reference alignment too narrow?

[danchurch]

Hello SINA team,

thanks for the really great aligner. I seem to be having troubles using my own MSA. I'm using an alignment provided by Cyanoseq (available here). I convert to an arb database as the documentation:

sina -i CyanoSeq_1.2.fasta -o CyanoSeq_1.2.arb --prealigned

No errors given. Then I attempt to align a set of additional Nostoc sequences (available here). I use the following:

sina \
  -i cyanoseqExtraNostocs_ours.fa \
  -o cyanoseqExtraNostocsOur16S.afa \
  --db CyanoSeq_1.2.arb 

I then get a lot of errors, and only 36 out of many sequences are aligned. The following error is repeated hundreds of times, for nearly all of the sequences in the reference MSA to which I am trying to align my Nostoc sequences:

[ARB I/O] loadKey failed: sequence 'Nodulariaceae_Purpureonostoc_tibetica_CHAB5880_MN381943.1' not found

I also receive the following error multiple times interspersed throughout:

[align] Internal error - incomplete data for alignment **(false-true-false)**

And the run ends unsuccessfully giving the following final error:

[SINA] Error during program execution: std::runtime_error ERROR: no space to left and right?? sequence longe than alignment?!

I assume there are multiple issues at work. The last error seems to be due to the fact that I have number of reads I would like to align that are longer than the number of columns reference alignment. Is this not possible, and if not, what can be done?

Thanks in advance.