assembly parameters for low depth of coverage

[zhenzhenyang-psu]

Hi Chan, I know the desired depth of coverage is 60, but in my case, I have nanopore reads of only 10x coverage. For desired output, is there any parameters that I shall change for a successful run?

Also, i have another issue regarding the support system for shasta. The server for which I have large RAM nodes is a centOS6, which complained about errors like "kernel too old, core dumped". When I switched to a centOS7 node, this error was avoided. However, I didn't have large fat nodes on that system. Do you have any suggestions?

thanks much, zhenzhen

[paoloczi]

To use Shasta on a Linux system with an old kernel, download shasta-OldLinux-0.5.0. Please let us know if you still have a problem with that on CentOS 6.

At coverage 10x it is going to be hard to achieve a good assembly.We have not had the time to optimize assembly parameters for low coverage, but there is some discussion of that in issue #7. In particular, here is a list of assembly parameters that should probably be reduced proportionally to coverage:

MinHash.maxBucketSize
MarkerGraph.minCoverage
MarkerGraph.maxCoverage
MarkerGraph.lowCoverageThreshold
MarkerGraph.highCoverageThreshold
MarkerGraph.edgeMarkerSkipThreshold

However, I would be surprised if you were able to obtain a good assembly at coverage 10x. But good luck!

[zhenzhenyang-psu]

I actually tried shasta-OldLinux-0.5.0, yet it still reported errors like "kernel too old". I am trying to build from source and see if it works.

While I was trying to build from source, there was an error while compiling package spoa, error message occurred while I typed "make -j all":

