Thanks, Aaron.
To follow up in case someone else has a similar error and comes looking for
the answer, I moved the alignment to a node with more memory and it ran
without a problem. I can't absolutely rule out /tmp but it was probably the
memory.
On Thu, Nov 26, 2015 at 6:44 PM, Aaron Darling <aaron.darl...@uts.edu.au>
wrote:
> 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
>
>
>
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