Segmentation fault: 11 on 2.2-e25c4ac

[Zhaoliang Liu]

Hi Paul, 

I finally managed to install majiq v2.2-e25c4ac successfully under a python virtual environment with the python version 3.8.6, at least it seems like. Under conda, I failed to install majiq 2.2, but successfully installed majiq v1.1.7a with a python version of 3.5.5.

I wanted to test if majiq 2.2 worked. However, when I ran the workshop example data with v2.2-e25c4ac, I had this "segmentation fault: 11" error,  and after I ran the command, python 3.8.6 crashed. I ran the the workshop example data with majiq 1.1.7a too, and it works just fine. I noticed there was a recent thread on the forum stating that she also used v2.2-e25c4ac, and had the same problem as me. But she said she had successfully ran the workshop example data with her majiq 2.2., which is a little bit different from me. And she did not report python crash. I don't know where is the issue, but I really want to make majiq work, because I think this is the best software suiting my needs of splicing analysis among the published splicing analysis softwares. Any help will be highly appreciated!

Here is the reported error by majiq 2.2.

/Users/zhaoliangliu/majiq_22/lib/python3.8/site-packages/majiq/src/config.py:81: UserWarning: sjdirs parameter not found in config file, using "./" instead
  warnings.warn(
2020-11-17 13:19:06,534 (PID:24973) - INFO - Majiq Build v2.2-e25c4ac
2020-11-17 13:19:06,534 (PID:24973) - INFO - Command: /Users/zhaoliangliu/majiq_22/bin/majiq build DB.gff3 -c majiq_build_config.ini -o ./build_majiq22
2020-11-17 13:19:06,534 (PID:24973) - INFO - Parsing GFF3
Segmentation fault: 11

The configuration file is like this:

info]
bamdirs=/Volumes/DataMining/Majiq/workshop_example/bam
genome=mm10

[experiments]
adr=workshop_Adr1,workshop_Adr2,workshop_Adr3
cer=workshop_Adr1,workshop_Adr2,workshop_Adr3

The version of htslib I am using is 1.11. The versions of other packages under the environment are as follows:

Click==7.0
Cython==0.29.14
Flask==1.0.2
Flask-Session==0.3.1
Flask-WTF==0.14.2
gitdb2==2.0.6
GitPython==3.0.5
gunicorn==19.9.0
h5py==2.10.0
itsdangerous==1.1.0
Jinja2==2.11.1
majiq==2.2
MarkupSafe==1.1.1
numpy==1.18.1
psutil==5.6.7
scipy==1.4.1
six==1.14.0
smmap2==2.0.5
waitress==1.1.0
Werkzeug==0.16.0
WTForms==2.2.1

The python crash report was attached.

Thanks a lot!

Zhaoliang

[Paul Jewell]

Hi Zhaoliang, 

Thank you for the report. I have heard a number of reports of issues in the last couple of months, related to OSX releasing some breaking changes. 

- Do you have access to a *Nix HPC system to use with majiq (It will be impractical to run most majiq analysis on your laptop itself, anyway), as a workaround?

- Could you please provide the basic outline of how you installed Majiq? This way, I can try to obtain a very recent OSX image and replicate the problem to check if there may be a ix or workaround from the majiq side. 

Thanks, 

-Paul

[Zhaoliang Liu]

Hi Paul,

Thank you very much! Unfortunately, I don't have access to *Nix HPC.

Here is how I installed majiq 2.2.

$ python3
Python 3.8.6 (v3.8.6:db455296be, Sep 23 2020, 13:31:39)
[Clang 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> exit()

