Phylogenetic placement error using iqtree2

[huanqihe]

Hello,

I follow this tutorial (http://www.iqtree.org/doc/recipes/phylogenetic-placement) to add new sequences from my samples into an exisiting tree. I ran the command line:

bin/iqtree2 -s sequences.fa -g iqtree.nex

But the error below persisted regardless of my efforts of shorten the sequence names or split the sequences into multiple lines.

"ERROR: Sequence RS_GCF_000770585.1NZ_JNCF01000026.1 contains too many characters (1539)
ERROR: Sequence GB_GCA_031291095.1JARLJR010000142.1 contains not enough characters (648)
ERROR: Sequence RS_GCF_900639985.1NZ_CAAAIM010000002.1 contains too many characters (1540)
ERROR: Sequence GB_GCA_013697955.1JACCVV010000041.1 contains not enough characters (336)
ERROR: Sequence RS_GCF_026191355.1~NZ_JAPHOQ010000001.1 contains too many characters (1540)"

What does this error mean? What is the length limit?

[roblanf]

The errrors suggest that there is something strange going on with your alignment. In an alignmnet, all sequences should be aligned to each other, and thus (with gaps) have the same length.

If you'd like help, please upload your command line, input files, and output files, and I'll take a look.