Closed zhaobo22 closed 10 months ago
Hi @zhaobo22, which version of ganon are you using? I just ran the same command here in v1.9.0 and it worked fine.
Thanks for reply! I used v1.9.0 ganon, too. This was really weird because it worked fine on my other server. I judged from the error message that raptor could not run properly. In fact, when I ran raptor -h, the following error occurred:
Illegal instruction (core dumped)
So I guess there should be a problem with the environment configuration, but I don't know exactly where the problem is. I can provide other error messages to help you determine the problem if you need.
Besides, I also got an error when I tried to compile from ganon source code with the following error message:
src/CMakeFiles/ganon-build-lib.dir/build.make:89: recipe for target 'src/CMakeFiles/ganon-build-lib.dir/ganon-build/GanonBuild.cpp.o' failed make[2]: [src/CMakeFiles/ganon-build-lib.dir/ganon-build/GanonBuild.cpp.o] Error 1 CMakeFiles/Makefile2:121: recipe for target 'src/CMakeFiles/ganon-build-lib.dir/all' failed make[1]: [src/CMakeFiles/ganon-build-lib.dir/all] Error 2 Makefile:145: recipe for target 'all' failed make: *** [all] Error 2
So are you using the conda version, right? Can you double check the version of raptor installed in that environment with conda list -n your_env -f raptor
.
To better help with the compilation I would have to see the full cmake
and make
command outputs.
Yes, I used the conda version. The version of raptor in ganon environment is as follows:
The cmake -DCMAKE_BUILD_TYPE=Release -DVERBOSE_CONFIG=ON -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCONDA=OFF -DLONGREADS=OFF ..
command output is as follows:
-- The CXX compiler identification is GNU 11.4.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11")
-- Finding SeqAn3 and checking requirements:
-- SeqAn3 include dir found: /home/zhaobo/tools/ganon/libs/seqan3/include
-- Detected as running from a repository checkout…
-- …adding submodule include: /home/zhaobo/tools/ganon/libs/seqan3/submodules/cereal/include
-- …adding submodule include: /home/zhaobo/tools/ganon/libs/seqan3/submodules/range-v3/include
-- …adding submodule include: /home/zhaobo/tools/ganon/libs/seqan3/submodules/sdsl-lite/include
-- C++ Standard-17 support: builtin
-- C++ Concepts support: via -fconcepts
-- C++ Filesystem header:
The make
command output is as follows:
[ 6%] Building CXX object src/CMakeFiles/ganon-classify-lib.dir/ganon-classify/GanonClassify.cpp.o
[ 12%] Building CXX object src/CMakeFiles/ganon-classify-lib.dir/ganon-classify/CommandLineParser.cpp.o
[ 18%] Building CXX object src/CMakeFiles/ganon-build-lib.dir/ganon-build/CommandLineParser.cpp.o
[ 25%] Building CXX object src/CMakeFiles/ganon-build-lib.dir/ganon-build/GanonBuild.cpp.o
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/detail/format_sam_base.hpp:26,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:23,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/output_format_concept.hpp:87:15: error: ‘std::optional’ has not been declared
87 | std::optional~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/core/platform.hpp:58:9: note: in definition of macro ‘SEQAN3_RETURN_TYPE_CONSTRAINT’
58 | {expression} -> concept_name<__VA_ARGS__>
| ^~~~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/record.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:30,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/record.hpp:82:5: note: ‘seqan3::field::ref_id’ declared here
82 | ref_id, //!< The identifier of the (reference) sequence that seqan3::field::seq was aligned to.
| ^~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/exception.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/concept.hpp:17,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/adaptation/char.hpp:28,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:22,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/output_format_concept.hpp:109:60: error: ‘ref_offset’ was not declared in this scope; did you mean ‘seqan3::field::ref_offset’?
109 | ref_offset,
| ^~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/core/platform.hpp:58:9: note: in definition of macro ‘SEQAN3_RETURN_TYPE_CONSTRAINT’
58 | {expression} -> concept_name<__VA_ARGS__>
| ^~~~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/record.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:30,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/record.hpp:84:5: note: ‘seqan3::field::ref_offset’ declared here
84 | ref_offset, //!< Sequence (seqan3::field::ref_seq) relative start position (0-based), unsigned value.
| ^~~~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/exception.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/concept.hpp:17,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/adaptation/char.hpp:28,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:22,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/output_format_concept.hpp:110:60: error: ‘align’ was not declared in this scope; did you mean ‘std::align’?
