Hi there,
I'm using progressive Mauve to align a draft genome (~2.8 Gbp) to the
mouse mm10 build (also ~2.8Gbp). Downloading the snapshot update of version
2.3.1 definitely helped get the alignment past the point of error that I was
previously encountering. I have at my disposal a computer with more than enough
memory to accommodate this, but the alignment as it stands has already been
running for over 72 hours. The last update shown on the Mauve console is as
follows:
Performing final pass iterative refinement
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Fix left ends
done.
root alignment has 85351 superintervals
root alignment length: 3971048854
The computer still shows that progressiveMauve is running, but there
has been no update to any of the files or the Mauve Console for ~8hrs. My first
question is whether or not this is normal? I just want to make sure something
hasn't gone wrong before I let it continue running. My second question is
whether or not I can split up my fast files and run multiple threads at once,
then combine these at the end to speed up the process? My IT guru tells me our
computer has enough memory to do this, but it's just whether or not the program
will allow this and/or if the alignment could be compromised in some way by
doing this.
Thanks for all the help.
Cheers,
Brianna Flynn------------------------------------------------------------------------------
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