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!