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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
302 stars 38 forks source link

Error installing on Debian (multiple versions) #94

Closed nuin closed 4 years ago

nuin commented 4 years ago

Hi

I am trying to install on Debian (9, 10 and 11) with the install script and getting the same error 

[ 10%] Building CXX object src/CMakeFiles/octopus.dir/main.cpp.o
[ 11%] Building CXX object src/CMakeFiles/octopus.dir/config/common.cpp.o
[ 11%] Building CXX object src/CMakeFiles/octopus.dir/config/config.cpp.o
[ 12%] Building CXX object src/CMakeFiles/octopus.dir/config/option_collation.cpp.o
[ 12%] Building CXX object src/CMakeFiles/octopus.dir/config/option_parser.cpp.o
[ 12%] Building CXX object src/CMakeFiles/octopus.dir/config/octopus_vcf.cpp.o
[ 13%] Building CXX object src/CMakeFiles/octopus.dir/exceptions/error.cpp.o
[ 13%] Building CXX object src/CMakeFiles/octopus.dir/exceptions/missing_file_error.cpp.o
[ 13%] Building CXX object src/CMakeFiles/octopus.dir/exceptions/malformed_file_error.cpp.o
[ 14%] Building CXX object src/CMakeFiles/octopus.dir/exceptions/missing_index_error.cpp.o
[ 14%] Building CXX object src/CMakeFiles/octopus.dir/exceptions/unwritable_file_error.cpp.o
[ 15%] Building CXX object src/CMakeFiles/octopus.dir/exceptions/unimplemented_feature_error.cpp.o
[ 15%] Building CXX object src/CMakeFiles/octopus.dir/exceptions/file_open_error.cpp.o
[ 15%] Building CXX object src/CMakeFiles/octopus.dir/basics/cigar_string.cpp.o
[ 16%] Building CXX object src/CMakeFiles/octopus.dir/basics/aligned_read.cpp.o
[ 16%] Building CXX object src/CMakeFiles/octopus.dir/basics/ploidy_map.cpp.o
[ 17%] Building CXX object src/CMakeFiles/octopus.dir/basics/pedigree.cpp.o
[ 18%] Building CXX object src/CMakeFiles/octopus.dir/basics/trio.cpp.o
[ 18%] Building CXX object src/CMakeFiles/octopus.dir/basics/read_pileup.cpp.o
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [src/CMakeFiles/octopus.dir/build.make:63: src/CMakeFiles/octopus.dir/main.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [src/CMakeFiles/octopus.dir/build.make:115: src/CMakeFiles/octopus.dir/config/option_collation.cpp.o] Error 1
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [src/CMakeFiles/octopus.dir/build.make:89: src/CMakeFiles/octopus.dir/config/common.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:281: src/CMakeFiles/octopus.dir/all] Error 2
make: *** [Makefile:130: all] Error 2

Any help appreciated.

dancooke commented 4 years ago

Looks like the OS killed the build process - maybe too many resources used. The default behaviour is to use as many processes as there are CPU cores for building, but you can set the number of threads with the --threads option. Maybe try with just a single thread to start with.

nuin commented 4 years ago

@dancooke Yep, you were right, works fine with --threads 1. Thanks for the quick reply.