Bug issue for the building of Primate phylogeny

[FabienCondamine]

Hi,

I am testing SUPERSMART with the Primate phylogeny. I connected myself to SUPERSMART_HOME following all instructions on the file README. At the step $ sh run.sh, I got the following message: INFO [/usr/local/src/supersmart/script/supersmart/infer_backbone.pl: 95] - patience please, running examples/primates/supermatrix.phy with starting tree examples/primates/user.dnd Can't locate object method "warn" via package "Bio::Phylo::PhyLoTA::Service::TreeService" at /usr/local/src/supersmart/lib/Bio/Phylo/PhyLoTA/Service/TreeService.pm line 152. finished reading config file Could not open file.

Don't see the solution.

[rvosa]

Hi Fabien,

can you do a 'git pull' on the source code? It appears you are working on an older version.

Rutger

On Fri, Mar 28, 2014 at 8:30 PM, FabienGaia notifications@github.comwrote:

Hi,

I am testing SUPERSMART with the Primate phylogeny. I connected myself to SUPERSMART_HOME following all instructions on the file README. At the step $ sh run.sh, I got the following message: INFO [/usr/local/src/supersmart/script/supersmart/infer_backbone.pl: 95]

• patience please, running examples/primates/supermatrix.phy with starting tree examples/primates/user.dnd Can't locate object method "warn" via package "Bio::Phylo::PhyLoTA::Service::TreeService" at /usr/local/src/supersmart/lib/Bio/Phylo/PhyLoTA/Service/TreeService.pm line 152. finished reading config file Could not open file.

Don't see the solution.

Reply to this email directly or view it on GitHubhttps://github.com/naturalis/supersmart/issues/17 .

[hettling]

Hi Fabien,

This was indeed a bug introduced by me, my apologies. I only saw and corrected it last week, so as Rutger pointed out, this should not be present in the current version.

Greetings,

Hannes

On 28 Mar 2014, at 22:04, Rutger Vos notifications@github.com wrote:

Hi Fabien,

can you do a 'git pull' on the source code? It appears you are working on an older version.

Rutger

On Fri, Mar 28, 2014 at 8:30 PM, FabienGaia notifications@github.comwrote:

Hi,

I am testing SUPERSMART with the Primate phylogeny. I connected myself to SUPERSMART_HOME following all instructions on the file README. At the step $ sh run.sh, I got the following message: INFO [/usr/local/src/supersmart/script/supersmart/infer_backbone.pl: 95]

• patience please, running examples/primates/supermatrix.phy with starting tree examples/primates/user.dnd Can't locate object method "warn" via package "Bio::Phylo::PhyLoTA::Service::TreeService" at /usr/local/src/supersmart/lib/Bio/Phylo/PhyLoTA/Service/TreeService.pm line 152. finished reading config file Could not open file.

Don't see the solution.

Reply to this email directly or view it on GitHubhttps://github.com/naturalis/supersmart/issues/17 .

— Reply to this email directly or view it on GitHub.

[FabienCondamine]

Hi Rutger and Hannes,

Thanks for your help. So I need to reinstall everything. But doing so I got weird outcome from my Terminal: Alex--Fabien-MacBook-Pro:conf fabien$ vagrant up Bringing machine 'default' up with 'virtualbox' provider... ==> default: Importing base box 'supersmart-fedora-18'... ==> default: Matching MAC address for NAT networking... ==> default: Setting the name of the VM: conf_default_1396355314773_32743 Vagrant cannot forward the specified ports on this VM, since they would collide with some other application that is already listening on these ports. The forwarded port to 8080 is already in use on the host machine.

To fix this, modify your current projects Vagrantfile to use another port. Example, where '1234' would be replaced by a unique host port:

config.vm.network :forwarded_port, guest: 80, host: 1234

Sometimes, Vagrant will attempt to auto-correct this for you. In this case, Vagrant was unable to. This is usually because the guest machine is in a state which doesn't allow modifying port forwarding.

