fail to build index

Hi

I was trying to build the sa index for a reference genome comprising all the microbial genomes and there were alot of ambiguous bases so HPG generated some warning and when it finished it did not generate the index file.

I replaced the ambiguous bases with 'N's but it failed to build the index as well.

Thank you.

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Unknown character Y at 31010902338 position
Unknown character K at 31010902347 position
Unknown character S at 31010902349 position
Unknown character R at 31010902360 position
Unknown character Y at 31010902363 position
Unknown character R at 31011381477 position
Unknown character K at 31041136755 position
Unknown character K at 31041136756 position
Unknown character W at 31041136758 position

setting chrom 59: length = 511236836 (but num_chroms = 61)
virtual_chr61
Unknown character W at 31548421032 position
reading 100.00 %...
Genome not supported: (microbiome_core_merged.fa)
Genome length: 31165433574
Number segments (chromosomes, scaffolds,...): 61

Genomes supported by HPG Aligner 2.0.1
Max. genome length: 4294967295
Max. number segments (chromosomes, scaffolds,...): 256