Mauve Activity
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Activity for Mauve
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Yong Yang created ticket #66
Exited with error code: 3
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mauve is not running
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Daniel Vieira da Silva created ticket #26
Caught signal 11
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Oren Milman posted a comment on ticket #64
I have created the ticket twice accidentally (on the first time, sourceforge told me that creating the ticket failed). I apologize. Please close (or delete, if possible) this duplicate.
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a workaround for mauveAligner: symbol lookup error: mauveAligner: undefined symbol: _ZN6genome10gnSequence10LoadSourceESs
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a workaround for mauveAligner: symbol lookup error: mauveAligner: undefined symbol: _ZN6genome10gnSequence10LoadSourceESs
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Gizem Avcı created ticket #62
Thread-7
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Devina Bhookhun-Seeruttun created ticket #61
Caught signal 11
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Ann Gill posted a comment on ticket #56
I have the same problem-- macOS Catalina v 10.15.4
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Ekaterina Bocharova posted a comment on ticket #56
Hi! I have the same error: gnDefs.cpp:8:7: error: 'abs' is missing exception specification 'throw()' int64 abs( int64 a ){ ^ throw() /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/stdlib.h:113:44: note: previous declaration is here inline _LIBCPP_INLINE_VISIBILITY long long abs(long long __x) _NOEXCEPT ... ^ 1 error generated. make[1]: [gnDefs.lo] Error 1 make[1]: Waiting for unfinished jobs.... make: *** [install-recursive] Error 1 I'm compiling...
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Anthony Einfeldt created ticket #60
Viewer stuck reading file
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printer error created ticket #59
java visualization errors
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John Joe posted a comment on ticket #58
That's weird - as far as I can tell the stream never closes itself until the program exits so output.flush() should have had the same effect. I had a similar problem a few days before you posted your issue where the file was not completely written and added output.flush() using a different method which solved it for me. The code is convoluted so I might be missing something. Well, as long as it eventually ended up working it's fine I guess.
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andrew davis posted a comment on ticket #58
Just FYI I changed: line 133 output.flush(); -> output.close(); The file was closing before it was done writing.
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Thanks John! That helped. I had to run: jar cf Mauve-2.jar ext images org
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I can't help you much with #1 since I never tried building from source myself, but for #2 make sure you still have the other necessary libraries in their proper place - your error isn't a version error but a "I can't find the stuff this program relies on error" Specifically, the file/folder layout should be (relative to Mauve.jar's directory) ./Mauve.jar ./ext/bytecode-1.9.2-SNAPSHOT.jar ./ext/commons-cli-1.2.jar ./ext/core-1.9.2-SNAPSHOT.jar ./ext/gui-1.9.2-SNAPSHOT.jar These libraries should have...
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I can't help you much with #1 since I never tried building from source myself, but for #2 make sure you still have the other necessary libraries in their proper place - your error isn't a version error but a "I can't find the stuff this program relies on error" Specifically, the file/folder layout should be (relative to Mauve.jar's directory) ./Mauve.jar ./ext/bytecode-1.9.2-SNAPSHOT.jar ./ext/commons-cli-1.2.jar ./ext/core-1.9.2-SNAPSHOT.jar ./ext/gui-1.9.2-SNAPSHOT.jar
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Thanks John for the quick reponse. I tried doing a fresh build in a docker container, following the build instructions (http://darlinglab.org/mauve/developer-guide/building.html) ran into a Makefile error: Makefile:761: recipe for target 'Aligner.lo' failed make[1]: [Aligner.lo] Error 1 make[1]: Leaving directory '/root/build/libMems/libMems' Makefile:546: recipe for target 'install-recursive' failed make: [install-recursive] Error 1 compiled SnpExporter.java into org/gel/mauve/analysis/ and re-created...
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Hello, I'm not the developer, but I think I know may know what is happening: If you downloaded it directly from the website (development snapshot 2015-02-26, or really any version that is older than the latest revision r4736 (made on 2016-06-08), using the SnpExporter may result in an incomplete output file. Your choices are: 1. Build Mauve from source 2. Take the code from https://sourceforge.net/p/mauve/code/HEAD/tree//mauve/trunk/src/org/gel/mauve/analysis/SnpExporter.java, compile it, so you...