Makes sense?

I have deleted all previous SUPERSMART folders of my computer.

Best,

Fabien

[hettling]

Hi Fabien,

could it be that you still have the old virtual machine running that is still forwarding to port 8080? Even if you deleted all SUPERSMART folders, the machine could still exist because they are usually stored in ~/VirtualBox VMs. You can also start the VirtualBox GUI and see all your virtual machines. To stop and remove a virtual machine completely, you can use "vagrant destroy".

Another possibility is that you have something else runnning on port 8080 (e.g. a Tomcat server) so that port is in use. I'm not sure about this though, since you had (as I understand) vagrant and SUPERSMART working before.

An easy hack would be to just forward the virtual machines port 80 to some other port than 8080 by adding a line in the config block of your Vagrantfile: config.vm.network "forwarded_port", guest: 80, host: 4567

However, I would first make sure that you do not have any more old virtual instances running.

All the Best,

Hannes

[FabienCondamine]

Hi Hannes,

Thanks a lot. You were right. And it works nice now.

I am training myself on the Primates and I got a new strange outcome for the last part of the analysis (the dating), below is the code lines:

Final tree written to: /usr/local/src/supersmart/examples/primates/ExaML_result.megatree.dnd Execution Log File written to: /usr/local/src/supersmart/examples/primates/ExaML_log.megatree.dnd Execution information file written to: /usr/local/src/supersmart/examples/primates/ExaML_info.megatree.dnd INFO [/usr/local/src/supersmart/script/supersmart/infer_backbone.pl: 100] - done, result written to examples/primates/megatree.dnd INFO [/usr/local/src/supersmart/script/supersmart/write_treepl_config.pl: 49] - reading tree from file examples/primates/megatree.dnd INFO [/usr/local/src/supersmart/script/supersmart/write_treepl_config.pl: 59] - reading fossils from file examples/primates/fossils2.tsv No file or folder of this type at /usr/local/src/supersmart/lib/Bio/Phylo/PhyLoTA/Service/CalibrationService.pm line 252, line 1. finished reading config file Could not open file.

Does it just need to put a file fossils2.tsv? In my folder that I downloaded, the file is fossils.tsv... Is thre something wrong in the VirtualMachine and the local folder?

Thanks again Hannes for the help,

Best regards,

Fabien

[hettling]

Hi Fabien,

Ruud had the same problems, in the 'run.sh' the file fossils2.tsv was given as fossiltable, this should be fossils.tsv. It's corrected on Github now, please tell me if the calibration works.

Cheers

Hannes

On 2 apr. 2014, at 19:10, FabienGaia notifications@github.com wrote:

Hi Hannes,

Thanks a lot. You were right. And it works nice now.

I am training myself on the Primates and I got a new strange outcome for the last part of the analysis (the dating), below is the code lines:

Final tree written to: /usr/local/src/supersmart/examples/primates/ExaML_result.megatree.dnd Execution Log File written to: /usr/local/src/supersmart/examples/primates/ExaML_log.megatree.dnd Execution information file written to: /usr/local/src/supersmart/examples/primates/ExaML_info.megatree.dnd INFO [/usr/local/src/supersmart/script/supersmart/infer_backbone.pl: 100] - done, result written to examples/primates/megatree.dnd INFO [/usr/local/src/supersmart/script/supersmart/write_treepl_config.pl: 49] - reading tree from file examples/primates/megatree.dnd INFO [/usr/local/src/supersmart/script/supersmart/write_treepl_config.pl: 59] - reading fossils from file examples/primates/fossils2.tsv No file or folder of this type at /usr/local/src/supersmart/lib/Bio/Phylo/PhyLoTA/Service/CalibrationService.pm line 252, line 1. finished reading config file Could not open file.

Does it just need to put a file fossils2.tsv? In my folder that I downloaded, the file is fossils.tsv... Is thre something wrong in the VirtualMachine and the local folder?

Thanks again Hannes for the help,

Best regards,

Fabien

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