progressivemauve sequences missing from output

[harry.pickering]

Dear all,

I recently ran a progressivemauve alignment of 266 bacterial sequences (~1x10^6 bp each). This completed with no errors, however the bbcols and backbone files only contain data for 241 sequences.

The xmfa file shows that all 266 were read in succesfully, but the alignments miss the final 20-odd sequences.

I ran an alignment with 260 copies of short made-up sequences to see if progressivemauve has a max sequence limit, but this completed properly.

Has anyone experienced a similar problem/have any ideas what might have caused the issue?

Thanks in advance,
Harry