110 | align,
| ^~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/core/platform.hpp:58:9: note: in definition of macro ‘SEQAN3_RETURN_TYPE_CONSTRAINT’
58 | {expression} -> concept_name<__VA_ARGS__>
| ^~~~~~
In file included from /usr/include/c++/11/memory:72,
from /home/zhaobo/tools/ganon/libs/robin-hood-hashing/src/include/robin_hood.h:46,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:3:
/usr/include/c++/11/bits/align.h:62:1: note: ‘std::align’ declared here
62 | align(size_t align, size_t size, void*& ptr, size_t& space) noexcept
| ^~~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/exception.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/concept.hpp:17,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/adaptation/char.hpp:28,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:22,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/output_format_concept.hpp:111:65: error: expected primary-expression before ‘,’ token
111 | cigar,
| ^
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/core/platform.hpp:58:9: note: in definition of macro ‘SEQAN3_RETURN_TYPE_CONSTRAINT’
58 | {expression} -> concept_name<__VA_ARGS__>
| ^~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/output_format_concept.hpp:112:60: error: ‘flag’ was not declared in this scope; did you mean ‘seqan3::field::flag’?
112 | flag,
| ^~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/core/platform.hpp:58:9: note: in definition of macro ‘SEQAN3_RETURN_TYPE_CONSTRAINT’
58 | {expression} -> concept_name<__VA_ARGS__>
| ^~~~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/record.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:30,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/record.hpp:87:5: note: ‘seqan3::field::flag’ declared here
87 | flag, //!< The alignment flag (bit information), uint16_t
value.
| ^~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/exception.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/concept.hpp:17,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/adaptation/char.hpp:28,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:22,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/output_format_concept.hpp:113:60: error: ‘mapq’ was not declared in this scope; did you mean ‘seqan3::field::mapq’?
113 | mapq,
| ^~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/core/platform.hpp:58:9: note: in definition of macro ‘SEQAN3_RETURN_TYPE_CONSTRAINT’
58 | {expression} -> concept_name<__VA_ARGS__>
| ^~~~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/record.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:30,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/record.hpp:89:5: note: ‘seqan3::field::mapq’ declared here
89 | mapq, //!< The mapping quality of the seqan3::field::seq alignment, usually a Phred-scaled score.
| ^~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/exception.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/concept.hpp:17,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/adaptation/char.hpp:28,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:22,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/output_format_concept.hpp:114:60: error: ‘mate’ was not declared in this scope; did you mean ‘seqan3::field::mate’?
114 | mate,
| ^~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/core/platform.hpp:58:9: note: in definition of macro ‘SEQAN3_RETURN_TYPE_CONSTRAINT’
58 | {expression} -> concept_name<__VA_ARGS__>
| ^~~~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/record.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:30,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/record.hpp:88:5: note: ‘seqan3::field::mate’ declared here
88 | mate, //!< The mate pair information given as a std::tuple of reference name, offset and template length.
| ^~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/utility/char_operations/pretty_print.hpp:17,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/exception.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/concept.hpp:17,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/alphabet/adaptation/char.hpp:28,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:22,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/output_format_concept.hpp:115:60: error: ‘tag_dict’ was not declared in this scope
115 | tag_dict,
| ^~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/core/platform.hpp:58:9: note: in definition of macro ‘SEQAN3_RETURN_TYPE_CONSTRAINT’
58 | {expression} -> concept_name<__VA_ARGS__>
| ^~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/output_format_concept.hpp:116:60: error: ‘e_value’ was not declared in this scope
116 | e_value,
| ^~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/core/platform.hpp:58:9: note: in definition of macro ‘SEQAN3_RETURN_TYPE_CONSTRAINT’
58 | {expression} -> concept_name<__VA_ARGS__>
| ^~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/output_format_concept.hpp:117:60: error: ‘bit_score’ was not declared in this scope; did you mean ‘seqan3::field::bit_score’?
117 | bit_score),
| ^~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/core/platform.hpp:58:9: note: in definition of macro ‘SEQAN3_RETURN_TYPE_CONSTRAINT’
58 | {expression} -> concept_name<__VA_ARGS__>
| ^~~~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/record.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:30,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/record.hpp:93:5: note: ‘seqan3::field::bit_score’ declared here
93 | bit_score, //!< The bit score (statistical significance indicator), unsigned value.
| ^~~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:23,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/detail/format_sam_base.hpp:102:54: error: ‘std::optional’ has not been declared
102 | void read_field(stream_view_type && stream_view, std::optional~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/detail/format_sam_base.hpp: In member function ‘void seqan3::detail::format_sam_base::read_header(stream_view_type&&, seqan3::sam_file_header~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/detail/format_sam_base.hpp:30:1: note: ‘std::optional’ is defined in header ‘~~~~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:25,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/input_format_concept.hpp: At global scope:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/input_format_concept.hpp:88:15: error: ‘std::optional’ has not been declared
88 | std::optional~
| seqan3::field::ref_id
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/record.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:30,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/record.hpp:82:5: note: ‘seqan3::field::ref_id’ declared here
82 | ref_id, //!< The identifier of the (reference) sequence that seqan3::field::seq was aligned to.
| ^~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:25,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/input_format_concept.hpp:112:31: error: ‘ref_offset’ was not declared in this scope; did you mean ‘seqan3::field::ref_offset’?
