Hi Becca, thanks for writing about this and for sending the console
output. It helps.
Exit code 137 is fairly generic, indicating the progressiveMauve process
was killed with signal 9, which is something that can either be done
manually or by the system I think. Insight here:
http://tldp.org/LDP/abs/html/exitcodes.html
Yes, progressiveMauve uses /tmp. If /tmp is limited you might try
pointing the software to store temporary files in another location by
setting $TMP or $TMPDIR . Apparently this hasn't been working for
everybody so I'd suggest testing on a small dataset first to confirm
that the rawseq* and guide tree etc temporary files land in the
specified directory before launching a long-running alignment.
It could also be a memory usage issue... you might wrap the call to
progressiveMauve with /usr/bin/time -v to get a record of the peak
memory allocation. linuxes will kill processes that consume too much
RAM, though different kernel versions behave differently in this regard.
Best,
-Aaron
On Wed, 2015-11-25 at 15:20 -0500, Becca Love wrote:
> 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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--
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
UTS CRICOS Provider Code: 00099F
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