astrid error

[Jason Bragg]

Hello,

Attempting to use ASTRID for the first time. Looks brilliant! Thanks for sharing it!
Having trouble running it with the dataset provided in the 'test' directory. (Note: generating same error on my data and the test data.)

I did sh install.sh
fastme, fastme2, etc, seemed to compile successfully.

I attempted to call ASTRID.py, and got a python error. Astral was called on a machine running ubuntu 14.04, with python 2.7.6. I am using ASTRID files that were downloaded from github 17 August 2015.

Apologies if I missed a dependency, or am doing something that is obviously incorrect!
I read http://pranjalv123.github.io/ASTRID/, 'python src/ASTRID.py -h', and https://github.com/pranjalv123/ASTRID/blob/master/README.md -- apologies if I missed other documentation that is available. 

I would be grateful if anyone has insights into the problem. 

Best, and Thanks,
Jason.


jgb@RSB000522:~/software/astrid/ASTRID-master$ python src/ASTRID.py -i test/song_mammals.424.gene.tre
reading trees
generating matrix
Traceback (most recent call last):
  File "src/ASTRID.py", line 127, in <module>
    a.run(method, fname)
  File "src/ASTRID.py", line 97, in run
    self.generate_matrix()
  File "src/ASTRID.py", line 41, in generate_matrix
    self.taxindices = dict([(j, i) for i, j in enumerate(sorted(list(self.tl.taxon_namespace)))])
AttributeError: 'TreeList' object has no attribute 'taxon_namespace'

[Pranjal Vachaspati]

Hi Jason,

Thanks for the report! ASTRID currently requires dendropy 4.0 or

greater, so installing that should fix the issue. This can be done with

pip install --upgrade dendropy

Thanks,

Pranjal

[Jason Bragg]

Dear Pranjal,

Many thanks for your help. I updated to dendropy 4, at your suggestion, and astrid is running on the test data.

Thanks again,

Jason.

On Wed, Aug 19, 2015 at 8:09 PM, Pranjal Vachaspati <p...@nj.al> wrote:

Hi Jason,

Thanks for the report! ASTRID currently requires dendropy 4.0 or
greater, so installing that should fix the issue. This can be done with

pip install --upgrade dendropy

Thanks,
Pranjal

[Pete Hosner]

Dear Pranjal,

First of all, many thanks for developing this package!

I too, am having an issue getting it running. When I run the test data, I get the following:

Hosner:src Grallaria$ python ASTRID.py -i /Users/Grallaria/Documents/PhylogeneticsSoftware/pranjalv123-ASTRID-262b3ea/test/song_mammals.424.gene.tre -o song.tre
reading trees
generating matrix
writing matrix None
inferring tree
/var/folders/js/gnnst_y53pxf33j92nsjr9jh0000gp/T/tmp0jzwlg_fastme.t

Traceback (most recent call last):

  File "ASTRID.py", line 127, in <module>
    a.run(method, fname)
  File "ASTRID.py", line 101, in run
    self.infer_tree(method)
  File "ASTRID.py", line 85, in infer_tree
    self.tree = dendropy.Tree.get_from_string(method(self.fname), 'newick')
  File "/Users/Grallaria/Documents/PhylogeneticsSoftware/pranjalv123-ASTRID-262b3ea/src/DistanceMethods.py", line 43, in fastme
    p = subprocess.Popen([fastme_exec, '-i', fname, '-o', fname + '_fastme.t'])
  File "/Users/Grallaria/anaconda/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/Users/Grallaria/anaconda/lib/python2.7/subprocess.py", line 1335, in _execute_child
    raise child_exception
OSError: [Errno 13] Permission denied

Do I need to change my permissions somewhere? Thanks,

-Pete

[Pranjal Vachaspati]

Hi Pete,

Thanks for the report. 

 - What operating system are you using?

 - Could you check that install.sh worked correctly? The distmethods

   folder should contain the fastme executable with the correct

   permissions (to verify this, you could just try running the fastme

   executable). 

--Pranjal

[Pete Hosner]

Pranjal,

Thanks for the quick response.

I am running Mac OSX Yosemite.

