IQtree failed the past 2 rebuild attempts with "Some sequences (see above) are problematic, please check your alignment again"

[corneliusroemer]

The 2 past rebuilds failed with the same error message from IQtree:

[batch] [2025-03-25T20:16:33+01:00]
[batch] [2025-03-25T20:16:34+01:00] [Tue Mar 25 19:16:34 2025]
[batch] [2025-03-25T20:16:34+01:00] Finished job 51.
[batch] [2025-03-25T20:16:34+01:00] 168 of 357 steps (47%) done
[batch] [2025-03-25T20:16:34+01:00] Select jobs to execute...
[batch] [2025-03-25T20:16:35+01:00] ERROR: Shell exited 2 when running: iqtree --threads-max 4 -s results/a/G/3y/G_aligned-delim.fasta -m GTR --ninit 2 -n 2 --epsilon 0.05 -T AUTO --redo -ninit 10 -n 4 -czb > results/a/G/3y/G_aligned-delim.iqtree.log
[batch] [2025-03-25T20:16:35+01:00] Command output was:
[batch] [2025-03-25T20:16:35+01:00]   ERROR: Some sequences (see above) are problematic, please check your alignment again
[batch] [2025-03-25T20:16:35+01:00] Building a tree via:
[batch] [2025-03-25T20:16:35+01:00] 	iqtree --threads-max 4 -s results/a/G/3y/G_aligned-delim.fasta -m GTR --ninit 2 -n 2 --epsilon 0.05 -T AUTO --redo -ninit 10 -n 4 -czb > results/a/G/3y/G_aligned-delim.iqtree.log
[batch] [2025-03-25T20:16:35+01:00] 	Nguyen et al: IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies.
[batch] [2025-03-25T20:16:35+01:00] 	Mol. Biol. Evol., 32:268-274. https://doi.org/10.1093/molbev/msu300
[batch] [2025-03-25T20:16:35+01:00] ERROR: TREE BUILDING FAILED
[batch] [2025-03-25T20:16:35+01:00] ERROR: Command '['/bin/bash', '-c', 'set -euo pipefail; iqtree --threads-max 4 -s results/a/G/3y/G_aligned-delim.fasta -m GTR --ninit 2 -n 2 --epsilon 0.05 -T AUTO --redo -ninit 10 -n 4 -czb > results/a/G/3y/G_aligned-delim.iqtree.log']' returned non-zero exit status 2.
[batch] [2025-03-25T20:16:35+01:00] Please see the log file for more details: results/a/G/3y/G_aligned-delim.iqtree.log
[batch] [2025-03-25T20:16:35+01:00] Building original tree took 0.15090155601501465 seconds
[batch] [2025-03-25T20:16:35+01:00] [Tue Mar 25 19:16:34 2025]
[batch] [2025-03-25T20:16:35+01:00] Error in rule tree:
[batch] [2025-03-25T20:16:35+01:00]     jobid: 108
[batch] [2025-03-25T20:16:35+01:00]     input: results/a/G/3y/G_aligned.fasta
[batch] [2025-03-25T20:16:35+01:00]     output: results/a/G/3y/tree_raw.nwk
[batch] [2025-03-25T20:16:35+01:00]     shell:
[batch] [2025-03-25T20:16:35+01:00]
[batch] [2025-03-25T20:16:35+01:00]         augur tree             --alignment results/a/G/3y/G_aligned.fasta             --output results/a/G/3y/tree_raw.nwk             --tree-builder-args '-ninit 10 -n 4 -czb'             --nthreads 4
[batch] [2025-03-25T20:16:35+01:00]
[batch] [2025-03-25T20:16:35+01:00]