Error: Tree building failed

[imdanique]

Hello! I'm trying to analyze sars-cov-2 and have this kind of error after 12 of 32 steps done.

ERROR: Shell exited 2 when running: iqtree2 -ninit 2 -n 2 -me 0.05 -nt AUTO -s results/global/aligned-delim.fasta -m GTR -ninit 10 -n 4 > results/global/aligned-delim.iqtree.log
Command output was:
  ERROR: Cannot read file results/global/aligned-delim.fasta

Building a tree via:
	iqtree2 -ninit 2 -n 2 -me 0.05 -nt AUTO -s results/global/aligned-delim.fasta -m GTR -ninit 10 -n 4 > results/global/aligned-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/aligned-delim.iqtree.log

Building original tree took 0.016222715377807617 seconds
Waiting at most 1000 seconds for missing files.

[ShawnSimp]

@imdanique Hi was a solution found for this error? i am experiencing the same issue.

[huddlej]

Hi @imdanique and @ShawnSimp, there are many different reasons why IQ-TREE can fail to build a tree. In my experience with SARS-CoV-2 analyses, these issues tend to be caused by unexpected issues with the input alignment (e.g., not enough valid sequences in the alignment, incorrect sequence type or format, etc.).

To get a better sense of what is happening in your cases, you'll need to look in the log file (e.g., results/global/aligned-delim.iqtree.log) and scan this for more details about the specific error. If you can share those here, that will help us troubleshoot whether the issue is with the ncov workflow itself or with the input alignment.