terminate called after throwing an instance of 'std::runtime_error'

[bellstwohearted]

root@lt5h8:~/dataset/hg38-1# cudamapper -a 2 hg38-1.mut hg38.fa
-C / --target-indices-in-host-memory not set, using -Q / --query-indices-in-host-memory value: 10
-c / --target-indices-in-device-memory not set, using -q / --query-indices-in-device-memory value: 5
Query file: hg38-1.mut, number of reads: 25
Target file: hg38.fa, number of reads: 25
Programmatically looking for max cached memory
Using device memory cache of 16376457462 bytes
Device 0 took batch 1 out of 9 batches in total
Aligning 0 overlaps (0x0) with batch size 0
terminate called after throwing an instance of 'std::runtime_error'
  what():  Max alignments must be at least 1.
Aborted (core dumped)

What causes this problem and how to fix it??

[ahehn-nv]

Hi @bellstwohearted ! I am sorry for the late reply. I just saw the issue now. We reorganized responsibilities end of November and this issue slipped our attention.
I think the problem is cudamapper not finding any overlaps to align. If this is the case, our error message isn't very helpful and we should definitely improve that.

However, it is hard to say for sure without knowing more about the data set.
If you are still interested in this, could you tell me how long the 25 reads are?
Furthermore, have you tried running with -a 1?