$ python3 -m venv majiq_22
$ export C_INCLUDE_PATH=/usr/local/include:$C_INCLUDE_PATH
$ export CPLUS_INCLUDE_PATH=/usr/local/include:
$ export LIBRARY_PATH=/usr/local/lib:$LIBRARY_PATH
$ export DYLD_LIBRARY_PATH=/usr/local/lib:$DYLD_LIBRARY_PATH
$ export HTSLIB_LIBRARY_DIR=/usr/local/bin/htslib/lib
$ export HTSLIB_INCLUDE_DIR=/usr/local/bin/htslib/include
$ export CC=/usr/local/bin/gcc-9
$ export CXX=/usr/local/bin/g++-9
$ source majiq_22/bin/activate
(majiq_22) $ pip install git+https://bitbucket.org/biociphers/majiq_academic.git#egg=majiq
Collecting majiq
  Cloning https://bitbucket.org/biociphers/majiq_academic.git to /private/var/folders/fb/c054_k9d5m72xznpbggpl57w0000gn/T/pip-install-uda54gqz/majiq
Collecting Click==7.0
  Using cached Click-7.0-py2.py3-none-any.whl (81 kB)
Processing ./Library/Caches/pip/wheels/db/06/c3/74b5ed9a4c9fe32f784d4bed0893bf80d76a1c97fae0f11ce2/Cython-0.29.14-cp38-cp38-macosx_10_9_x86_64.whl
Collecting Flask==1.0.2
  Using cached Flask-1.0.2-py2.py3-none-any.whl (91 kB)
Collecting Flask-Session==0.3.1
  Using cached Flask_Session-0.3.1-py2.py3-none-any.whl (7.5 kB)
Collecting Flask-WTF==0.14.2
  Using cached Flask_WTF-0.14.2-py2.py3-none-any.whl (14 kB)
Collecting gitdb2==2.0.6
  Using cached gitdb2-2.0.6-py2.py3-none-any.whl (63 kB)
Collecting GitPython==3.0.5
  Using cached GitPython-3.0.5-py3-none-any.whl (455 kB)
Collecting gunicorn==19.9.0
  Using cached gunicorn-19.9.0-py2.py3-none-any.whl (112 kB)
Collecting h5py==2.10.0
  Using cached h5py-2.10.0-cp38-cp38-macosx_10_9_x86_64.whl (3.0 MB)
Collecting itsdangerous==1.1.0
  Using cached itsdangerous-1.1.0-py2.py3-none-any.whl (16 kB)
Collecting Jinja2==2.11.1
  Using cached Jinja2-2.11.1-py2.py3-none-any.whl (126 kB)
Collecting MarkupSafe==1.1.1
  Using cached MarkupSafe-1.1.1-cp38-cp38-macosx_10_9_x86_64.whl (16 kB)
Collecting numpy==1.18.1
  Using cached numpy-1.18.1-cp38-cp38-macosx_10_9_x86_64.whl (15.2 MB)
Processing ./Library/Caches/pip/wheels/c9/ca/61/9ce825d7f8fe0d1ed07f3d914d5b998540f205d39c742380ca/psutil-5.6.7-cp38-cp38-macosx_10_9_x86_64.whl
Collecting scipy==1.4.1
  Using cached scipy-1.4.1-cp38-cp38-macosx_10_9_x86_64.whl (28.8 MB)
Collecting six==1.14.0
  Using cached six-1.14.0-py2.py3-none-any.whl (10 kB)
Collecting smmap2==2.0.5
  Using cached smmap2-2.0.5-py2.py3-none-any.whl (24 kB)
Collecting waitress==1.1.0
  Using cached waitress-1.1.0-py2.py3-none-any.whl (114 kB)
Collecting Werkzeug==0.16.0
  Using cached Werkzeug-0.16.0-py2.py3-none-any.whl (327 kB)
Collecting WTForms==2.2.1
  Using cached WTForms-2.2.1-py2.py3-none-any.whl (166 kB)
Using legacy 'setup.py install' for majiq, since package 'wheel' is not installed.
Installing collected packages: Click, Cython, MarkupSafe, Jinja2, Werkzeug, itsdangerous, Flask, Flask-Session, WTForms, Flask-WTF, smmap2, gitdb2, GitPython, gunicorn, numpy, six, h5py, psutil, scipy, waitress, majiq
    Running setup.py install for majiq ... done
Successfully installed Click-7.0 Cython-0.29.14 Flask-1.0.2 Flask-Session-0.3.1 Flask-WTF-0.14.2 GitPython-3.0.5 Jinja2-2.11.1 MarkupSafe-1.1.1 WTForms-2.2.1 Werkzeug-0.16.0 gitdb2-2.0.6 gunicorn-19.9.0 h5py-2.10.0 itsdangerous-1.1.0 majiq-2.2 numpy-1.18.1 psutil-5.6.7 scipy-1.4.1 six-1.14.0 smmap2-2.0.5 waitress-1.1.0
WARNING: You are using pip version 20.2.1; however, version 20.2.4 is available.
You should consider upgrading via the '/Users/zhaoliangliu/majiq_22/bin/python3 -m pip install --upgrade pip' command.
(majiq_22) $ majiq -v
2.2-e25c4ac