GRIT installed ok, test tutorial doesn't run

[Susan C]

Hi, 

I installed GRIT 1.1.3 on Python 2.7.6, on a Centos 5 system. The installation went fine, with no obvious errors. However, running the test suite gives me lots of errors:

[susanc@p19 GRITdir]$ run_grit.py --rnaseq-reads AdMatedF_Ecl_20days_Heads.biorep1.rnaseq.chr4.bam  \

>             --cage-reads AdMatedF_Ecl_20days_Heads.biorep1.cage.chr4.bam \

>             --polya-reads AdMatedF_Ecl_20days_Heads.biorep2.passeq.chr4.bam \

>             --reference flybase-r5.45.chr4.gtf

Process Process-2:

Traceback (most recent call last):

  File "/usr/local/Python/2.7.6/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap

    self.run()

  File "/usr/local/Python/2.7.6/lib/python2.7/multiprocessing/process.py", line 114, in run

    self._target(*self._args, **self._kwargs)

  File "/usr/local/Python/2.7.6/lib/python2.7/curses/wrapper.py", line 43, in wrapper

    return func(stdscr, *args, **kwds)

  File "build/bdist.linux-x86_64/egg/grit/lib/logging.py", line 13, in manage_curses_display

    curses.curs_set(0)

error: curs_set() returned ERR

Traceback (most recent call last):

  File "/usr/local/Python/2.7.6/bin/run_grit.py", line 5, in <module>

    pkg_resources.run_script('GRIT==1.1.3', 'run_grit.py')

  File "/usr/local/Python/2.7.6/lib/python2.7/site-packages/pkg_resources.py", line 488, in run_script

    self.require(requires)[0].run_script(script_name, ns)

  File "/usr/local/Python/2.7.6/lib/python2.7/site-packages/pkg_resources.py", line 1345, in run_script

    exec(script_code, namespace, namespace)

  File "/usr/local/Python/2.7.6/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit.py", line 515, in <module>

    

  File "/usr/local/Python/2.7.6/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit.py", line 510, in main

    

  File "build/bdist.linux-x86_64/egg/grit/build_transcripts.py", line 948, in build_and_quantify_transcripts

  File "build/bdist.linux-x86_64/egg/grit/build_transcripts.py", line 873, in spawn_and_manage_children

  File "build/bdist.linux-x86_64/egg/grit/build_transcripts.py", line 754, in worker

  File "build/bdist.linux-x86_64/egg/grit/build_transcripts.py", line 472, in build_design_matrices_worker

  File "build/bdist.linux-x86_64/egg/grit/f_matrix.py", line 834, in __init__

  File "build/bdist.linux-x86_64/egg/grit/f_matrix.py", line 693, in _build_rnaseq_arrays

  File "build/bdist.linux-x86_64/egg/grit/f_matrix.py", line 600, in cluster_rows

TypeError: object of type 'generator' has no len()

Process Process-6:

Traceback (most recent call last):

  File "/usr/local/Python/2.7.6/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap

    self.run()

  File "/usr/local/Python/2.7.6/lib/python2.7/multiprocessing/process.py", line 114, in run

    self._target(*self._args, **self._kwargs)

  File "build/bdist.linux-x86_64/egg/grit/build_transcripts.py", line 575, in write_finished_data_to_disk

    write_type, key = data.finished_queue.get(timeout=0.1)

  File "<string>", line 2, in get

  File "/usr/local/Python/2.7.6/lib/python2.7/multiprocessing/managers.py", line 758, in _callmethod

    conn.send((self._id, methodname, args, kwds))

IOError: [Errno 32] Broken pipe

The created bed file has some size, but the other files are all empty except for some header information. 

Any ideas what the problem might be?

Thanks for suggestions,

Susan.