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Snp file from a command line
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Jarrett F. Lebov created ticket #57
Exited with error code: -1073741676
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Marius Walter created ticket #56
Error when compiling
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Pat created ticket #55
Score an assembly Error
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Yaser Alsahafi posted a comment on ticket #52
I faced the same problem when aligning multiple genomes in .gb format. However, I was able to overcome it be using only on file in .gb format, which was my reference genome, and the other files in .fasta format. This was I was ablt to compute the DJC distance. I tried to contact the email listed in the erorr, but did get any response. In interpretation, I hope somebody could help in resolving this issue.
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Kazi Ahsan created ticket #54
Mauve Contig Mover: getting error while reordering genbank output
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James Abbott created ticket #53
Additional header required for recent boost versions
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seshank created ticket #52
DCJ rearrangement analysis error
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Harry Pickering created ticket #51
progressivemauve sequences missing from output
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Jessie created ticket #50
Mauve Error 134 with move contigs
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Elham Elkrewi created ticket #25
error code 3
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Thomas Rattei created ticket #49
Alignment errors or missing annotations when using gbk files from RefSeq
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Bhavya Papudeshi created ticket #48
Cant look up annotation features when using a genbank file (.gbk)
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Yongan posted a comment on ticket #47
I found there are RC sequences. My bad. Please close the ticket!
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concatenated block sequences are different from original sequences
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Gert Wollny created ticket #46
libMems does not compile with g++-6 [patch]
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Aaron Darling committed [r4736]
need to flush the output buffer!
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Anirvan Chatterjee posted a comment on ticket #45
Dear Aaron, thank you for your reply. The duplication was an error. However rectifying...
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It looks like progressiveMauve is unable to open the first sequence file. I notice...
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eror 136
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Fabrice Touzain created ticket #44
No contig names display in Mauve GUI on Windows 7 when reading a xmfa file
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remove unimplemented --input-id-matrix option (...
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Ivan Alexandrov created ticket #43
Mauve error code 139
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Cristina created ticket #42
trouble with contig coordinates in the backbone file
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Joaquim Martins Jr created ticket #41
progressiveMauve2.3.1 error
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thekswenson posted a comment on ticket #40
Hi Aaron, I am using 2.3.1build1! Sorry about that... I should have checked for a...
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Hi Krister, looks like you're on linux, do you know which JVM version you've got...
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"align" button off window boarder
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enable selection of multiple sequence files at ...
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Change defaults to compensate for triplet indel...
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Fix to triplet indel bias
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disconnect testing command line
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fixes for linux build
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Changes to introduce gene-awareness and elimina...
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enable allocation of histograms smaller than th...
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updated with new deployment address
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norhan mahfouz created ticket #39
Mauve aligner without SML files
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update with new target name
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workaround for boost memory mapped file corrupt...
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Hi Sarah, your attachment didn't show up. I would suggest reading this page to understand...
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Sarah posted a comment on ticket #38
Hi Aaron, I've been looking over the .backbone file (attached) but I'm seeing negative...
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Thanks Sarah, I'll check out that code. In the meantime, I suggest you have a look...
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You're correct, the format of the text is output from a code I found in a publication....
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Hi Sarah, the text screenshot does not appear to correspond to an XMFA file. Could...
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GUI vs XMFA Text File
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bugfix
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build with -O0 until clang/llvm bug with except...
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update snapshots to new web host
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ant build now requires java 7
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updated binaries and build for 2.4.0 release
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update to current repository and server location
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updated to deploy to new server
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potential fix for msvc compiler error
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fix for windows build
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need to copy with ditto to preserve executable ...
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binaries for 2.4.0 release, taken from the 2012...
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improved error message when output file is unwr...
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bugfix
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fix typo
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revisions for more robust build system
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workaround for strange behavior with boost 1.57...
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add java runtime to OS X build, other refinements
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include rt.jar from java 1.6 in bootclasspath t...
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use svn urls instead of http
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DeMaere special request: improved responsivenes...
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updates to os X disk image packaging
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move empty check further down to allow empty ob...
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don't keep changelog in mauve repo, master copy...
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re-add shell script, prep for 2.4.0 release
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updating classpath to include latest biojava
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removing 32-bit support
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custom biojava with parsing fix for Prokka-gene...
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updates for server migration
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drop linux 32 bit support
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update biojava to 1.9.1 release
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fix for OS X binary path problem
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site migration, clean some OS X cruft
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Fix off-by-one, clean up some cruft
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switch to platform-specific command keys
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Switch to platform-specific command keys, launc...
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