Scanning dependencies of target spoa [ 20%] Building CXX object CMakeFiles/spoa.dir/src/alignment_engine.cpp.o [ 40%] Building CXX object CMakeFiles/spoa.dir/src/dispatcher.cpp.o [ 60%] Building CXX object CMakeFiles/spoa.dir/src/graph.cpp.o [ 80%] Building CXX object CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o In file included from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.hpp:14, from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/alignment_engine.cpp:12: /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:30: error: expected nested-name-specifier before 'Alignment' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:30: error: 'Alignment' has not been declared /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:30: error: expected ';' before '=' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:30: error: expected unqualified-id before '=' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:50: error: 'Alignment' does not name a type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:53: error: 'Alignment' does not name a type In file included from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/alignment_engine.cpp:12: /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.hpp:30: error: expected ';' before 'override' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.hpp:32: error: 'Alignment' does not name a type /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.hpp:47: error: 'Alignment' does not name a type /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.hpp:50: error: 'Alignment' does not name a type /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.hpp:53: error: 'Alignment' does not name a type /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.hpp:60: error: expected ';' before 'noexcept' In file included from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/alignment_engine.cpp:13: /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine.hpp:43: error: expected ';' before 'override' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine.hpp:45: error: 'Alignment' does not name a type /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine.hpp:61: error: expected constructor, destructor, or type conversion before 'linear' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine.hpp:65: error: expected constructor, destructor, or type conversion before 'affine' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine.hpp:69: error: expected constructor, destructor, or type conversion before 'convex' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine.hpp:78: error: expected initializer before 'noexcept' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/alignment_engine.cpp: In function 'std::unique_ptr<spoa::AlignmentEngine, std::default_delete > spoa::createAlignmentEngine(spoa::AlignmentType, int8_t, int8_t, int8_t, int8_t, int8_t, int8_t)': /tmp/shasta-build.bY1y/spoa-v3.4.0/src/alignment_engine.cpp:64: error: 'nullptr' was not declared in this scope /tmp/shasta-build.bY1y/spoa-v3.4.0/src/alignment_engine.cpp: At global scope: /tmp/shasta-build.bY1y/spoa-v3.4.0/src/alignment_engine.cpp:77: error: 'Alignment' does not name a type make[2]: [CMakeFiles/spoa.dir/src/alignment_engine.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... In file included from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.cpp:10: /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:24: error: expected nested-name-specifier before 'Alignment' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:24: error: 'Alignment' has not been declared /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:24: error: expected ';' before '=' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:24: error: expected unqualified-id before '=' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:53: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:53: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:53: error: 'void spoa::Graph::add_alignment(int)' cannot be overloaded /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: with 'void spoa::Graph::add_alignment(int)' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:56: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:56: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:56: error: 'void spoa::Graph::add_alignment(int)' cannot be overloaded /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: with 'void spoa::Graph::add_alignment(int)' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:59: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:59: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:59: error: 'void spoa::Graph::add_alignment(int)' cannot be overloaded /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: with 'void spoa::Graph::add_alignment(int)' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:63: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:63: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:63: error: 'void spoa::Graph::add_alignment(int)' cannot be overloaded /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: with 'void spoa::Graph::add_alignment(int)' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:66: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:66: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:66: error: 'void spoa::Graph::add_alignment(int)' cannot be overloaded /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: with 'void spoa::Graph::add_alignment(int)' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:81: error: 'Alignment' has not been declared /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:165: error: a class-key must be used when declaring a friend /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:165: error: friend declaration does not name a class or function /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:191: error: a class-key must be used when declaring a friend /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:191: error: friend declaration does not name a class or function /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:192: error: a class-key must be used when declaring a friend /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:192: error: friend declaration does not name a class or function In file included from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.hpp:14, from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.cpp:11: /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:30: error: expected nested-name-specifier before 'Alignment' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:30: error: 'Alignment' has not been declared /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:30: error: expected ';' before '=' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:30: error: expected unqualified-id before '=' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:50: error: 'Alignment' does not name a type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:53: error: 'Alignment' does not name a type In file included from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.cpp:11: /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.hpp:30: error: expected ';' before 'override' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.hpp:32: error: 'Alignment' does not name a type /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.hpp:47: error: 'Alignment' does not name a type /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.hpp:50: error: 'Alignment' does not name a type /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.hpp:53: error: 'Alignment' does not name a type /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.hpp:60: error: expected ';' before 'noexcept' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.cpp:15: error: 'constexpr' does not name a type /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.cpp: In function 'std::unique_ptr<spoa::AlignmentEngine, std::default_delete > spoa::createSisdAlignmentEngine(spoa::AlignmentType, spoa::AlignmentSubtype, int8_t, int8_t, int8_t, int8_t, int8_t, int8_t)': /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.cpp:23: error: cannot allocate an object of abstract type 'spoa::SisdAlignmentEngine' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.hpp:25: note: because the following virtual functions are pure within 'spoa::SisdAlignmentEngine': /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:47: note: virtual void spoa::AlignmentEngine::prealloc(uint32_t, uint32_t) /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.cpp: In constructor 'spoa::SisdAlignmentEngine::Implementation::Implementation()': /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.cpp:37: error: 'nullptr' was not declared in this scope /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.cpp: At global scope: /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.cpp:53: error: no 'void spoa::SisdAlignmentEngine::prealloc(uint32_t, uint32_t)' member function declared in class 'spoa::SisdAlignmentEngine' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.cpp: In member function 'void spoa::SisdAlignmentEngine::realloc(uint32_t, uint32_t, uint32_t)': /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.cpp:72: error: 'nullptr' was not declared in this scope /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.cpp: At global scope: /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.cpp:95: error: expected initializer before 'noexcept' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/sisd_alignment_engine.cpp:912: error: expected '}' at end of input make[2]: [CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o] Error 1 In file included from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp:13: /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:24: error: expected nested-name-specifier before 'Alignment' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:24: error: 'Alignment' has not been declared /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:24: error: expected ';' before '=' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:24: error: expected unqualified-id before '=' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:53: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:53: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:53: