iqtree v 2.1.3 - assertion error in alignment.cpp:77

[iqtree]

iqtree v 2.1.3 - assertion error in alignment.cpp:77

[corneliusroemer]

I also got this error, but now in 2.1.4-beta on macOS and it drove me mad.

I couldn't pin it down. A reboot fixed it. Very strange.

IQ-TREE multicore version 2.1.4-beta COVID-edition for Mac OS X 64-bit built Jun 24 2021

 ERROR: alignment.cpp:77: std::__1::string &Alignment::getSeqName(int): Assertion `i >= 0 && i < (int)seq_names.size()' failed.

[corneliusroemer]

Now I got the error using version 2.2.0-beta on centOS.

When I downloaded the fasta file to my local computer and ran the same command that errored on the cluster, no error was thrown.

When I deleted the log files and the potentially corrupted output tree from previous runs it ran through without error. So I guess as a workaround, one can try to remove intermediary output files from iqtree.

By the way, in the new version, the code line has changed, in case anyone googles this.

ERROR: alignment.cpp:80: std::__1::string &Alignment::getSeqName(int): Assertion `i >= 0 && i < (int)seq_names.size()' failed.

[corneliusroemer]

I found this relevant message from the maintainer @bqminh in the Google group:

This line in the log is relevant (just printed right before the error messages):

NOTE: Restoring information from model checkpoint file AS.pruning-0.5.model.gz

It means that you had a previous (unfinished) run and IQ-TREE loaded the checkpoint file. From what you wrote below, I’m guessing that you now change the alignment file (-s option). This causes incompability between the checkpoint and the alignment.

So try to run again with another --prefix and see how it goes.

https://groups.google.com/g/iqtree/c/Gii__XoEIdU/m/w0JsQqEKCwAJ

And indeed, I think I also aborted a previous run and that's when the error appeared.

I'm not quite sure what the easiest workaround is when one hits this error. I also think it would be nice if iqtree would not error in this situation.

[bqminh]

Yes, it would have been nice to print such more informative error message... But since you found the answer I'll close this issue.