iqtree COVID-19 release - assertion error in alignment.cpp:77

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giusepp...@gmail.com

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Aug 30, 2021, 5:56:51 AM8/30/21
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Hi all,

After successfully creating the varsites file we ran across the following error while using iqtree2 v 2.1.2, 2.1.3 and 2.1.4-beta (all fresh runs from scratch):

ERROR: alignment.cpp:77: std::__cxx11::string &Alignment::getSeqName(int): Assertion `i >= 0 && i < (int)seq_names.size()' 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: AS.pruning-0.5.log
ERROR: *** Alignment files (if possible)

I am attaching the log file in the case of version 2.1.3
AS.pruning-0.5.log

We also tried with "-keep_empty_seq" without any luck.

Could you please help us in handling this error?

Thanks in advance.

Minh Bui

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Sep 1, 2021, 8:31:16 PM9/1/21
to IQ-TREE, giusepp...@gmail.com
Hi there,

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.

Cheers,
Minh

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