g++: error: htslib/libhts.a: No such file or directory

[tseemann]

gcc-5 -g -Wall -O2 -I.  -c -o bgzip.o bgzip.c
gcc-5 -g -Wall -O2 -I.  -c -o htsfile.o htsfile.c
gcc-5 -g -Wall -O2 -I.  -c -o tabix.o tabix.c
gcc-5 -g -Wall -O2 -I.  -c -o hts.o hts.c
ar -csru libbwa.a utils.o bwt.o bntseq.o QSufSort.o bwt_gen.o bwtindex.o
ar: `u' modifier ignored since `D' is the default (see `U')

gcc-5 -g -Wall -O3 main.o -o bwt_index -L. -lbwa -lm -lz
make[1]: Leaving directory '/home/linuxbrew/git/MapCaller/BWT_Index'
g++ -D NDEBUG -O3 -m64 main.o GetData.o VariantCalling.o ReadMapping.o AlignmentRescue.o ReadAlign
ment.o AlignmentProfile.o SamReport.o tools.o bwt_index.o bwt_search.o nw_alignment.o KmerAnalysis.o -o MapCaller -lz -lm -lpthread -lstdc++ htslib/libhts.a -lbz2 -llzma
g++: error: htslib/libhts.a: No such file or directory
make[1]: *** [makefile:16: main] Error 1
make[1]: Leaving directory '/home/linuxbrew/git/MapCaller/src'
make: *** [makefile:9: main] Error 2
make: *** Waiting for unfinished jobs....

Because of this error, I think it is linking against my htslib I have installed?

[tseemann]

This also explains why I have to run make twice (2 times) to get the binaries created.

[hsinnan75]

I don't understand why you have to run make twice. If you run "make" under the MapCaller folder, it will build all the binaries at the same time. Could you please show me how to fix the problem?

[tseemann]

I SOLVED THE PROBLEM.

Your makefile does not work with make -j 2 because the dependencies are not correct.

main depends on htslib so they should not be built in parallel.

[hsinnan75]

Do you have any suggestions how I should modify the makefile to prevent from parallel compiling?

[tseemann]

This will allow all the cpus to be used to build MapCaller but ensure that HTSLIB is built before MapCaller tries to use it:

.PHONY: htslib

all:            bwt_index MapCaller

MapCaller: htslib
                make -C src
                mv src/$@ .

bwt_index:
                make -C BWT_Index
                mv BWT_Index/$@ .

htslib:
                make -C src/htslib

[hsinnan75]

Thank you very much! I've updated the makefile.

[tseemann]

https://github.com/hsinnan75/MapCaller/commit/b9fdf32f463c54ca1bf5b719897689f95bb45be9