k-mer counts were clipped to 255

[a-kroh]

Hi,

Gap2Seq looks like a great tool and mostly performed well when I tested it (closing most smaller [<1000 bp] gaps in my test dataset). However, I always get an error message while the program runs and I am worrying that this might affect the ability of the program to close larger gaps. Here is the error message (plus adjacent lines from the log):

2018-09-07 17:41:37: Round 62, 0% nodes remaining
2018-09-07 17:41:37: Assigning values
2018-09-07 17:41:39: Setting abundances of 42410107 kmers.
2018-09-07 17:41:52: WARNING: 100379 k-mer counts were clipped to 255
2018-09-07 17:42:11: Saving mphf to disk

I assume it means that the program was not able to correctly store kmer counts due to some memory limitation. Increasing the memory available to the program (to 200 GB) does not seem to make a difference though.

Any ideas? All the best Andreas