about reproducibility

[EugeneKim76]

Hi all
I have a question about the reproducibility of canu1.3.
I used same parameters and same pacbio subreads fasta file.
However, results show slightly different genome size (1st run: 11,327,374bp, 2nd run: 11,327,379bp).
Is there any way to explain the difference?
best

[brianwalenz]

There is slight non-determinism in the order evidence reads are used during read correction and contig consensus. I suspect you're seeing the latter. The difference is typically a few indel events. I suspect these are ties -- four reads say TTGCC and four reads say TTCC -- but haven't looked in detail.

You are aware that 1.3 is extremely old, right?

[skoren]

Answered, closing. Please open a new issue if you encounter other issues with the latest code.