Hey Aaron,
I used Mauve as a standalone application many years ago. Recently I started using it again through the plugin interface in Geneious Prime. It seems to be a potentially great solution for analyzing the polished contig data generated by Plasmidsaurus (https://plasmidsaurus.com/bacteria_sequencing).
However, when I try to align more than about 5 bacterial genomes, I get an error message (below).
Genious suggested this was due to a Windows memory leak error.
I know Mauve was released a long time ago, but I'm curious if you think you'll ever have time to investigate where this memory leak might be coming from.
Thanks,
Dan
Mauve exited with abnormal exit code: -1073741811 For help with this issue, send the details along with your files/document using 'support' button in Toolbar. Details from standard error: Details from standard output: storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4618.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve1182067682795937448.fasta 3567409 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4638.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve15883018511461415970.fasta 3572661 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4668.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve3445774262338665250.fasta 3567506 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4688.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve3227101329016086766.fasta 3573090 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw46b8.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve18359883362699538498.fasta 3567407 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw46e8.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve8109322732495249038.fasta 3567437 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4708.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve1057208941296962951.fasta 3572652 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4738.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve7046801981060835674.fasta 3568567 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4768.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve6309044540007114920.fasta 3570023 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4798.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve870851801642912132.fasta 3567550 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw47b8.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve10263980973674758848.fasta 3564740 base pairs. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 0 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. 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%..done. using default bp penalty: 152369 using default bp estimate min score: 457108 starting with 760 multi-matches computing genome content distance matrix... genome conservation distance matrix: 0 0.000575725 0.00133688 0.000910944 0.001455 0.000741769 0.00133772 0.00077035 0.00138443 0.000748923 0.000751718 0.0013401 0.00091613 0.00111311 0.000621811 0.000378034 0.000575725 0 0.000838573 0.000341598 0.000912766 0.000187114 0.000785766 0.000682221 0.00084893 0.000180946 0.000194121 0.000824149 0.000355754 0.000543141 0.000494274 0.000214376 0.00133688 0.000838573 0 0.00115141 0.00041688 0.000995815 7.66935e-005 0.0014325 0.000318087 0.000990773 0.00100338 7.44544e-005 0.00115253 0.00135293 0.00120925 0.00102444 0.000910944 0.000341598 0.00115141 0 0.00124954 0.000167716 0.00109988 0.00100011 0.0011629 0.000160709 0.000177105 0.00114609 8.96718e-006 0.000201679 0.000812297 0.000531726 0.001455 0.000912766 0.00041688 0.00124954 0 0.00108667 0.000399387 0.00156688 0.000464857 0.00108891 0.00108303 0.000418559 0.00126103 0.00145106 0.000940312 0.00112256 0.000741769 0.000187114 0.000995815 0.000167716 0.00108667 0 0.000949459 0.000840514 0.00101388 7.00789e-006 2.80314e-005 0.000981674 0.000181449 0.000369328 0.000654668 0.000378148 0.00133772 0.000785766 7.66935e-005 0.00109988 0.000399387 0.000949459 0 0.00142452 0.000326764 0.000939235 0.00095254 8.50907e-005 0.00110688 0.00130141 0.001222 0.00097288 0.00077035 0.000682221 0.0014325 0.00100011 0.00156688 0.000840514 0.00142452 0 0.00146553 0.000837992 0.000846958 0.00142173 0.000996605 0.00120239 0.00110315 0.000871525 0.00138443 0.00084893 0.000318087 0.0011629 0.000464857 0.00101388 0.000326764 0.00146553 0 0.00100226 0.00103111 0.000340199 0.00116892 0.00136443 0.00124312 0.00103588 0.000748923 0.000180946 0.000990773 0.000160709 0.00108891 7.00789e-006 0.000939235 0.000837992 0.00100226 0 1.63984e-005 0.000985455 0.000169677 0.000362323 0.000651725 0.000371138 0.000751718 0.000194121 0.00100338 0.000177105 0.00108303 2.80314e-005 0.00095254 0.000846958 0.00103111 1.63984e-005 0 0.00099344 0.000191118 0.000378716 0.000664335 0.000387538 0.0013401 0.000824149 7.44544e-005 0.00114609 0.000418559 0.000981674 8.50907e-005 0.00142173 0.000340199 0.000985455 0.00099344 0 0.00114441 0.00134761 0.00121864 0.00101912 0.00091613 0.000355754 0.00115253 8.96718e-006 0.00126103 0.000181449 0.00110688 0.000996605 0.00116892 0.000169677 0.000191118 0.00114441 0 0.000210645 0.000834298 0.000540698 0.00111311 0.000543141 0.00135293 0.000201679 0.00145106 0.000369328 0.00130141 0.00120239 0.00136443 0.000362323 0.000378716 0.00134761 0.000210645 0 0.00101374 0.000733189 0.000621811 0.000494274 0.00120925 0.000812297 0.000940312 0.000654668 0.001222 0.00110315 0.00124312 0.000651725 0.000664335 0.00121864 0.000834298 0.00101374 0 0.000280622 0.000378034 0.000214376 0.00102444 0.000531726 0.00112256 0.000378148 0.00097288 0.000871525 0.00103588 0.000371138 0.000387538 0.00101912 0.000540698 0.000733189 0.000280622 0 writing guide tree to c:\users\d89659k\appdata\local\temp\gui976b.tmp storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4618.tmp
Hey Aaron,
I used Mauve as a standalone application many years ago. Recently I started using it again through the plugin interface in Geneious Prime. It seems to be a potentially great solution for analyzing the polished contig data generated by Plasmidsaurus (https://plasmidsaurus.com/bacteria_sequencing).