112 | ref_offset,
| ^~~~~~
| seqan3::field::ref_offset
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/record.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:30,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/record.hpp:84:5: note: ‘seqan3::field::ref_offset’ declared here
84 | ref_offset, //!< Sequence (seqan3::field::ref_seq) relative start position (0-based), unsigned value.
| ^~~~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:25,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/input_format_concept.hpp:113:31: error: ‘align’ was not declared in this scope; did you mean ‘std::align’?
113 | align,
| ^~~~~
| std::align
In file included from /usr/include/c++/11/memory:72,
from /home/zhaobo/tools/ganon/libs/robin-hood-hashing/src/include/robin_hood.h:46,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:3:
/usr/include/c++/11/bits/align.h:62:1: note: ‘std::align’ declared here
62 | align(size_t align, size_t size, void*& ptr, size_t& space) noexcept
| ^~~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:25,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/input_format_concept.hpp:114:36: error: expected primary-expression before ,’ token
114 | cigar,
| ^
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/input_format_concept.hpp:115:31: error: ‘flag’ was not declared in this scope; did you mean ‘seqan3::field::flag’?
115 | flag,
| ^~~~
| seqan3::field::flag
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/record.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:30,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/record.hpp:87:5: note: ‘seqan3::field::flag’ declared here
87 | flag, //!< The alignment flag (bit information), uint16_t
value.
| ^~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:25,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/input_format_concept.hpp:116:31: error: ‘mapq’ was not declared in this scope; did you mean ‘seqan3::field::mapq’?
116 | mapq,
| ^~~~
| seqan3::field::mapq
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/record.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:30,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/record.hpp:89:5: note: ‘seqan3::field::mapq’ declared here
89 | mapq, //!< The mapping quality of the seqan3::field::seq alignment, usually a Phred-scaled score.
| ^~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:25,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/input_format_concept.hpp:117:31: error: ‘mate’ was not declared in this scope; did you mean ‘seqan3::field::mate’?
117 | mate,
| ^~~~
| seqan3::field::mate
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/record.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:30,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/record.hpp:88:5: note: ‘seqan3::field::mate’ declared here
88 | mate, //!< The mate pair information given as a std::tuple of reference name, offset and template length.
| ^~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:25,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/input_format_concept.hpp:118:31: error: ‘tag_dict’ was not declared in this scope
118 | tag_dict,
| ^~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/input_format_concept.hpp:119:31: error: ‘e_value’ was not declared in this scope
119 | e_value,
| ^~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/input_format_concept.hpp:120:31: error: ‘bit_score’ was not declared in this scope; did you mean ‘seqan3::field::bit_score’?
120 | bit_score)};
| ^~~~~
| seqan3::field::bit_score
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/record.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:30,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/record.hpp:93:5: note: ‘seqan3::field::bit_score’ declared here
93 | bit_score, //!< The bit score (statistical significance indicator), unsigned value.
| ^~~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:220:33: error: ‘std::optional’ has not been declared
220 | std::optional~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:38:1: note: ‘std::optional’ is defined in header ‘~~~~~
| default_align_t
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp: In member function ‘void seqan3::format_sam::read_alignment_record(stream_type&, const seqan3::sam_file_input_options~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:388:77: note: ‘std::optional’ is defined in header ‘~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/submodules/range-v3/include/range/v3/view/drop.hpp:30,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/std/ranges:120,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/in_file_iterator.hpp:16,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:28,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/submodules/range-v3/include/range/v3/utility/optional.hpp:53:32: note: ‘ranges::nullopt’ declared here
53 | inline constexpr nullopt_t nullopt{nullopt_t::tag{}};
| ^~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp: At global scope:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:635:48: error: ‘std::optional’ has not been declared
635 | std::optional~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:675:99: note: ‘std::optional’ is defined in header ‘~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:680:98: note: ‘std::optional’ is defined in header ‘~~~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:690:25: error: template argument 2 is invalid
690 | std::equality_comparable_with<gap, std::ranges::range_reference_t<decltype(std::get<0>(align))>> &&
| ^~~~~~~~~~~~~~~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:691:86: error: template argument 1 is invalid
691 | std::equality_comparable_with<gap, std::ranges::range_reference_t<decltype(std::get<1>(align))>>),
| ^~~~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:691:25: error: template argument 2 is invalid
691 | std::equality_comparable_with<gap, std::ranges::range_reference_t<decltype(std::get<1>(align))>>),
| ^~~~~~~~~~~~~~~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:706:69: error: ‘mate’ was not declared in this scope; did you mean ‘seqan3::field::mate’?