error: 'void spoa::Graph::add_alignment(int)' cannot be overloaded /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: with 'void spoa::Graph::add_alignment(int)' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:56: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:56: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:56: error: 'void spoa::Graph::add_alignment(int)' cannot be overloaded /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: with 'void spoa::Graph::add_alignment(int)' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:59: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:59: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:59: error: 'void spoa::Graph::add_alignment(int)' cannot be overloaded /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: with 'void spoa::Graph::add_alignment(int)' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:63: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:63: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:63: error: 'void spoa::Graph::add_alignment(int)' cannot be overloaded /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: with 'void spoa::Graph::add_alignment(int)' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:66: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:66: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:66: error: 'void spoa::Graph::add_alignment(int)' cannot be overloaded /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: with 'void spoa::Graph::add_alignment(int)' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:81: error: 'Alignment' has not been declared /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:165: error: a class-key must be used when declaring a friend /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:165: error: friend declaration does not name a class or function /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:191: error: a class-key must be used when declaring a friend /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:191: error: friend declaration does not name a class or function /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:192: error: a class-key must be used when declaring a friend /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:192: error: friend declaration does not name a class or function /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp:17: error: 'constexpr' does not name a type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp: In static member function 'static std::unique_ptr<spoa::Node, std::default_delete > spoa::Graph::createNode(uint32_t, uint32_t)': /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:168: error: 'spoa::Node::Node(uint32_t, uint32_t)' is private /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp:20: error: within this context /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp: In member function 'bool spoa::Node::successor(uint32_t&, uint32_t) const': /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp:33: error: expected initializer before ':' token /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp:791: error: expected primary-expression at end of input /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp:791: error: expected ';' at end of input /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp:791: error: expected primary-expression at end of input /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp:791: error: expected ')' at end of input /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp:791: error: expected statement at end of input /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp:791: error: expected '}' at end of input /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp:791: warning: no return statement in function returning non-void /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp: At global scope: /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp:31: warning: unused parameter 'dst' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp:31: warning: unused parameter 'label' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/graph.cpp:791: error: expected '}' at end of input make[2]: [CMakeFiles/spoa.dir/src/graph.cpp.o] Error 1 In file included from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine_impl.hpp:24, from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/dispatcher.cpp:7: /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:24: error: expected nested-name-specifier before 'Alignment' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:24: error: 'Alignment' has not been declared /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:24: error: expected ';' before '=' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:24: error: expected unqualified-id before '=' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:53: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:53: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:53: error: 'void spoa::Graph::add_alignment(int)' cannot be overloaded /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: with 'void spoa::Graph::add_alignment(int)' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:56: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:56: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:56: error: 'void spoa::Graph::add_alignment(int)' cannot be overloaded /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: with 'void spoa::Graph::add_alignment(int)' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:59: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:59: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:59: error: 'void spoa::Graph::add_alignment(int)' cannot be overloaded /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: with 'void spoa::Graph::add_alignment(int)' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:63: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:63: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:63: error: 'void spoa::Graph::add_alignment(int)' cannot be overloaded /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: with 'void spoa::Graph::add_alignment(int)' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:66: error: ISO C++ forbids declaration of 'Alignment' with no type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:66: error: expected ',' or '...' before '&' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:66: error: 'void spoa::Graph::add_alignment(int)' cannot be overloaded /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:50: error: with 'void spoa::Graph::add_alignment(int)' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:81: error: 'Alignment' has not been declared /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:165: error: a class-key must be used when declaring a friend /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:165: error: friend declaration does not name a class or function /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:191: error: a class-key must be used when declaring a friend /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:191: error: friend declaration does not name a class or function /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:192: error: a class-key must be used when declaring a friend /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/graph.hpp:192: error: friend declaration does not name a class or function In file included from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine.hpp:14, from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine_impl.hpp:25, from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/dispatcher.cpp:7: /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:30: error: expected nested-name-specifier before 'Alignment' /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:30: error: 'Alignment' has not been declared /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:30: error: expected ';' before '=' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:30: error: expected unqualified-id before '=' token /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:50: error: 'Alignment' does not name a type /tmp/shasta-build.bY1y/spoa-v3.4.0/include/spoa/alignment_engine.hpp:53: error: 'Alignment' does not name a type In file included from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine_impl.hpp:25, from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/dispatcher.cpp:7: /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine.hpp:43: error: expected ';' before 'override' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine.hpp:45: error: 'Alignment' does not name a type /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine.hpp:61: error: expected constructor, destructor, or type conversion before 'linear' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine.hpp:65: error: expected constructor, destructor, or type conversion before 'affine' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine.hpp:69: error: expected constructor, destructor, or type conversion before 'convex' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine.hpp:78: error: expected initializer before 'noexcept' In file included from /tmp/shasta-build.bY1y/spoa-v3.4.0/src/dispatcher.cpp:7: /tmp/shasta-build.bY1y/spoa-v3.4.0/src/simd_alignment_engine_impl.hpp:32: error: expected initializer before 'noexcept' /tmp/shasta-build.bY1y/spoa-v3.4.0/src/dispatcher.cpp:61: error: expected '}' at end of input make[2]: [CMakeFiles/spoa.dir/src/dispatcher.cpp.o] Error 1 make[1]: [CMakeFiles/spoa.dir/all] Error 2 make: *** [all] Error 2

Do you happen to know how to fix this compiliationi error? By the way, I will try the low depth parameters, thanks much, zhenzhen

[zhenzhenyang-psu]

Hi, sorry for the long error message. It was fixed with newer version of gcc and g++ and pass it to cmake. the following commands worked for me in the end:

module load apps/cmake/3.7.0-rc3 module load compiler/gnu/5.5.0 module load apps/glib/2.14

cmake -DCMAKE_C_COMPILER=/public/software/compiler/gnu/5.5.0/bin/gcc -DCMAKE_CXX_COMPILER=/public/software/compiler/gnu/5.5.0/bin/g++ ../spoa-v3.4.0 -DBUILD_SHARED_LIBS=OFF

thanks, zhenzhen

[paoloczi]

Regarding building Shasta on CentOS6 6, please see my comments on issue #157.