N<4, iqtree: ERROR: It makes no sense to perform bootstrap with less than 4 sequences.

[cmkobel]

Either there should be an if statement that shuts bootstrapping off when N<4, or this error should be simply ignored. I guess FastTree is good enough when N<4.

Activating conda environment: ../../../../../../conda-envs/108c93bf8519b05838cdca347b9bf6fa
IQ-TREE multicore version 2.2.5 COVID-edition for Linux 64-bit built Sep 15 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    threadripper (AVX2, FMA3, 503 GB RAM)
Command: iqtree -s results_ac2/roary/core_gene_alignment.aln -m GTR --boot 100 --prefix results_ac2/iqtree/core_genome_iqtree -redo
Seed:    488167 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Fri Feb  2 12:58:02 2024
Kernel:  AVX+FMA - 1 threads (128 CPU cores detected)

HINT: Use -nt option to specify number of threads because your CPU has 128 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.

Reading alignment file results_ac2/roary/core_gene_alignment.aln ... Fasta format detected
Reading fasta file: done in 0.100144 secs using 95.78% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.505062 secs using 31.51% CPU
Alignment has 3 sequences with 1882304 columns, 105 distinct patterns
0 parsimony-informative, 10079 singleton sites, 1872225 constant sites
       Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 7.54371e-06 secs
   1  116_2    0.65%    passed     98.28%
   2  E8202    0.84%    passed     99.89%
   3  SRR24    0.78%    passed     99.22%
****  TOTAL    0.76%  0 sequences failed composition chi2 test (p-value<5%; df=3)
NOTE: minimal branch length is reduced to 0.000000053126 for long alignment
ERROR: It makes no sense to perform bootstrap with less than 4 sequences.

[cmkobel]

A possible solution would be to make a checkpoint that checks if there is enough samples, but it seems a bit overengineered.