hal2maf error: when I used cactus-hal2maf to convert Hal output into MAF output, it had no output

[Windyxia11]

Hello,
When I used the cactus-hal2maf to convert Hal output into MAF output, it just outputed : ##maf version=1;without anything else. My HAL output was created by using Cactus to align 7 very small gene's sequences(~200-500bp) . The command lines I had run as follows:
cactus ../output/result ./species-1.txt ../output/Align-1.hal
cactus-hal2maf ../output/result ../output/Align-1.hal ../output/Align-1.maf --refGenome NC_031164 --chunkSize 1000000 --dupeMode single --noAncestors
I don't know why this happen, please give me some suggestions, any help would be greatly appreciated!

[glennhickey]

You may want to use halStats to verify if anything aligned. You can also try running cactus-hal2maf with --refGenome Anc0 to make a MAF on the ancestor to see if there are any alignments there.

I suspect the small sequence size (smaller than we usually support) may be the underlying issue.