[Mauve-users] Fwd: Reorder issue

[mali s. <ma...@ar...>]

Dear users
I try to reorder assembled contigs (de novo assembly of 500Mb plant genome.
I have ~1M scaffolds) based on reference genome.
I used the command
nohup java  -Xmx100G -cp /home/mauve_2.3.1/Mauve.jar
org.gel.mauve.contigs.ContigOrderer
-output ./ -ref /data/genomes/vitis/ref.fa -draft ../scafSeq &
The program finish running without errors, but except of the alignment1
directory, no output files were created.

The last lines in the log file, and the content of alignment1 directory are
below
Any idea what got wrong?
Thanks
Mali

Greedy BPE
Scoring with scaled breakpoint penalty: 4000
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%..done
Arrived at 180991 intervals
Adding unaligned intervals
addUnalignedIntervals yields 540256 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 180991 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 9.25996e+09
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search

The alignment1 directory contains the following files:
472M  ref.fa
640M scafSeq
2.0G ref.fa.sslist
2.6G scafSeq.sslist
0 alignment1 (empty)
31 alignment1.guide_tree




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Mali Salmon-Divon, PhD
Department of Molecular Biology
Ariel University
Ariel, ISRAEL
Phone: +972-546-350197 <ma...@ar...>
Email: ma...@ar...