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secastel / phaser

phasing and Allele Specific Expression from RNA-seq
GNU General Public License v3.0
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Error running phaser #71

Closed Arkosen closed 3 years ago

Arkosen commented 3 years ago

Hi I tried compiling phaser using the instructions laid out in the how-to section. I got the following output

(base) -bash-4.2$ python setup.py build_ext --inplace Compiling read_variant_map.py because it changed. [1/1] Cythonizing read_variant_map.py /iblm/netapp/home/asen/.local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /iblm/netapp/home/asen/phaser/phaser/read_variant_map.py tree = Parsing.p_module(s, pxd, full_module_name) running build_ext building 'read_variant_map' extension creating build creating build/temp.linux-x86_64-3.7 /iblm/netapp/home/asen/myconda/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /iblm/netapp/home/asen/myconda/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /iblm/netapp/home/asen/myconda/include -fPIC -I/iblm/netapp/home/asen/myconda/include/python3.7m -c read_variant_map.c -o build/temp.linux-x86_64-3.7/read_variant_map.o x86_64-conda_cos6-linux-gnu-gcc -pthread -shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-rpath,/iblm/netapp/home/asen/myconda/lib -L/iblm/netapp/home/asen/myconda/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-rpath,/iblm/netapp/home/asen/myconda/lib -L/iblm/netapp/home/asen/myconda/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/iblm/netapp/home/asen/myconda/lib -Wl,-rpath-link,/iblm/netapp/home/asen/myconda/lib -L/iblm/netapp/home/asen/myconda/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /iblm/netapp/home/asen/myconda/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /iblm/netapp/home/asen/myconda/include build/temp.linux-x86_64-3.7/read_variant_map.o -o /iblm/netapp/home/asen/phaser/phaser/read_variant_map.cpython-37m-x86_64-linux-gnu.so

Then I tried to running phaser.py and got the following error.

FATAL ERROR: Read Variant Mapper module must be compiled by running 'python setup.py build_ext --inplace'.

which suggest that the compilation wasnt correct.

Any suggestions?

Thanks

secastel commented 3 years ago

Not entirely sure what is going on here. What version of Python are you using? If you are using 3.x can you try with 2.x?

Arkosen commented 3 years ago

I tried Py27 and it worked. Thanks!. I do have another question where can I extract the information of which alleles have been phased? I want to see what percent of variants at a particular read depth are phased?

secastel commented 3 years ago

Glad to hear that worked for you. As for your followup question, you can look in the outputted VCF or the haplotypes.txt file to determine which variants were phased. You'll need to do your own processing of those outputs to get the answer.