706 | static_assert(((std::ranges::forward_range<decltype(std::get<0>(mate))> ||
| ^~~~
| seqan3::field::mate
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/record.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:30,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/record.hpp:88:5: note: ‘seqan3::field::mate’ declared here
88 | mate, //!< The mate pair information given as a std::tuple of reference name, offset and template length.
| ^~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:706:34: error: template argument 1 is invalid
706 | static_assert(((std::ranges::forward_range<decltype(std::get<0>(mate))> ||
| ^~~~~~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:707:55: error: template argument 1 is invalid
707 | std::integral<std::remove_cvref_t<decltype(std::get<0>(mate))>> ||
| ^~~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:707:26: error: template argument 1 is invalid
707 | std::integral<std::remove_cvref_t<decltype(std::get<0>(mate))>> ||
| ^~~~~~~~~~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:708:104: error: template argument 1 is invalid
708 | detail::is_type_specialisation_of_v<std::remove_cvref_t<decltype(std::get<0>(mate))>, std::optional>) &&
| ^
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:708:112: error: ‘optional’ is not a member of ‘std’
708 | detail::is_type_specialisation_of_v<std::remove_cvref_t<decltype(std::get<0>(mate))>, std::optional>) &&
| ^~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:708:112: note: ‘std::optional’ is defined in header ‘~~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:709:25: error: template argument 1 is invalid
709 | (std::integral<std::remove_cvref_t<decltype(std::get<1>(mate))>> ||
| ^~~~~~~~~~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:710:103: error: template argument 1 is invalid
710 | detail::is_type_specialisation_of_v<std::remove_cvref_t<decltype(std::get<1>(mate))>, std::optional>) &&
| ^
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:710:111: error: ‘optional’ is not a member of ‘std’
710 | detail::is_type_specialisation_of_v<std::remove_cvref_t<decltype(std::get<1>(mate))>, std::optional>) &&
| ^~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:710:111: note: ‘std::optional’ is defined in header ‘~~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:711:24: error: template argument 1 is invalid
711 | std::integral<std::remove_cvref_t<decltype(std::get<2>(mate))>>),
| ^~~~~~~~~~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:717:53: error: template argument 1 is invalid
717 | if constexpr (std::integral<std::remove_cvref_t<decltype(std::get<0>(mate))>> ||
| ^~~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:717:24: error: template argument 1 is invalid
717 | if constexpr (std::integral<std::remove_cvref_t<decltype(std::get<0>(mate))>> ||
| ^~~~~~~~~~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:718:102: error: template argument 1 is invalid
718 | detail::is_type_specialisation_of_v<std::remove_cvref_t<decltype(std::get<0>(mate))>, std::optional>)
| ^
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:718:110: error: ‘optional’ is not a member of ‘std’
718 | detail::is_type_specialisation_of_v<std::remove_cvref_t<decltype(std::get<0>(mate))>, std::optional>)
| ^~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:718:110: note: ‘std::optional’ is defined in header ‘~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:731:99: note: ‘std::optional’ is defined in header ‘~~~~~
| seqan3::field::ref_offset
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/record.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:30,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/record.hpp:84:5: note: ‘seqan3::field::ref_offset’ declared here
84 | ref_offset, //!< Sequence (seqan3::field::ref_seq) relative start position (0-based), unsigned value.
| ^~~~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:786:50: error: ‘flag’ was not declared in this scope; did you mean ‘seqan3::field::flag’?
786 | stream_it.write_number(static_castuint16_t
value.
| ^~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:795:107: error: ‘optional’ is not a member of ‘std’
795 | else if constexpr (detail::is_type_specialisation_of_v<std::remove_reference_t~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:795:107: note: ‘std::optional’ is defined in header ‘~~~~~
| seqan3::field::ref_offset
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/detail/record.hpp:19,
from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:30,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/record.hpp:84:5: note: ‘seqan3::field::ref_offset’ declared here
84 | ref_offset, //!< Sequence (seqan3::field::ref_seq) relative start position (0-based), unsigned value.
| ^~~~~~
In file included from /home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sequence_file/input.hpp:32,
from /home/zhaobo/tools/ganon/src/utils/include/utils/dna4_traits.hpp:10,
from /home/zhaobo/tools/ganon/src/ganon-build/GanonBuild.cpp:10:
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:818:50: error: ‘mapq’ was not declared in this scope; did you mean ‘seqan3::field::mapq’?
