Problem with Combine Alignments

[DNAjunk]

Hi

We're using Ion Proton with the latest Torrent Suite (3.4.1).
When we would like to merge data from different runs belonging to the same project, then suddenly the alignment rate of the combined alignment drops to less than 20% although the alignment rates of the individual (not merged) runs were 95%.
Has anyone seen this problem before and do you know the reason/solution ?
Many thanks!

[DNAjunk]

PS: It seems that the merged bam file is present and correct and only the presentation of the alignment (rate in percentage and curve) is wrong in the torrent suite browser. Although the combine alignments process is terminated, the browser indicates "Still calculating."

[GenoMax]

Sounds like you need to get in touch with Ion Proton support. Not many on this group have Ion Protons yet.