Running ASTRID... First steps

[Francesco Asnicar]

Hi all,

I'm trying to running ASTRID but I got an error.

I downloaded the Linux executable from here https://github.com/pranjalv123/ASTRID/releases and I executed both ./ASTRID and ./ASTRID -h.

In both cases I got the usage message.

The problem is when I run ./ASTRID -i test/song_mammals.424.gene.tre it generates the following error:

generating matrix

0.117029905319 seconds

inferring tree

/tmp/_MEI48uYxF/fastme: /usr/lib/x86_64-linux-gnu/libgomp.so.1: version `GOMP_4.0' not found (required by /tmp/_MEI48uYxF/fastme)

Traceback (most recent call last):

  File "build/bin/ASTRID", line 46, in <module>

  File "build/bin/lib/python/ASTRID/ASTRID.py", line 87, in run

  File "build/bin/lib/python/ASTRID/ASTRID.py", line 67, in infer_tree

  File "build/bin/lib/python/ASTRID/DistanceMethods.py", line 86, in fastme2_bal_nni

  File "build/bin/lib/python/ASTRID/DistanceMethods.py", line 71, in fastme2

IOError: [Errno 2] No such file or directory: '/tmp/tmpYWC9tk_fastme2.t'

Failed to execute script ASTRID

Does anyone know what's happening?

Many thanks,

Francesco

[Tomáš Fér]

Hi,

I have been testing ASTRID binary on many Linux distributions and observed the error described below only on Ubuntu 14.04. Other distributions I tried (Fedora/OpenSUSE, CentOS, Debian) were OK and ASTRID was running without any problems. Does anybody know what's going on here?

Thanks,

Tomas

Dne úterý 13. září 2016 17:49:30 UTC+2 Francesco Asnicar napsal(a):

[Francesco Asnicar]

Hi Tomas,

thanks for your answer and pointing out this fact. Indeed, I am trying ASTRID on Ubuntu 14.04.4, so maybe the operating system is the problem...

I didn't tried ASTRID on different operating systems because all the servers I have access to have the same Ubuntu 14.04.4.

Thanks,

Francesco

[Pranjal Vachaspati]

Hi all,

Sorry for the delay - there is a new distribution format of ASTRID
available at
https://github.com/pranjalv123/ASTRID/releases/download/v1.4/ASTRID.zip
that should solve your problems. Just unzip it and run ASTRID (not
ASTRID.py) that is in the folder.

Pranjal Vachaspati writes:

> Hi Tomas and Francesco,
>
> Thanks for pointing out this issue. I'm loading up a computer with
> Ubuntu 14.04.4 to resolve this issue.
>
> --Pranjal

[Pranjal Vachaspati]

Hi all,

I have updated the ASTRID-linux binary (available at
https://github.com/pranjalv123/ASTRID/releases/tag/v1.4) so that it
should be compatible with older versions of Ubuntu, glibc, and
GOMP. Please let me know if you continue to have problems running on
these systems.

Thanks,
Pranjal

[Francesco Asnicar]

Hello Pranjal,

I tried ASTRID today and it worked! :)

Many thanks for the support,

Francesco