Error: tree building failed

Hello, I am a new for nextstrain. I have the problem when I follow the tutorial. I appreciate if you give me some suggestion. Thank you.

Here is logs/tree_global.txt
ERROR: b’ERROR: \nERROR: *** IQ-TREE CRASHES WITH SIGNAL ILLEGAL INSTRUCTION\nERROR: *** For bug report please send to developers:\nERROR: *** Log file: results/global/subsampled_alignment-delim.fasta.log\nERROR: *** Alignment files (if possible)\n/bin/bash: line 1: 35314 Illegal instruction: 4 iqtree -ninit 2 -n 2 -me 0.05 -nt 4 -s results/global/subsampled_alignment-delim.fasta -m GTR -ninit 10 -n 4 > results/global/subsampled_alignment-delim.iqtree.log\n’
shell exited 132 when running: iqtree -ninit 2 -n 2 -me 0.05 -nt 4 -s results/global/subsampled_alignment-delim.fasta -m GTR -ninit 10 -n 4 > results/global/subsampled_alignment-delim.iqtree.log

Building a tree via:
iqtree -ninit 2 -n 2 -me 0.05 -nt 4 -s results/global/subsampled_alignment-delim.fasta -m GTR -ninit 10 -n 4 > results/global/subsampled_alignment-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/global/subsampled_alignment-delim.iqtree.log

Building original tree took 2.101897954940796 seconds

Thank you.
Yan

Hi I am still waiting the answers,
I find more information about error, maybe useful, thanks.

**** TOTAL 1.10% 0 sequences failed composition chi2 test (p-value<5%; df=3)
NOTE: France_DELIM-MQNWQTYYSCTNUJKVNVAA_10060KV_DELIM-MQNWQTYYSCTNUJKVNVAA_2020 is identical to Wuhan_DELIM-MQNWQTYYSCTNUJKVNVAA_Hu-1_DELIM-MQNWQTYYSCTNUJKVNVAA_2019 but kept for subsequent analysis
NOTE: USA_DELIM-MQNWQTYYSCTNUJKVNVAA_CA-CZB-1097_DELIM-MQNWQTYYSCTNUJKVNVAA_2020 is identical to ENV_DELIM-MQNWQTYYSCTNUJKVNVAA_USA_DELIM-MQNWQTYYSCTNUJKVNVAA_UF-11_DELIM-MQNWQTYYSCTNUJKVNVAA_2020 but kept for subsequent analysis
NOTE: France_DELIM-MQNWQTYYSCTNUJKVNVAA_10078MA_DELIM-MQNWQTYYSCTNUJKVNVAA_2020 is identical to France_DELIM-MQNWQTYYSCTNUJKVNVAA_10006HC_DELIM-MQNWQTYYSCTNUJKVNVAA_2020 but kept for subsequent analysis
NOTE: France_DELIM-MQNWQTYYSCTNUJKVNVAA_40003KA_DELIM-MQNWQTYYSCTNUJKVNVAA_2020 is identical to France_DELIM-MQNWQTYYSCTNUJKVNVAA_10015BY_DELIM-MQNWQTYYSCTNUJKVNVAA_2020 but kept for subsequent analysis
NOTE: Greece_DELIM-MQNWQTYYSCTNUJKVNVAA_259_31928_DELIM-MQNWQTYYSCTNUJKVNVAA_2020 is identical to Greece_DELIM-MQNWQTYYSCTNUJKVNVAA_139_32716_DELIM-MQNWQTYYSCTNUJKVNVAA_2020 but kept for subsequent analysis
NOTE: USA_DELIM-MQNWQTYYSCTNUJKVNVAA_CA-CZB-1085_DELIM-MQNWQTYYSCTNUJKVNVAA_2020 is identical to USA_DELIM-MQNWQTYYSCTNUJKVNVAA_CA-CZB-1045_DELIM-MQNWQTYYSCTNUJKVNVAA_2020 but kept for subsequent analysis
NOTE: 3 identical sequences (see below) will be ignored for subsequent analysis
NOTE: USA_DELIM-MQNWQTYYSCTNUJKVNVAA_VA-DCLS-0018_DELIM-MQNWQTYYSCTNUJKVNVAA_2020 (identical to ENV_DELIM-MQNWQTYYSCTNUJKVNVAA_USA_DELIM-MQNWQTYYSCTNUJKVNVAA_UF-11_DELIM-MQNWQTYYSCTNUJKVNVAA_2020) is ignored but added at the end
NOTE: USA_DELIM-MQNWQTYYSCTNUJKVNVAA_WA4-UW2_DELIM-MQNWQTYYSCTNUJKVNVAA_2020 (identical to ENV_DELIM-MQNWQTYYSCTNUJKVNVAA_USA_DELIM-MQNWQTYYSCTNUJKVNVAA_UF-11_DELIM-MQNWQTYYSCTNUJKVNVAA_2020) is ignored but added at the end
NOTE: Greece_DELIM-MQNWQTYYSCTNUJKVNVAA_37_35684_DELIM-MQNWQTYYSCTNUJKVNVAA_2020 (identical to Greece_DELIM-MQNWQTYYSCTNUJKVNVAA_139_32716_DELIM-MQNWQTYYSCTNUJKVNVAA_2020) is ignored but added at the end

For your convenience alignment with unique sequences printed to results/global/subsampled_alignment-delim.fasta.uniqueseq.phy

Create initial parsimony tree by phylogenetic likelihood library (PLL)… 0.011 seconds

NOTE: 5 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)

  1. Initial log-likelihood: -43876.481
    ERROR:
    ERROR: *** IQ-TREE CRASHES WITH SIGNAL ILLEGAL INSTRUCTION
    ERROR: *** For bug report please send to developers:
    ERROR: *** Log file: results/global/subsampled_alignment-delim.fasta.log
    ERROR: *** Alignment files (if possible)

Hi, @Yan, welcome!

Unfortunately, this appears to be a bug in IQ-TREE itself, not Augur or Nextstrain’s usage of it. I would suggest doing what the error message suggests and filing a bug report with the IQ-TREE developers (including the log + alignment files).