Bug in table based normalization with custom databases

[ctSkennerton]

terminal output is shown below, I'm using version 2.3.3-connor on brown.

app_make_results.pl -threads 20 -c app_265.config -b ~/db/ppk/ppk.fasta -t ~/db/ppk/ppk.nds.1 
---------------------------------------------------------------- 
 /srv/whitlam/bio/apps/sw/app/2.3.3-connor/app_make_results.pl
 Version 2.3.3
 Copyright (C) 2011 Michael Imelfort and Paul Dennis

 This program comes with ABSOLUTELY NO WARRANTY;
 This is free software, and you are welcome to redistribute it
 under certain conditions: See the source for more details.
---------------------------------------------------------------- 
app_analysis_20121008/results/table_based
Checking if all the config checks out...        /srv/whitlam/home/projects/EBPR_PHAGE/pyrotags/265/QA/qiime_mapping.txt ...Processing 23 samples
Finding normalisation size automatically
Normalised sample size calculated at: 1500 reads
Using taxonomy file: /srv/whitlam/home/users/uqcskenn/db/ppk/ppk.nds.1
Using blast file: /srv/whitlam/home/users/uqcskenn/db/ppk/ppk.fasta
Using aligned blast file: /srv/whitlam/bio/db/gg/qiime_default/gg_otus_4feb2011/rep_set/gg_99_otus_4feb2011_aligned.fasta
Using imputed file: /srv/whitlam/bio/db/gg/qiime_default/core_set_aligned.fasta.imputed
All good!
----------------------------------------------------------------
Start TABLE BASED NORMALISATION data set processing...
----------------------------------------------------------------
Copying reads for analysis...
Beginning OTU and Taxonomy module...
Picking OTUs for non normalised data set...
    pick_otus.py -o app_analysis_20121008/processing/table_based/uclust_picked_otus -s 0.97 -i app_analysis_20121008/processing/table_based/non_normalised.fa

Getting a representative set...
    pick_rep_set.py -i app_analysis_20121008/processing/table_based/uclust_picked_otus/non_normalised_otus.txt -f app_analysis_20121008/processing/table_based/non_normalised.fa

Assigning taxonomy for non normalised data set...
Assign taxonomy method: blast
    assign_taxonomy.py -a 20 -o app_analysis_20121008/processing/table_based -m blast -t /srv/whitlam/home/users/uqcskenn/db/ppk/ppk.nds.1 -i app_analysis_20121008/processing/table_based/non_normalised.fa_rep_set.fasta -e 0.001 -b /srv/whitlam/home/users/uqcskenn/db/ppk/ppk.fasta

Making NON NORMALISED otu table...
    make_otu_table.py -o app_analysis_20121008/results/table_based/non_normalised_otu_table.txt -t app_analysis_20121008/processing/table_based/non_normalised.fa_rep_set_tax_assignments.txt -i app_analysis_20121008/processing/table_based/uclust_picked_otus/non_normalised_otus.txt

Making NON NORMALISED otu table (Extended format)...
    reformat_otu_table.py -o app_analysis_20121008/results/table_based/non_normalised_otu_table_expanded.tsv -t app_analysis_20121008/processing/table_based/non_normalised.fa_rep_set_tax_assignments.txt -i app_analysis_20121008/results/table_based/non_normalised_otu_table.txt

Rarefaction...
    multiple_rarefactions.py -n 50 -o app_analysis_20121008/processing/table_based/rarefied_otu_tables/ -s 50 -m 50 -i app_analysis_20121008/results/table_based/non_normalised_otu_table.txt -x 19190

Normalizing non normalised table at 1500 sequences... [1500, 1000]
    multiple_rarefactions_even_depth.py -n 1000 -o app_analysis_20121008/processing/table_based/rare_tables/ -i app_analysis_20121008/results/table_based/non_normalised_otu_table.txt -d 1500 --lineages_included --k

Calculating centroid subsampled table...
Calculating centroid OTU table from tables in app_analysis_20121008/processing/table_based/rare_tables/...
  --start loading data...
  --data loaded, calculating centroid...
  --calculating distances of tables to centroid...
  --table: -1 is the centroid table
Problem running this R command:
mantel.otu <- mantel(ave,big_frame[,,min_index]);

Got the error:
'x' and 'y' must have the same length
Warning message:
In as.dist.default(ydis) : non-square matrix