iqtree2 failure for monkeypox - wrong outgroup header in nextalign.aligned.fasta

[uphl-biongs]

iqtree2 failure for monkeypox - wrong outgroup header in nextalign.aligned.fasta

[DrB-S]

I created a fastas directory and added NC_063383.1.fasta to the dir.
This time Cecret completed successfully and iqtree2 created a tree, but NC_063383.1 was represented twice in both snp-dists.txt and iqtree2 as:
NC_063383.1
and
ref_in_coord

annotation:vadr (QC metrics) failed (as it has been doing) and I received the following warning:

WARN: Input tuple does not match input set cardinality declared by process summary -- offending value: [AZMPXV-0001, 11581, 185612, 0, 197193, Consensus_AZMPXV-0001.consensus_threshold_0.6_quality_20, fastp 0.23.2, minimap2 : 2.24-r1122, iVar version 1.3.1, 6401948, 3259911, 3259911, 0.21 0.21, 91.03, 64, 67, 0, 100, 18.3682, 179560, null, null]

[erinyoung]

I ran into this same issue. Stand by.

[DrB-S]

I think I found it in your documentation.
I cannot specify the outgroup in params.iqtree2_outgroup AND params.iqtree2_options in the config file.
I commented out the first mention and am testing:
//params.iqtree2_outgroup = 'NC_063383.1'
params.iqtree2_options = '-ninit 2 -n 2 -me 0.05 -m GTR -o NC_063383.1'

[erinyoung]

Yeah. That'll fail things. I separated the two variables so that it was easier to specify the outgroup.