Error installing miso
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Entering edit mode
6.0 years ago

Hello,

       I used pip to install misopy. All went well.

import misopy and import pysplicing ok.

module_availability checked, all modules available.

Testing MISO fails with errors (see further):

The command used: (As per the manual)

python2.7 -m unittest discover misopy

Errors found:

 

Testing gene-level Psi...

Executing: python /usr/local/lib/python2.7/site-packages/misopy/index_gff.py --index /usr/local/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /usr/local/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed
Indexing GFF...
/usr/local/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff appears to already be indexed. Aborting.
Executing: python /usr/local/lib/python2.7/site-packages/misopy/run_events_analysis.py  --compute-genes-psi /usr/local/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed /usr/local/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /usr/local/lib/python2.7/site-packages/misopy/test-output/gene-psi-output --read-len 36  --paired-end 250 30 --use-cluster
MISO (Mixture of Isoforms model)
To run MISO, please use "miso" instead.
.Testing single-end SE event interface...
Executing: python /usr/local/lib/python2.7/site-packages/misopy/run_events_analysis.py  --compute-events-psi se-sample /usr/local/lib/python2.7/site-packages/misopy/test-data/se-counts/se_test.counts --output-dir /usr/local/lib/python2.7/site-packages/misopy/test-output/SE-output --read-len 35 --overhang-len 4  --event-type SE --use-cluster
MISO (Mixture of Isoforms model)
To run MISO, please use "miso" instead.
.Testing fr-unstranded...
Checking read  f_read  against  +
Checking read  f_read  against  -
Checking read  r_read  against  +
Checking read  r_read  against  -
Testing fr-firststrand...
.Testing conversion of SAM to BAM...
Executing: sam_to_bam --convert /usr/local/lib/python2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam /usr/local/lib/python2.7/site-packages/misopy/test-output/sam-output
Converting SAM to BAM...
Traceback (most recent call last):
  File "/usr/local/bin/sam_to_bam", line 9, in <module>
    load_entry_point('misopy==0.5.3', 'console_scripts', 'sam_to_bam')()
  File "/usr/local/lib/python2.7/site-packages/misopy/sam_to_bam.py", line 63, in main
    sam_to_bam(sam_filename, output_dir, header_ref=ref)
  File "/usr/local/lib/python2.7/site-packages/misopy/sam_to_bam.py", line 13, in sam_to_bam
    os.makedirs(output_dir)
  File "/usr/local/lib/python2.7/os.py", line 150, in makedirs
    makedirs(head, mode)
  File "/usr/local/lib/python2.7/os.py", line 157, in makedirs
    mkdir(name, mode)
OSError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/site-packages/misopy/test-output'
FTesting gene-level Psi...
Testing GFF indexing of: /usr/local/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
Executing: index_gff --index /usr/local/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /usr/local/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed
Traceback (most recent call last):
  File "/usr/local/bin/index_gff", line 9, in <module>
    load_entry_point('misopy==0.5.3', 'console_scripts', 'index_gff')()
  File "/usr/local/lib/python2.7/site-packages/misopy/index_gff.py", line 188, in main
    os.makedirs(output_dir)
  File "/usr/local/lib/python2.7/os.py", line 150, in makedirs
    makedirs(head, mode)
  File "/usr/local/lib/python2.7/os.py", line 157, in makedirs
    mkdir(name, mode)
OSError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1'
Executing: miso --run /usr/local/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed /usr/local/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /usr/local/lib/python2.7/site-packages/misopy/test-output/gene-psi-output --read-len 36
MISO (Mixture of Isoforms model)
Probabilistic analysis of RNA-Seq data for detecting differential isoforms
Use --help argument to view options.

Using MISO settings file: /usr/local/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
Traceback (most recent call last):
  File "/usr/local/bin/miso", line 9, in <module>
    load_entry_point('misopy==0.5.3', 'console_scripts', 'miso')()
  File "/usr/local/lib/python2.7/site-packages/misopy/miso.py", line 563, in main
    main_logger = get_main_logger(logs_output_dir)
  File "/usr/local/lib/python2.7/site-packages/misopy/miso.py", line 54, in get_main_logger
    fh = logging.FileHandler(logger_fname)
  File "/usr/local/lib/python2.7/logging/__init__.py", line 911, in __init__
    StreamHandler.__init__(self, self._open())
  File "/usr/local/lib/python2.7/logging/__init__.py", line 941, in _open
    stream = open(self.baseFilename, self.mode)
IOError: [Errno 2] No such file or directory: '/usr/local/lib/python2.7/site-packages/misopy/test-output/gene-psi-output/logs/main.2015-08-17_08-31-02.log'
.
======================================================================
FAIL: test_a_sam_to_bam (misopy.test_miso.TestMISO)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/misopy/test_miso.py", line 51, in test_a_sam_to_bam
    "c2c12.Atp2b1.sorted.bam")))
AssertionError

----------------------------------------------------------------------
Ran 5 tests in 1.276s

FAILED (failures=1)

 

Can you please help me...

 

 

RNA-Seq tool MISO • 3.9k views
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OSError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/site-packages/misopy/test-output'
OSError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1'
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yeah... thanx i tried running it with root and it worked ...

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you don't need to run the software with root, instead install it with root and run as user. You could use programs like Anaconda, which makes life easier for managing python packages.

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conda install -c bioconda misopy Collecting package metadata (repodata.json): done Solving environment: done

All requested packages already installed.

i installed like this. still getting error ~/anaconda3/pkgs/misopy-0.5.4-py27h516909a_2/lib/python2.7/site-packages/misopy$ python gff_utils.py Traceback (most recent call last): File "gff_utils.py", line 34, in <module> import misopy ImportError: No module named misopy

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I am abolutely new to this. How to go about the miso pipeline right from the stratch?

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