Question: Please Help For Effest "Segmentation Fault (Core Dumped)" In The Rlsim Package
1
gravatar for Allen Kao
5.8 years ago by
Allen Kao10
Ghent, Belgium
Allen Kao10 wrote:

Hi all,

When using rlsim for simulating RNA-seq reads, I tried to estimate parameters by effest in the following command:

$ effest -v -f ref.fas aln1.sam
[13-04-23 02:27:51] Assumed mean efficiency: 0.87
[13-04-23 02:27:51] Number of PCR cycles: 11
[13-04-23 02:27:51] Sliding window step ratio: 5
[13-04-23 02:27:51] Minimum mapping quality: 10
[13-04-23 02:27:51] Saving estimated raw parameters to file: raw_params.json
[13-04-23 02:27:51] Parsing fragments from file: aln1.sam
Segmentation fault (core dumped)

As described, effest resulted in Segmentation fault. Is it because I failed to install HTSeq provided in the rlsim package properly? I directly installed HTSeq-0.5.3p3-hack but it seems that some critical files were missing:

$ python setup.py install --user
running install
running bdist_egg
running egg_info
writing HTSeq.egg-info/PKG-INFO
writing top-level names to HTSeq.egg-info/top_level.txt
writing dependency_links to HTSeq.egg-info/dependency_links.txt
file HTSeq/StepVector.py (for module HTSeq.StepVector) not found
reading manifest file 'HTSeq.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching 'example_data'
no previously-included directories found matching 'test'
warning: no previously-included files found matching 'todo.txt'
writing manifest file 'HTSeq.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
file HTSeq/StepVector.py (for module HTSeq.StepVector) not found
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/HTSeq
copying HTSeq/__init__.py -> build/lib.linux-x86_64-2.7/HTSeq
copying HTSeq/_HTSeq_internal.py -> build/lib.linux-x86_64-2.7/HTSeq
copying HTSeq/_version.py -> build/lib.linux-x86_64-2.7/HTSeq
creating build/lib.linux-x86_64-2.7/HTSeq/scripts
copying HTSeq/scripts/__init__.py -> build/lib.linux-x86_64-2.7/HTSeq/scripts
copying HTSeq/scripts/qa.py -> build/lib.linux-x86_64-2.7/HTSeq/scripts
copying HTSeq/scripts/count.py -> build/lib.linux-x86_64-2.7/HTSeq/scripts
file HTSeq/StepVector.py (for module HTSeq.StepVector) not found
running build_ext
building 'HTSeq._HTSeq' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c src/_HTSeq.c -o build/temp.linux-x86_64-2.7/src/_HTSeq.o -w
gcc: error: src/_HTSeq.c: No such file or directory
gcc: fatal error: no input files
compilation terminated.
error: command 'gcc' failed with exit status 4

After copying StepVector.py and _HTSeq.c from HTSeq-0.5.3p2.tar.gz (downloaded from https://pypi.python.org/packages/source/H/HTSeq/), the installation process finished successfully, but it still resulted in Segmentation fault while running effest.

Does anyone encounter the same problem? Any response is appreciated!

• 3.3k views
ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Allen Kao10
0
gravatar for Botond Sipos
5.8 years ago by
Botond Sipos1.7k
United Kingdom
Botond Sipos1.7k wrote:

It seems that there was an issue with the packaging of the modified HTSeq. The modifications are actually in the .pyx files which generate StepVector.py and _HTSeq.c, hence copying those from the official package will not solve the segfault issue.

I have updated the modified HTSeq in the rlsim repo, please let me know if it is still broken.

ADD COMMENTlink written 5.8 years ago by Botond Sipos1.7k
0
gravatar for Allen Kao
5.8 years ago by
Allen Kao10
Ghent, Belgium
Allen Kao10 wrote:

Thank you for replying me, Botond. Not sure if I manipulate it correctly or not.
I downloaded the modified HTSeq package again and tried to use it in two ways:
1. Install it the official way:

$ python setup.py install --user
running install
running bdist_egg
running egg_info
writing HTSeq.egg-info/PKG-INFO
writing top-level names to HTSeq.egg-info/top_level.txt
writing dependency_links to HTSeq.egg-info/dependency_links.txt
file HTSeq/StepVector.py (for module HTSeq.StepVector) not found
reading manifest file 'HTSeq.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching 'example_data'
no previously-included directories found matching 'test'
warning: no previously-included files found matching 'todo.txt'
writing manifest file 'HTSeq.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
file HTSeq/StepVector.py (for module HTSeq.StepVector) not found
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/HTSeq
copying HTSeq/__init__.py -> build/lib.linux-x86_64-2.7/HTSeq
copying HTSeq/_HTSeq_internal.py -> build/lib.linux-x86_64-2.7/HTSeq
copying HTSeq/_version.py -> build/lib.linux-x86_64-2.7/HTSeq
creating build/lib.linux-x86_64-2.7/HTSeq/scripts
copying HTSeq/scripts/__init__.py -> build/lib.linux-x86_64-2.7/HTSeq/scripts
copying HTSeq/scripts/qa.py -> build/lib.linux-x86_64-2.7/HTSeq/scripts
copying HTSeq/scripts/count.py -> build/lib.linux-x86_64-2.7/HTSeq/scripts
file HTSeq/StepVector.py (for module HTSeq.StepVector) not found
running build_ext
building 'HTSeq._HTSeq' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c src/_HTSeq.c -o build/temp.linux-x86_64-2.7/src/_HTSeq.o -w
gcc: error: src/_HTSeq.c: No such file or directory
gcc: fatal error: no input files
compilation terminated.
error: command 'gcc' failed with exit status 4

2. Let htseq-count and htseq-qa be executable, then create soft link to PATH

$ chmod +x ./rlsim-master/misc/HTSeq-0.5.3p3-hack/scripts/htseq*; ln -s `pwd`/rlsim-master/misc/HTSeq-0.5.3p3-hack/scripts/htseq* ~/bin/

Both the above methods resulted in segmentation fault again.
Wondering how HTseq involved in effest, and how to install the modified HTseq after downloading it, thank you.

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Allen Kao10

Interesting. I would like to ask you to download the modified package once again and try to install it the "official" way. If still fails, then please run the build_it script in unpacked HTSeq directory before trying to install.

BTW, you do not need the htseq-count and htseq-qa scripts as effest only uses the HTSeq API.

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by Botond Sipos1.7k
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