IQ-Tree does some sanity checks before it starts the analysis. Likely, the problem is really what it says: The sequence has a different length than the other sequences. All sequences must have identical length. If you have problems checking this, try to save the alignment in FASTA format or convert the phylip formated file to FASTA format using EMBOSS seqret and try again. Another problem may be that the sequence identifier is too long for phylip format. Then again, IQ-Tree runs fine on FASTA files with no restrictions on identifier length.

I am going to assume that all your sequences have the same length, as most alignment programs take care of this properly. If so, it is likely that you have two sequences with the same name, or a very similar name over most of its length. Sequence names must be unique.