[miso-users] minpack2.so problem

[Zhao, Hao]

Hi all,

I installed the latest MISO (0.4.3). And I passed Testing the Installation:
all the required modules are available and misopy, pysplicing could be
imported. However, I was stuck when running test_miso.py.  It said "..
python-2.7.2/lib/python2.7/site-packages/scipy/optimize/minpack2.so: file
too short'. Then I checked the size of /RIS/HPC_apps/AMD/python/
python-2.7.2/lib/python2.7/site-packages/scipy/optimize/minpack2.so. Its
size is zero. So I guess Scipy was not properly installed.

Yarden said "*It does sound like a scipy error as you suggest.  I've never
seen this error, so I'm not sure what could be causing it*."

So I posted the error message here, as Yarden suggested. I will ask our
Unix admin to see  if this is indeed associated with the minpack2.so file.

Thank you.

[xx at xxxsapp06p misopy]$ python test_miso.py
Testing conversion of SAM to BAM...
Executing: python /RIS/home/hzhao1/tools/misopy-0.4.3/misopy/sam_to_bam.py
--convert
/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/test-data/sam-data/c2c12.Atp2b1.sam
/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/test-output/sam-output
Converting SAM to BAM...
  - Executing: samtools view -Sbh
/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/test-data/sam-data/c2c12.Atp2b1.sam
 >
/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/test-output/sam-output/c2c12.Atp2b1.bam
[samopen] SAM header is present: 35 sequences.
Sorting BAM file...
  - Executing: samtools sort
/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/test-output/sam-output/c2c12.Atp2b1.bam
/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/test-output/sam-output/c2c12.Atp2b1.sorted
Indexing BAM...
  - Executing: samtools index
/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
Conversion took 0.00 minutes.
.Testing gene-level Psi...
Testing GFF indexing of:
/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
Executing: python /RIS/home/hzhao1/tools/misopy-0.4.3/misopy/index_gff.py
--index
/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/gff-events/mm9/genes/Atp2b1/indexed
Indexing GFF...
/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
appears to already be indexed. Aborting.
Executing: python
/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/run_events_analysis.py
 --compute-genes-psi
/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/gff-events/mm9/genes/Atp2b1/indexed
/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
--output-dir
/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/test-output/gene-psi-output
--read-len 35
Traceback (most recent call last):
  File "/RIS/home/hzhao1/tools/misopy-0.4.3/misopy/run_events_analysis.py",
line 13, in <module>
    import misopy.run_miso as run_miso
  File
"/RIS/home/hzhao1/tools/MISO/lib/python2.7/site-packages/misopy/run_miso.py",
line 14, in <module>
    import misopy.hypothesis_test as ht
  File
"/RIS/home/hzhao1/tools/MISO/lib/python2.7/site-packages/misopy/hypothesis_test.py",
line 7, in <module>
    from scipy import stats
  File
"/RIS/HPC_apps/AMD/python/python-2.7.2/lib/python2.7/site-packages/scipy/stats/__init__.py",
line 322, in <module>
    from stats import *
  File
"/RIS/HPC_apps/AMD/python/python-2.7.2/lib/python2.7/site-packages/scipy/stats/stats.py",
line 198, in <module>
    import distributions
  File
"/RIS/HPC_apps/AMD/python/python-2.7.2/lib/python2.7/site-packages/scipy/stats/distributions.py",
line 14, in <module>
    from scipy import optimize
  File
"/RIS/HPC_apps/AMD/python/python-2.7.2/lib/python2.7/site-packages/scipy/optimize/__init__.py",
line 128, in <module>
    from optimize import *
  File
"/RIS/HPC_apps/AMD/python/python-2.7.2/lib/python2.7/site-packages/scipy/optimize/optimize.py",
line 28, in <module>
    from linesearch import \
  File
"/RIS/HPC_apps/AMD/python/python-2.7.2/lib/python2.7/site-packages/scipy/optimize/linesearch.py",
line 1, in <module>
    from scipy.optimize import minpack2
ImportError:
/RIS/HPC_apps/AMD/python/python-2.7.2/lib/python2.7/site-packages/scipy/optimize/minpack2.so:
file too short
.
----------------------------------------------------------------------
Ran 2 tests in 1.369s

OK
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