ERROR: Tree file does not start with an opening-bracket '(' (line 1 column 1)

[srgirard]

Hello, I am trying to get bootstraps, gCF, and sCF on a concatenated/supermatrix tree using the command:

iqtree2 -t <supermatrix_tree> --gcf <concat_loci> -p <align_directory> --scf 100 --prefix final -B 1000 -T 4

This is running for a few hours before failing with a ERROR: Tree file does not start with an opening-bracket '(' (line 1 column 1)

Does anyone know what is causing this?

Thanks!!

[roblanf]

@srgirard it's hard to help without more information. If you are able to post your input files and log file, that would help a lot.

In the absence of that information - have you double checked the treefile? Does the error message help? It's very specific.

[srgirard]

Hi, thanks for the reply.

I looked closer into the log file and I realized that I used the wrong file as the --gcf input file. But now that I have the right file I am still having issues because all of the trees in my loci.treefile file have less tips than my concatenated supermatrix tree made from the same alignment files.

I used this for the reference tree
iqtree2 -p <alignment_directory> --prefix concat -B 1000 -T AUTO

To make the loci.tree file I used
iqtree2 -S <alignment_directory> --prefix loci -T AUTO

And I used the same command as the original post (but now with the right -- gcf input file) and am getting the error
ERROR: Tree taxa and alignment sequence do not match
Do you know why they would have a different number of tips? It appears that all the trees in the loci.treefile have between 87-107 tips even though my input taxa and reference tree both are at 111.

Thanks

Here's the last 50 lines or so from the log file
bs_gcf_scf_log.txt

[thomaskf]

Hi srgirard, Can you try the latest version like 2.3.x ? The issue you encountered appeared in the previous version but it should have been fixed in the latest version. Thanks, Thomas

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On Thu, Apr 25, 2024 at 9:35 PM srgirard ***@***.***> wrote: Hi, thanks for the reply. I looked closer into the log file and I realized that I used the wrong file as the --gcf input file. But now that I have the right file I am still having issues because all of the trees in my loci.treefile file have less tips than my concatenated supermatrix tree made from the same alignment files. I used this for the reference tree iqtree2 -p <alignment_directory> --prefix concat -B 1000 -T AUTO To make the loci.tree file I used iqtree2 -S <alignment_directory> --prefix loci -T AUTO And I used the same command as the original post (but now with the right -- gif input file) and am getting the error ERROR: Tree taxa and alignment sequence do not match Do you know why they would have a different number of tips? It appears that all the trees in the loci.treefile have between 87-107 tips even though my input taxa and reference tree both are at 111. Thanks Here's the last 50 lines or so from the log file bs_gcf_scf_log.txt <https://github.com/iqtree/iqtree2/files/15108955/bs_gcf_scf_log.txt> — Reply to this email directly, view it on GitHub <#178 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AENQCRS3MHQKYNS55AVGQBLY7DS65AVCNFSM6AAAAABGV32SYOVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TEMRUGIYTS> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[srgirard]

Hello, thanks for the reply. When I first tried I was using 2.3.0, and I have updated to 2.3.3 and I am still getting the same exact error, with he same exact individuals shown in the new log. The log I posted and the new log are identical. I tried making a brand new supermatrix tree and a new loci.tree file but still the same error.

[thomaskf]

Hi Srgirard, Thanks for your question. Can I confirm whether you used the latest version to run the following commands to make the loci tree file again? iqtree2 -S <alignment_directory> --prefix loci -T AUTO If so, then can you send us the data files, perhaps by email if more convenient for you, and the whole (not partial) log file? We will then have a check. Thanks, Thomas

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On Sat, Apr 27, 2024 at 1:53 AM srgirard ***@***.***> wrote: Hello, thanks for the reply. When I first tried I was using 2.3.0, and I have updated to 2.3.3 and I am still getting the same exact error, with he same exact individuals shown in the new log. The log I posted and the new log are identical. I tried making a brand new supermatrix tree and a new loci.tree file but still the same error. — Reply to this email directly, view it on GitHub <#178 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AENQCRXK3SFGC2U6V2635TDY7JZ73AVCNFSM6AAAAABGV32SYOVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TEMZZGEZDC> . You are receiving this because you commented.Message ID: ***@***.***>

[srgirard]

Hello, yes! I just reran it using v2.3.3 and I am getting the same missing tips errors as when I was using an older 2.2.x version. What is the email I could get the log file and input data files to you?

[thomaskf]

Hi, Got it. You can send the data files to me at ***@***.*** I will check and let you know. Thanks. Thomas

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On Tue, 30 Apr 2024 at 3:08 AM, srgirard ***@***.***> wrote: Hello, yes! I just reran it using v2.3.3 and I am getting the same missing tips errors as when I was using an older 2.2.x version. What is the email I could get the log file and input data files to you? — Reply to this email directly, view it on GitHub <#178 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AENQCRUTYQDG2ATDN2VTRWTY7Z5ALAVCNFSM6AAAAABGV32SYOVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TENRVHA2TI> . You are receiving this because you commented.Message ID: ***@***.***>

[thomaskf]

Hi @srgirard

Sorry for the delay of the reply.
These were the commands you used:
a. Build a loci tree for each locus alignment:
iqtree2 -S align_directory --prefix loci -nt 20
b. Build a tree for the concatenate alignment:
iqtree2 -p align_directory --prefix concat -B 1000 -T 20
c. Perform gcf and scf analysis
iqtree2 -t concat.treefile --gcf loci.treefile -p align_directory --scf 100 --prefix final -B 1000 -nt 20

However, for step c, you should not include "-B 1000", because you have already did that in step b.
If you change the command in step c as follows, then it should complete successfully:
iqtree2 -t concat.treefile --gcf loci.treefile -p align_directory --scf 100 --prefix final -nt 20

Thanks for @bqminh 's help in coming up with the above answer.

Thomas