Tree building failed

1 
ERROR: Shell exited from fatal signal SIGABRT when running: iqtree -ninit 2 -n 2 -me 0.05 -nt 8 -s results/indonesia/masked_masked-delim.fasta -m GTR -ninit 10 -n 4 > results/indonesia/masked_masked-delim.iqtree.log

Command output was:

  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: results/indonesia/masked_masked-delim.fasta.log

  ERROR: ***    Alignment files (if possible)

  /bin/bash: line 1:   516 Aborted                 iqtree -ninit 2 -n 2 -me 0.05 -nt 8 -s results/indonesia/masked_masked-delim.fasta -m GTR -ninit 10 -n 4 > results/indonesia/masked_masked-delim.iqtree.log

7 masking sites read from defaults/sites_ignored_for_tree_topology.txt

Building a tree via:

  iqtree -ninit 2 -n 2 -me 0.05 -nt 8 -s results/indonesia/masked_masked-delim.fasta -m GTR -ninit 10 -n 4 > results/indonesia/masked_masked-delim.iqtree.log

  Nguyen et al: IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies.

  Mol. Biol. Evol., 32:268-274. https://doi.org/10.1093/molbev/msu300

ERROR: TREE BUILDING FAILED

Please see the log file for more details: results/indonesia/masked_masked-delim.iqtree.log

Building original tree took 21.314745664596558 seconds

Please help me.
Thanks

Rian

2

Hi @riannuryadin. This appears to be a bug in IQ-TREE but may also be bad input files. In order for the Nextstrain team or the IQ-TREE to help further, please share the following three files:

  • results/indonesia/masked_masked-delim.fasta.log
  • results/indonesia/masked_masked-delim.iqtree.log
  • results/indonesia/masked_masked-delim.fasta (if possible)
3

Hi there - I just commented on a (closed) issue that mentioned a very similar error. At the risk of being redundant: I hit this same error and found this post on the iqtree forum.

Prior to hitting this error I had changed the input data used for my Nextstrain run. I.e. the series of events was:

  1. start a nextstrain build but don’t complete it
  2. add new data to the input data
  3. continue nextstrain build

In the linked post Minh Bui states that “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.” Since my sequence of actions might have led to the situation Dr Bui describes. I deleted my (partial) results, re-ran the Nextstrain build and it got past the tree building with no issues.