bbuchfink
make: *** [diamond] Error 1
I am trying to own a diamond v0.7.10 (which version is a dependency of another tool) on our computer cluster. But I am getting an error which persists.
Also install the CONDA version before that "conda install -c bioconda diamond = 0.7.10 "but diamond does not always work.
(plantiSMASH_py27) [amissino@genossh:plantiSMASH] $ conda install -c bioconda diamond=0.7.10 (plantiSMASH_py27) [amissino@genossh:plantiSMASH] $ more slurm-1399411.out ERROR: Failed to locate file: 'diamond' ERROR: Failed to locate file: 'diamond' ERROR: Not all prerequisites met
$ wget http://github.com/bbuchfink/diamond/archive/v0.7.10.tar.gz
$ tar xzf v0.7.10.tar.gz
$ cd diamond-0.7.10/src
$ ./install-boost
$ [...]
$ make
gcc -O3 -DNDEBUG -c -o algo/blast/core/raw_scoremat.o algo/blast/core/raw_scoremat.c gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_query_info.o algo/blast/core/blast_query_info.c gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_seg.o algo/blast/core/blast_seg.c g++ -O3 -DNDEBUG -Iboost/include -Wall -Wno-uninitialized -march=native -c -o main.o main.cpp In file included from run/../search/align.h:28, from run/../search/align_range.h:24, from run/master_thread.h:32, from main.cpp:28: run/../search/../search/sse_dist.h: In function ‘unsigned int match_block_reduced(const _val*, const _val*) [with _val = Value_type<Letter_prot>]’: run/../search/../search/sse_dist.h:81: warning: dereferencing pointer ‘s’ does break strict-aliasing rules run/../search/../search/sse_dist.h:78: note: initialized from here run/../search/../search/sse_dist.h:81: note: initialized from here run/../search/../search/sse_dist.h:81: warning: dereferencing pointer ‘s’ does break strict-aliasing rules run/../search/../search/sse_dist.h:78: note: initialized from here run/../search/../search/sse_dist.h:81: note: initialized from here run/../search/../search/sse_dist.h: In function ‘unsigned int match_block_reduced(const _val*, const _val*) [with _val = Value_type<Letter_nucl>]’: run/../search/../search/sse_dist.h:81: warning: dereferencing pointer ‘s’ does break strict-aliasing rules run/../search/../search/sse_dist.h:78: note: initialized from here run/../search/../search/sse_dist.h:81: note: initialized from here run/../search/../search/sse_dist.h:81: warning: dereferencing pointer ‘s’ does break strict-aliasing rules run/../search/../search/sse_dist.h:78: note: initialized from here run/../search/../search/sse_dist.h:81: note: initialized from here g++ -O3 -DNDEBUG -Iboost/include -Wall -Wno-uninitialized -march=native -c -o basic/options.o basic/options.cpp g++ -O3 -DNDEBUG -Iboost/include -Wall -Wno-uninitialized -march=native -c -o util/tinythread.o util/tinythread.cpp g++ -o ../bin/diamond algo/blast/core/blast_encoding.o algo/blast/core/blast_stat.o algo/blast/core/blast_filter.o algo/blast/core/blast_util.o algo/blast/core/blast_message.o algo/blast/core/ncbi_erf.o algo/blast/core/blast_options.o algo/blast/core/ncbi_math.o algo/blast/core/blast_program.o algo/blast/core/ncbi_std.o algo/blast/core/blast_psi_priv.o algo/blast/core/raw_scoremat.o algo/blast/core/blast_query_info.o algo/blast/core/blast_seg.o main.o basic/options.o util/tinythread.o boost/lib/libboost_thread.a boost/lib/libboost_system.a boost/lib/libboost_timer.a boost/lib/libboost_chrono.a boost/lib/libboost_iostreams.a boost/lib/libboost_program_options.a -lpthread -lz -lrt g++: boost/lib/libboost_iostreams.a: No such file or directory gcc -O3 -DNDEBUG -c -o algo/blast/core/raw_scoremat.o algo/blast/core/raw_scoremat.c gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_query_info.o algo/blast/core/blast_query_info.c gcc -O3 -DNDEBUG -c -o algo/blast/core/blast_seg.o algo/blast/core/blast_seg.c g++ -O3 -DNDEBUG -Iboost/include -Wall -Wno-uninitialized -march=native -c -o main.o main.cpp In file included from run/../search/align.h:28, from run/../search/align_range.h:24, from run/master_thread.h:32, from main.cpp:28: run/../search/../search/sse_dist.h: In function ‘unsigned int match_block_reduced(const _val*, const _val*) [with _val = Value_type<Letter_prot>]’: run/../search/../search/sse_dist.h:81: warning: dereferencing pointer ‘s’ does break strict-aliasing rules run/../search/../search/sse_dist.h:78: note: initialized from here run/../search/../search/sse_dist.h:81: note: initialized from here run/../search/../search/sse_dist.h:81: warning: dereferencing pointer ‘s’ does break strict-aliasing rules run/../search/../search/sse_dist.h:78: note: initialized from here run/../search/../search/sse_dist.h:81: note: initialized from here run/../search/../search/sse_dist.h: In function ‘unsigned int match_block_reduced(const _val*, const _val*) [with _val = Value_type<Letter_nucl>]’: run/../search/../search/sse_dist.h:81: warning: dereferencing pointer ‘s’ does break strict-aliasing rules run/../search/../search/sse_dist.h:78: note: initialized from here run/../search/../search/sse_dist.h:81: note: initialized from here run/../search/../search/sse_dist.h:81: warning: dereferencing pointer ‘s’ does break strict-aliasing rules run/../search/../search/sse_dist.h:78: note: initialized from here run/../search/../search/sse_dist.h:81: note: initialized from here g++ -O3 -DNDEBUG -Iboost/include -Wall -Wno-uninitialized -march=native -c -o basic/options.o basic/options.cpp g++ -O3 -DNDEBUG -Iboost/include -Wall -Wno-uninitialized -march=native -c -o util/tinythread.o util/tinythread.cpp g++ -o ../bin/diamond algo/blast/core/blast_encoding.o algo/blast/core/blast_stat.o algo/blast/core/blast_filter.o algo/blast/core/blast_util.o algo/blast/core/blast_message.o algo/blast/core/ncbi_erf.o algo/blast/core/blast_options.o algo/blast/core/ncbi_math.o algo/blast/core/blast_program.o algo/blast/core/ncbi_std.o algo/blast/core/blast_psi_priv.o algo/blast/core/raw_scoremat.o algo/blast/core/blast_query_info.o algo/blast/core/blast_seg.o main.o basic/options.o util/tinythread.o boost/lib/libboost_thread.a boost/lib/libboost_system.a boost/lib/libboost_timer.a boost/lib/libboost_chrono.a boost/lib/libboost_iostreams.a boost/lib/libboost_program_options.a -lpthread -lz -lrt g++: boost/lib/libboost_iostreams.a: No such file or directory make: *** [diamond] Error 1
(plantiSMASH_py27) [amissino@genossh:plantiSMASH] $ more slurm-1399414.out ERROR: Failed to locate file: 'diamond' ERROR: Failed to locate file: 'diamond' ERROR: Not all prerequisites met
Thank your help
It seems like Boost is not installed correctly on your system. Try to install it through the package manager and leave out the ./install-boost. There should also be a compiled binary of that Diamond version available for download that is attached to the release.