Fastme2 executes on its own.

The install.sh script seems to have worked correctly, although I needed to use sudo or it would give a ton of warnings. I've attached a log, if that helps.

Cheers,

-Pete

 

------------------------
Peter A. Hosner
Postdoctoral Associate

P.O. Box 118525

Dept. of Biology

University of Florida

Gainesville, FL 32611

cell: 785-331-7583

On Mon, Aug 24, 2015 at 12:53 PM, Pranjal Vachaspati <p...@nj.al> wrote:

Hi Pete,

Thanks for the report.

 - What operating system are you using?
 - Could you check that install.sh worked correctly? The distmethods
   folder should contain the fastme executable with the correct
   permissions (to verify this, you could just try running the fastme
   executable).

--Pranjal

[Pete Hosner]

Pranjal,

All right. I still got the same error with fastme, but it ran with the -m fastme2 option.

Thanks for the help,

Cheers,

-Pete

------------------------
Peter A. Hosner
Postdoctoral Associate

P.O. Box 118525

Dept. of Biology

University of Florida

Gainesville, FL 32611

cell: 785-331-7583

On Mon, Aug 24, 2015 at 1:48 PM, Pranjal Vachaspati <pranjal.v...@gmail.com> wrote:

Hi Pete,

I have not yet tested ASTRID on OSX, so thanks for letting me know about
this.

Try going into the distmethods directory and doing

sudo chmod a+x fastme fastme2

ASTRID is still configured to use fastme 1 by default, so if it still
doesn't work you could try running ASTRID with the
 -m fastme2
option.

[Kavya Kannan]

Hi Pranjal,

I am having problems running ASTRID on my data.

I get this following error:

/home/apps/python/python-2.7.3/lib/python2.7/site-packages/numpy/ma/core.py:3900: UserWarning: Warning: converting a masked element to nan.

  warnings.warn("Warning: converting a masked element to nan.")

Exception in thread "main" java.lang.NumberFormatException: For input string: "nan"

at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)

at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)

at java.lang.Double.parseDouble(Double.java:538)

at java.lang.Double.<init>(Double.java:608)

at PhyDstar.main(PhyDstar.java:440)

Traceback (most recent call last):

  File "ASTRID/src/ASTRID.py", line 127, in <module>

    a.run(method, fname)

  File "ASTRID/src/ASTRID.py", line 101, in run

    self.infer_tree(method)

  File "ASTRID/src/ASTRID.py", line 85, in infer_tree

    self.tree = dendropy.Tree.get_from_string(method(self.fname), 'newick')

  File "build/bdist.linux-x86_64/egg/dendropy/datamodel/basemodel.py", line 248, in get_from_string

  File "build/bdist.linux-x86_64/egg/dendropy/datamodel/treemodel.py", line 2517, in _parse_and_create_from_stream

  File "build/bdist.linux-x86_64/egg/dendropy/dataio/ioservice.py", line 361, in read_tree_lists

  File "build/bdist.linux-x86_64/egg/dendropy/dataio/newickreader.py", line 317, in _read

  File "build/bdist.linux-x86_64/egg/dendropy/dataio/newickreader.py", line 296, in tree_iter

  File "build/bdist.linux-x86_64/egg/dendropy/dataio/newickreader.py", line 354, in _parse_tree_statement

  File "build/bdist.linux-x86_64/egg/dendropy/dataio/tokenizer.py", line 159, in require_next_token

dendropy.dataio.tokenizer.UnexpectedEndOfStreamError: Error parsing data source on line 1 at column 0: Unexpected end of stream

this is the command I used: python ASTRID/src/ASTRID.py -i gene_tree_test_abc_aplha_0.5-2gt-stM-astral-MS75-p6S-1-OA-iterative-CM-wqmc-R2 -o output_tree

Would you be knowing why such an error is returned. Thanks!

Kavya

[Pranjal Vachaspati]

Hi Kavya,

Have you tried using the most recent version of ASTRID from GitHub? I

think this is an error that has been fixed in the latest version. 

(https://github.com/pranjalv123/ASTRID)

Thanks,

Pranjal