Hi all,
I'm trying to align three closely-related invertebrate genomes of about 275
Mbp using progressiveMauve (console output pasted below). I have previously
aligned similar genomes, but this time I'm getting an error code of 137,
which I haven't seen described elsewhere. I have 70G RAM and should have
sufficient hard drive space, though there could possibly be a conflict with
large backups being temporarily written to /tmp overnight.
So my questions are:
1.) does error code 137 signify a disk space shortage, and if not,
2.) can you give me any other information on this code?
Thanks,
Becca
##console output:
trying path ./linux-x64/progressiveMauve
Running alignment.
Executing
progressiveMauve
--output=taxon1-taxon2-outgroup
--output-guide-tree=taxon1-taxon2-outgroup.guide_tree
--backbone-output=taxon1-taxon2-outgroup.backbone
/media/labcomp/NGSdata/taxon1.fa
/media/labcomp/NGSdata/taxon2.fa
/media/labcomp/NGSdata/outgroup.fa
Storing raw sequence at /tmp/rawseq12032.000
Sequence loaded successfully.
/media/labcomp/NGSdata/taxon1.fa 273109044 base pairs.
Storing raw sequence at /tmp/rawseq12032.001
Sequence loaded successfully.
/media/labcomp/NGSdata/taxon2.fa 273109044 base pairs.
Storing raw sequence at /tmp/rawseq12032.002
Sequence loaded successfully.
/media/labcomp/NGSdata/outgroup.fa 283828998 base pairs.
Using weight 19 mers for initial seeds
Creating sorted mer list
Create time was: 48 seconds.
Creating sorted mer list
Create time was: 48 seconds.
Creating sorted mer list
Create time was: 44 seconds.
0%..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%..done.
using default bp penalty: 196306
using default bp estimate min score: 588917
Starting with 9524545 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0.104825 0.439205
0.104825 0 0.441706
0.439205 0.441706 0
Writing guide tree to taxon1-taxon2-outgroup.guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 327147 initial LCBs
Using scaled bp penalty: 378169
Pair (0,1) has 1 well-supported breakpoints
Pair 0, 2 has 1022274 initial LCBs
Using scaled bp penalty: 58246.4
Pair (0,2) has 1791 well-supported breakpoints
Pair 1, 2 has 1042887 initial LCBs
Using scaled bp penalty: 57214.3
Pair (1,2) has 1817 well-supported breakpoints
genome content distance matrix:
0 0.104825 0.439205
0.104825 0 0.441706
0.439205 0.441706 0
bp distance matrix:
0.9 0.000216867 0.38841
0.000216867 0.9 0.394048
0.38841 0.394048 0.9
Aligning...
Aligning node 3 to 4 via 1!
get ancestral matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 2488444 tracking matches
There are 4976888 / 12442220 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 327509 pairwise LCBs
scaling bp penalty by conservation weight:
0.104825
scaling bp penalty by bp weight:
0.000216867
Greedy BPE
Scoring with scaled breakpoint penalty: 126002
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%..done
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 3 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(3) has 1 intervals
descendant 1(4) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 1.26132e+10
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 2 new matches outside LCBs
0,0 has an additional 17332 matches
Restoring backed up alignment tree...
1,0 has 17332 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 2202926 tracking matches
There are 4405852 / 11014630 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 348 pairwise LCBs
scaling bp penalty by conservation weight:
0.104825
scaling bp penalty by bp weight:
0.000216867
Greedy BPE
Scoring with scaled breakpoint penalty: 126002
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%..done
Arrived at 3 intervals
Adding unaligned intervals
addUnalignedIntervals yields 11 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(3) has 1 intervals
descendant 1(4) has 1 intervals
propagateDescendantBreakpoints yields 3 intervals
Creating ancestral ordering
Previous anchoring score: 1.26132e+10, new anchor score: 1.12416e+10
propagating ancestral breakpoints
performing a gapped alignment
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.
Aligning node 1 to 2 via 0!
get ancestral matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
construct LCB tracking matches
There are 3284810 tracking matches
There are 13008197 / 16424050 components used
init tracking match LCB tracking
pairwise score tracking matches
get pairwise LCBs
there are 2179961 pairwise LCBs
scaling bp penalty by conservation weight:
0.439205
0.441706
scaling bp penalty by bp weight:
0.38841
0.394048
Greedy BPE
Scoring with scaled breakpoint penalty: 7262.22
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%..done
Arrived at 10742 intervals
Adding unaligned intervals
addUnalignedIntervals yields 32131 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 1 intervals
descendant 1(2) has 1 intervals
propagateDescendantBreakpoints yields 10742 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 1.6137e+10
Backing up alignment tree...
propagating ancestral breakpoints
Exited with error code: 137
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