU time) ERROR: Alignment sequence AY278489|SARS-CoV_GD01|Betacoronavirus does not appear in the tree ERROR: Alignment sequence AY390556|SARS-CoV_GZ02|Guangzhou|Betacoronavirus does not appear in ERROR: Alignment sequence AY485277|SARS-CoV_Sino1-11|Betacoronavirus does not appear in the tr ERROR: Alignment sequence AY508724|SARS-CoV_NS-1|Betacoronavirus does not appear in the tree ERROR: Alignment sequence KT444582|WIV16|Yunnan|Betacoronavirus does not appear in the tree ERROR: Alignment sequence KY417146|Rs4231|Yunnan|Betacoronavirus does not appear in the tree ERROR: Alignment sequence KY417151|Rs7327|Yunnan|Betacoronavirus does not appear in the tree ERROR: Alignment sequence KY417152|Rs9401|Yunnan|Betacoronavirus does not appear in the tree ERROR: Alignment sequence MK211376|BtRs-BetaCoV/YN2018B|Yunnan|Betacoronavirus does not appear (KJ473815|BtRs-BetaCoV/GX2013|Guangxi|Betacoronavirus,JX993988|Yunnan2011|Betacoronavirus,(((( ERROR: Tree taxa and alignment sequence do not match (see above) -----------> It is about the taxon name error. However, it run accurately in IQTREE (Version 1.6.12). I am waiting for a reply from you. Tanks. Sincerely Zhenzhi Han — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#11>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADRTPU5EYBYXZSN4MRVQBLTSOOD4VANCNFSM4TMIAPRA>.

[hansir8]

Dear Bui Quang Minh:
Unfortunately, I also meet the same error in the IQ-TREE2 (multicore version 2.1.0 for Linux 64-bit built Jul 18 2020).

Tanks.
Sincerely
Zhenzhi Han

[bqminh]

Then how about https://github.com/iqtree/iqtree2/releases/tag/v2.0.8? <https://github.com/iqtree/iqtree2/releases/tag/v2.0.8?> Sorry, I need too trace back to the version that this works. If this still does not work, please help us to go earlier, and let the know the 2.X version that it works. Thanks!

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On 4 Dec 2020, at 7:15 pm, Zhenzhi ***@***.***> wrote: Dear Bui Quang Minh: Unfortunately, I also meet the same error in the IQ-TREE2 (multicore version 2.1.0 for Linux 64-bit built Jul 18 2020). Tanks. Sincerely Zhenzhi Han — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#11 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADRTPU2VWO2SYZ4OZWW5GHTSTCLD7ANCNFSM4TMIAPRA>.

[hansir8]

I used older version you told me and meet another error in the IQ-TREE2 (IQ-TREE multicore version 2.0.8 for Linux 64-bit built Jul 9 2020).
------->
Creating fast initial parsimony tree by random order stepwise addition...
ERROR: phylotreepars.cpp:1053: virtual int PhyloTree::computeParsimonyTree(const char *, Alignment *, int *): Assertion `leafNum == 3' failed.
ERROR: STACK TRACE FOR DEBUGGING:
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: *** Log file: 3.fas.log
ERROR: *** Alignment files (if possible)
-------->
And the older version before 2.0.7, only contain the source code. Could you send me the compiled version of that for me? So that I could assess the error for older version of IQTREE2.
Tanks.
Sincerely
Zhenzhi Han

[bqminh]

The release for earlier versions are posted here: https://github.com/Cibiv/IQ-TREE/releases <https://github.com/Cibiv/IQ-TREE/releases> Can you check them? Thanks!

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On 5 Dec 2020, at 6:04 pm, Zhenzhi ***@***.***> wrote: I used older version you told me and meet another error in the IQ-TREE2 (IQ-TREE multicore version 2.0.8 for Linux 64-bit built Jul 9 2020). -------> Creating fast initial parsimony tree by random order stepwise addition... ERROR: phylotreepars.cpp:1053: virtual int PhyloTree::computeParsimonyTree(const char *, Alignment *, int *): Assertion `leafNum == 3' failed. ERROR: STACK TRACE FOR DEBUGGING: ERROR: ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED ERROR: *** For bug report please send to developers: ERROR: *** Log file: 3.fas.log ERROR: *** Alignment files (if possible) --------> And the older version before 2.0.7, only contain the source code. Could you send me the compiled version of that for me? So that I could assess the error for older version of IQTREE2. Tanks. Sincerely Zhenzhi Han — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#11 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADRTPU7CRBZVYPQQOGEYKF3STHLQFANCNFSM4TMIAPRA>.

[hansir8]

Dear Bui Quang Minh:
I have checked five versions, including the version 2.0.4-2.0.8. And I found the error begin at the version 2.0.8. Previous versions could run normally for this dataset. Please check the error information about the new versions described above.

Tanks.
Sincerely
Zhenzhi Han

[iqtree]

Thanks, @james: can you please check this? To rule out that it’s not due to your new code, before I will have a look. thanks

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On 10 Dec 2020, at 12:11 pm, Zhenzhi ***@***.*** ***@***.***>> wrote: Dear Bui Quang Minh: I have checked five versions, including the version 2.0.4-2.0.8. And I found the error begin at the version 2.0.8. Previous versions could run normally for this dataset. Please check the error information about the new versions described above. Tanks. Sincerely Zhenzhi Han — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#11 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGG7OVYXYJTQU5PDSXY45KTSUAN5FANCNFSM4TMIAPRA>.

--- Minh Bui, PhD Lecturer Research School of Computer Science & Research School of Biology The Australian National University Canberra, ACT 2600, Australia Hanna Neumann Building, Room 4.35 145 Science Rd https://bqminh.github.io

[andersgs]

I have run into the same issue. Specifying --keep-ident seems to fix things. My guess is that the comparison between alignment and the tree is being done with the processed alignment.