Please Help For Effest "Segmentation Fault (Core Dumped)" In The Rlsim Package

Question

[Allen Kao]

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!

Answer 1

[Botond Sipos]

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.

Answer 2

[Allen Kao]

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.

[Botond Sipos]

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.