Dependencies errors

[amrdavila]

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 ?

[claczny]

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

[amrdavila]

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

[claczny]

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

[amrdavila]

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:

[claczny]

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