no edit summary
===error: zlib.h: No such file or directory===
1) libStatGen/Makefiles/Makefile.src, edit the settings for OPT_BUILD, DEBUG_BUILD, and PROFILE_BUILD to be (the new part is in bold):
OPT_BUILD = $(CXX) $(COMPFLAGS) $(USER_LINK_OPTIONS) -o $(PROG_OPT) $(OBJECTS_OPT) $(USER_LIBS) $(REQ_LIBS_OPT) -lm $(ZLIB_LIB) $(OTHER_LIBS)DEBUG_BUILD = $(CXX) $(COMPFLAGS) $(USER_LINK_OPTIONS) -o $(PROG_DEBUG) $(OBJECTS_DEBUG) $(USER_LIBS) $(REQ_LIBS_DEBUG) -lm $(ZLIB_LIB) $(OTHER_LIBS)PROFILE_BUILD = $(CXX) $(COMPFLAGS) $(USER_LINK_OPTIONS) -o $(PROG_PROFILE) $(OBJECTS_PROFILE) $(USER_LIBS) $(REQ_LIBS_PROFILE) -lm $(ZLIB_LIB) $(OTHER_LIBS)
2) raremetal/src/Makefile, add: (I added it on the line right after USER_LIBS is defined.)
OTHER_LIBS = -lgfortran NOTE: this has been fixed by
idenifying a bug in makefile. If you still see the same error message, please try the above solutions.
===error while loading shared libraries===
make: *** [samtools] Error 2
make: *** [../../libStatGen/libStatGen. a] Error 2
If you are using version 0.4.4 and under, please go to our wiki page to download the newest version [[
[RAREMETAL ]]]. There was a bug in makefile in older versions of RAREMETAL that could cause this error and it has been fixed. For a quick fix, please go to /raremetal/src and open "Makefile". Then comment out the lines at the bottom of raremetal/src/Makefile that set LD_LIBRARY_PATH. Try compiling and see if it works.
===error: BGZF EOF marker is missing in
Loading input files...
Loading DAT files ... done.
Loading PED files ... done.
BGZF EOF marker is missing in
reffhsexome_v2.vcf.gzExiting, exception thrown: FAIL_IO: Failed to open reffhsexome_v2.vcf.gz
This problem has been solved. If you are using version 0.4.5 or older, please download the newest version
[[[RAREMETALWORKER ]]], and then in your command line, add --noeof. If you still see the error message, then you need to check if your bgzip has been updated to current version.
The ideal would be to send us your data so that we can debug. But if data sharing is not an option, you can use the following strategy to generate a backtrace and send it to us, without sharing the raw data.