Open amrdavila opened 4 years ago
Dear @amrdavila,
thank you for posting the issue.
It seems that you are trying to build VizBin from scratch. This is, however, not needed if you just want to use it to visualize and bin your metagenomic data. You should be able to download releases via https://github.com/claczny/VizBin/releases.
Could you please try if downloading, unzipping and running the application from the Releases page would work?
Best,
Cedric
Thanks ! The compiled .jar works. However, by using a 269MB fasta file just got this error:
2019-12-04 10:29:47 | 967 DEBUG [main] (MainFrame.java:109) - Init of Main application frame | |||
---|---|---|---|---|
2019-12-04 10:29:48 | 016 DEBUG [main] (MainFrame.java:114) - Property changed: defaultCloseOperation. Old: 1 New: 3 | |||
2019-12-04 10:29:48 | 054 DEBUG [main] (MainFrame.java:114) - Property changed: font. Old: null New: java.awt.Font[family=Dialog | name=Dialog | style=plain | size=12] |
2019-12-04 10:29:48 | 054 DEBUG [main] (MainFrame.java:114) - Property changed: foreground. Old: null New: java.awt.SystemColor[i=9] | |||
2019-12-04 10:30:06 | 037 DEBUG [AWT-EventQueue-0] (MainFrame.java:114) - Property changed: custom:workspaceName. Old: null New: all.fasta | |||
2019-12-04 10:30:41 | 210 DEBUG [AWT-EventQueue-0] (ProcessInput.java:70) - Init of ProcessInput | |||
2019-12-04 10:30:41 | 215 DEBUG [Thread-0] (ObjectWithProperties.java:33) - Property changed: FINISHED. Old: true New: false | |||
2019-12-04 10:30:41 | 215 DEBUG [Thread-0] (ProcessInput.java:123) - /tmp | |||
2019-12-04 10:30:41 | 229 DEBUG [Thread-0] (ProcessInput.java:132) - Loading data from file. | |||
Contig length treshold: 500 | ||||
2019-12-04 10:30:41 | 229 DEBUG [Thread-0] (ProcessInput.java:99) - Loading fasta file: /path/all.fasta | |||
2019-12-04 10:30:48 | 682 DEBUG [Thread-0] (DataSetFactory.java:443) - Zero sequences loaded from the file! Check file and parameters. | |||
2019-12-04 10:30:53 | 335 DEBUG [Thread-0] (ProcessInput.java:99) - | |||
2019-12-04 10:30:53 | 336 DEBUG [Thread-0] (ObjectWithProperties.java:33) - Property changed: FINISHED. Old: false New: true |
That is strange indeed. From the log, I can gather
Zero sequences loaded from the file! Check file and parameters.
Can you please check the input file? Is it properly formatted? Maybe you could share a snippet?
Thank you! Best,
Cedric
The fasta file is OK, just checked it. However, I also got the warning window below, looks like it reads the fasta file but cannot find any contigs, no matter the "contig size" I ask to find:
I just tried the 1.0.0 release on EqualSet01.fa and it worked fine.
It seems that, for some unclear reason, you have many sequences that are recognized as "short". In fact, it seems that your file has ~2.5Mio entries (i.e., sequences). Is that correct?
Would there be any chance you could share, say, the first 150 sequences > 1kbp with me, e.g., via email? That might help trace back the issue you are facing.
Best,
Cedric
Just downloaded the latest version from GitHub:
https://github.com/claczny/VizBin
when running the setup I got these errors:
Downloads/VizBin/setupUbuntu.sh Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'libgsl-dev' instead of 'libgsl0-dev' Package openjdk-7-jre is not available, but is referred to by another package. This may mean that the package is missing, has been obsoleted, or is only available from another source
Package libgsl0ldbl is not available, but is referred to by another package. This may mean that the package is missing, has been obsoleted, or is only available from another source However the following packages replace it: libgsl2 libgsl2:i386
Package openjdk-7-jdk is not available, but is referred to by another package. This may mean that the package is missing, has been obsoleted, or is only available from another source
E: Package 'openjdk-7-jre' has no installation candidate E: Package 'libgsl0ldbl' has no installation candidate E: Package 'openjdk-7-jdk' has no installation candidate
real 0m0.399s user 0m0.376s sys 0m0.012s fatal: destination path 'osxcross' already exists and is not an empty directory. Downloads/VizBin/setupUbuntu.sh: line 14: cd: tarballs: No such file or directory Downloads/VizBin/setupUbuntu.sh: line 18: ./build.sh: No such file or directory
real 0m0.000s user 0m0.000s sys 0m0.000s Downloads/VizBin/setupUbuntu.sh: line 19: ./build_gcc.sh: No such file or directory
real 0m0.000s user 0m0.000s sys 0m0.000s mkdir: cannot create directory ‘boost’: File exists --2019-12-03 12:06:39-- http://downloads.sourceforge.net/project/boost/boost/1.55.0/boost_1_55_0.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fboost%2Ffiles%2Fboost%2F1.55.0%2F&ts=1402397648&use_mirror=softlayer-ams Resolving downloads.sourceforge.net (downloads.sourceforge.net)... 216.105.38.13 Connecting to downloads.sourceforge.net (downloads.sourceforge.net)|216.105.38.13|:80... connected. HTTP request sent, awaiting response... 403 Forbidden 2019-12-03 12:06:39 ERROR 403: Forbidden.
fatal: destination path 'mxe' already exists and is not an empty directory. make: *** No rule to make target 'gcc'. Stop.
real 0m0.003s user 0m0.000s sys 0m0.000s
I already has openjdk-8 (jdk and jre) installed and cannot downgrade to openjdk-7 because I am using Linux Mint Sarah 18
My (Mint) system:
4.4.0-21-generic #37-Ubuntu SMP Mon Apr 18 18:33:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Any tips ?