pplacer question

[bfp7]

Can anyone please help out with the following error message I am getting from pplacer??

Running pplacer v1.1.alpha17-6-g5cecf99 analysis on Q2KYQ0_BORA1.fasta...
Didn't find any reference sequences in given alignment file. Using supplied reference alignment.
Warning: using a statistics file directly is now deprecated. We suggest using a reference package. If you already are, then please use the latest version of taxtastic.
WARNING: your stats file is from RAxML 8.2.8; RAxML has been tested with the following versions: 7.0.4; 7.2.3; 7.2.5; 7.2.6; 7.2.7
I'm going to try parsing as if this was version 7.2.3Problem parsing info or stats fileRAxML_info.10_Q2KYQ0
Uncaught exception: Parse_stats.Stats_parsing_error("too many partitions. Only one is allowed.")

I included a reference alignment in fasta format but pplacer does not like it. The alignment was generated with muscle and the nucleotide sequences are derived from a Uniref90 cluster (we used a script to acquire the corresponding DNA sequences from the Uniref90 protein sequences). Jeff Bowman indicates that the reference sequences need to be aligned against an existing reference alignment. What does this mean?? Do I also need to align the query reads???

Does pplacer not like RAxML v8.2? Should I use an earlier version??

Thanks!!
Brian