[Mauve-users] Fwd: Reorder issue
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From: mali s. <ma...@ar...> - 2016-08-15 06:50:03
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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 -- ================================ Mali Salmon-Divon, PhD Department of Molecular Biology Ariel University Ariel, ISRAEL Phone: +972-546-350197 <ma...@ar...> Email: ma...@ar... |