818 | stream_it.write_number(static_cast~~~
| rna5_vector
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:850:57: error: template argument 1 is invalid
850 | if constexpr (std::integral<std::remove_reference_t<decltype(get<0>(mate))>>)
| ^~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:850:24: error: template argument 1 is invalid
850 | if constexpr (std::integral<std::remove_reference_t<decltype(get<0>(mate))>>)
| ^~~~~~~~~~~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:854:106: error: template argument 1 is invalid
854 | else if constexpr (detail::is_type_specialisation_of_v<std::remove_reference_t<decltype(get<0>(mate))>, std::optional>)
| ^
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:854:114: error: ‘optional’ is not a member of ‘std’
854 | else if constexpr (detail::is_type_specialisation_of_v<std::remove_reference_t<decltype(get<0>(mate))>, std::optional>)
| ^~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:854:114: note: ‘std::optional’ is defined in header ‘~~~
/home/zhaobo/tools/ganon/libs/seqan3/include/seqan3/io/sam_file/format_sam.hpp:870:105: note: ‘std::optional’ is defined in header ‘~~~
src/CMakeFiles/ganon-build-lib.dir/build.make:89: recipe for target 'src/CMakeFiles/ganon-build-lib.dir/ganon-build/GanonBuild.cpp.o' failed
make[2]: [src/CMakeFiles/ganon-build-lib.dir/ganon-build/GanonBuild.cpp.o] Error 1
CMakeFiles/Makefile2:121: recipe for target 'src/CMakeFiles/ganon-build-lib.dir/all' failed
make[1]: [src/CMakeFiles/ganon-build-lib.dir/all] Error 2
make[1]: Waiting for unfinished jobs....
[ 31%] Linking CXX static library libganon-classify-lib.a
[ 31%] Built target ganon-classify-lib
Makefile:145: recipe for target 'all' failed
make: [all] Error 2
I'm not sure what is the issue with the pre-compiled conda version of raptor. Try to install raptor from source (https://pirovc.github.io/ganon/#installing-raptor-optional) and tell ganon to use it with --raptor-path
. Make sure is version 3.0.0.
The compilation error is probably due to the GCC 11, not tested with ganon yet. But I guess the conda version will work fine for you, once you get raptor to work.
Thanks for you advice! I have successfuly installed the raptor. When I run the ganon build
command, there are still errors. However, the error message had changed this time:
Building index (raptor) raptor prepare [Error] Expected one of the following valid extensions: [embl, fasta, fa, fna, ffn, faa, frn, fas, fastq, fq, genbank, gb, gbk, sam]! Got fna.gz instead! The following command failed to run: /home/zhaobo/tools/raptor/build/bin//raptor prepare --input 'a_rs_files/build/hibf.txt' --output 'a_rs_files/build/' --kmer 19 --window 31 --quiet --threads 32
Error code: 255
Thank you very much for your help!
I found this error because I was using raptor v3.1.0, but it worked fine when I used raptor v3.0.0. However, on another device, I was able to compile raptor v3.1.0 but was unable to compile v3.0.0. I have also tried different versions of gcc, but none of them compile properly.
Thank you again!
Great to hear you got it working. Right now ganon and raptor are compiling on different versions of gcc, what makes it tricky to compile locally as you noticed. The next release of ganon will update the gcc supported to the most current versions and include raptor as a library, so I hope this process will be easier.
Hi there, Thanks for building this greate tool. I am encountering an issue while using ganon for the build database process, and I'm seeking your assistance in resolving it. The error message I'm facing is as follows:
Building index (raptor) raptor prepare The following command failed to run: /miniconda3/envs/ganon/bin/raptor prepare --input 'a_rs_files/build/hibf.txt' --output 'a_rs_files/build/' --kmer 19 --window 31 --quiet --threads 48
Error code: -4
I initiated the build process with the following specific command: ganon build --source refseq --organism-group archaea --threads 48 --hibf --level species --db-prefix a_rs
I would greatly appreciate your guidance on how to address this error and successfully complete the ganon build. Any insights or suggestions you can provide would be immensely helpful.
Thank you for your time and expertise!