Hi Aaron,
> As for the problem on windows, would you be able to send a bit more of
> the text preceding the exit error message? It would help to know what
> the aligner was doing right before it crashed.
I get the same crash on Windows (7.1, x64, Java x64) with the new Mauve
release 2.4, regardless if I use a Genbank or a Fasta file. The error with
the Genbank File is slightely different. Here is the full log:
Exception in thread "AWT-EventQueue-0" java.lang.InternalError: Unable to
bind D:\Dropbox\tmp\RSA493.gbk to parent
at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source)
at sun.awt.shell.Win32ShellFolder2$4.call(Unknown Source)
at sun.awt.shell.Win32ShellFolderManager2$ComInvoker.invoke(Unknown Source)
at sun.awt.shell.ShellFolder.invoke(Unknown Source)
at sun.awt.shell.Win32ShellFolder2.getIShellFolder(Unknown Source)
at sun.awt.shell.Win32ShellFolder2.access$200(Unknown Source)
at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source)
at sun.awt.shell.Win32ShellFolder2$16.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at sun.awt.shell.Win32ShellFolderManager2$ComInvoker$3.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Running alignment.
Executing
win64\progressiveMauve
--output=E:\Temp\Mauve\493_C2
--output-guide-tree=E:\Temp\Mauve\493_C2.guide_tree
--backbone-output=E:\Temp\Mauve\493_C2.backbone
D:\Dropbox\tmp\RSA493.gbk\RSA493.gbk
D:\Dropbox\tmp\C2\C2.fasta
Exception FileNotOpened thrown from
Unknown() in ..\libGenome\gnFileSource.cpp 67
Called by Unknown()
Exited with error code: -1073741676
Just by replacing the Genbank file by its corresponding file starts the
alignment process but stops with the same error code a few seconds later:
Running alignment.
Executing
win64\progressiveMauve
--output=E:\Temp\Mauve\493_C2
--output-guide-tree=E:\Temp\Mauve\493_C2.guide_tree
--backbone-output=E:\Temp\Mauve\493_C2.backbone
D:\Dropbox\tmp\RSA493\PacBio\RSA493_i2.fa
D:\Dropbox\tmp\C2\C2.fasta
Storing raw sequence at C:\Windows\TEMP\rawF18F.tmp
Sequence loaded successfully.
D:\Dropbox\tmp\RSA493\PacBio\RSA493_i2.fa 2032763 base pairs.
Storing raw sequence at C:\Windows\TEMP\rawF1FD.tmp
Sequence loaded successfully.
D:\Dropbox\tmp\C2\C2.fasta 1996544 base pairs.
Using weight 15 mers for initial seeds
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: 146595
using default bp estimate min score: 439784
Starting with 92 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0.00996889
0.00996889 0
Writing guide tree to E:\Temp\Mauve\493_C2.guide_tree
Exited with error code: -1073741819
--
Kind regards,
Mathias
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