However, when I try to align more than about 5 bacterial genomes, I get an error message (below).
Genious suggested this was due to a Windows memory leak error.
I know Mauve was released a long time ago, but I'm curious if you think you'll ever have time to investigate where this memory leak might be coming from.
Thanks,
Dan
Mauve exited with abnormal exit code: -1073741811 For help with this issue, send the details along with your files/document using 'support' button in Toolbar. Details from standard error: Details from standard output: storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4618.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve1182067682795937448.fasta 3567409 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4638.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve15883018511461415970.fasta 3572661 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4668.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve3445774262338665250.fasta 3567506 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4688.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve3227101329016086766.fasta 3573090 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw46b8.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve18359883362699538498.fasta 3567407 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw46e8.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve8109322732495249038.fasta 3567437 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4708.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve1057208941296962951.fasta 3572652 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4738.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve7046801981060835674.fasta 3568567 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4768.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve6309044540007114920.fasta 3570023 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4798.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve870851801642912132.fasta 3567550 base pairs. storing raw sequence at c:\users\d89659k\appdata\local\temp\raw47b8.tmp sequence loaded successfully. c:\users\d89659k\geneious 2025.1 data\transient\1744306972930\x\21\mauve10263980973674758848.fasta 3564740 base pairs. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 0 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. creating sorted mer list create time was: 1 seconds. 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%..done. using default bp penalty: 152369 using default bp estimate min score: 457108 starting with 760 multi-matches computing genome content distance matrix... genome conservation distance matrix: 0 0.000575725 0.00133688 0.000910944 0.001455 0.000741769 0.00133772 0.00077035 0.00138443 0.000748923 0.000751718 0.0013401 0.00091613 0.00111311 0.000621811 0.000378034 0.000575725 0 0.000838573 0.000341598 0.000912766 0.000187114 0.000785766 0.000682221 0.00084893 0.000180946 0.000194121 0.000824149 0.000355754 0.000543141 0.000494274 0.000214376 0.00133688 0.000838573 0 0.00115141 0.00041688 0.000995815 7.66935e-005 0.0014325 0.000318087 0.000990773 0.00100338 7.44544e-005 0.00115253 0.00135293 0.00120925 0.00102444 0.000910944 0.000341598 0.00115141 0 0.00124954 0.000167716 0.00109988 0.00100011 0.0011629 0.000160709 0.000177105 0.00114609 8.96718e-006 0.000201679 0.000812297 0.000531726 0.001455 0.000912766 0.00041688 0.00124954 0 0.00108667 0.000399387 0.00156688 0.000464857 0.00108891 0.00108303 0.000418559 0.00126103 0.00145106 0.000940312 0.00112256 0.000741769 0.000187114 0.000995815 0.000167716 0.00108667 0 0.000949459 0.000840514 0.00101388 7.00789e-006 2.80314e-005 0.000981674 0.000181449 0.000369328 0.000654668 0.000378148 0.00133772 0.000785766 7.66935e-005 0.00109988 0.000399387 0.000949459 0 0.00142452 0.000326764 0.000939235 0.00095254 8.50907e-005 0.00110688 0.00130141 0.001222 0.00097288 0.00077035 0.000682221 0.0014325 0.00100011 0.00156688 0.000840514 0.00142452 0 0.00146553 0.000837992 0.000846958 0.00142173 0.000996605 0.00120239 0.00110315 0.000871525 0.00138443 0.00084893 0.000318087 0.0011629 0.000464857 0.00101388 0.000326764 0.00146553 0 0.00100226 0.00103111 0.000340199 0.00116892 0.00136443 0.00124312 0.00103588 0.000748923 0.000180946 0.000990773 0.000160709 0.00108891 7.00789e-006 0.000939235 0.000837992 0.00100226 0 1.63984e-005 0.000985455 0.000169677 0.000362323 0.000651725 0.000371138 0.000751718 0.000194121 0.00100338 0.000177105 0.00108303 2.80314e-005 0.00095254 0.000846958 0.00103111 1.63984e-005 0 0.00099344 0.000191118 0.000378716 0.000664335 0.000387538 0.0013401 0.000824149 7.44544e-005 0.00114609 0.000418559 0.000981674 8.50907e-005 0.00142173 0.000340199 0.000985455 0.00099344 0 0.00114441 0.00134761 0.00121864 0.00101912 0.00091613 0.000355754 0.00115253 8.96718e-006 0.00126103 0.000181449 0.00110688 0.000996605 0.00116892 0.000169677 0.000191118 0.00114441 0 0.000210645 0.000834298 0.000540698 0.00111311 0.000543141 0.00135293 0.000201679 0.00145106 0.000369328 0.00130141 0.00120239 0.00136443 0.000362323 0.000378716 0.00134761 0.000210645 0 0.00101374 0.000733189 0.000621811 0.000494274 0.00120925 0.000812297 0.000940312 0.000654668 0.001222 0.00110315 0.00124312 0.000651725 0.000664335 0.00121864 0.000834298 0.00101374 0 0.000280622 0.000378034 0.000214376 0.00102444 0.000531726 0.00112256 0.000378148 0.00097288 0.000871525 0.00103588 0.000371138 0.000387538 0.00101912 0.000540698 0.000733189 0.000280622 0 writing guide tree to c:\users\d89659k\appdata\local\temp\gui976b.tmp storing raw sequence at c:\users\d89659k\appdata\local\temp\raw4618.tmp