30
edits
Changes
From Genome Analysis Wiki
no edit summary
[[Category:RAREMETAL]]
[[Category:RAREMETALWORKER]]
==COMPILE PROBLEMS==
===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 identifying a bug in makefile. If you still see the same error message, please try the above solutions.
===error while loading shared libraries===
make[1]: *** [samtools] Error 2
make: *** [../../libStatGen/libStatGen. a] Error 2
====SOLUTION====
If you are using version 0.4.4 and under, please go to our wiki page to download the newest version [[RAREMETAL_Documentation#Where_to_Download | '''download 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: can not find Makefile.base ===
../libStatGen/Makefiles/Makefile.tool:4: Makefile.base: No such file or directory
../libStatGen/Makefiles/Makefile.tool:23: *** first argument to `word' function must be greater than 0. Stop.
====SOLUTION====
==RUNTIME ERRORS=====error: BGZF EOF marker is missing in reffhsexome_v2xxx.vcf.gz===
Loading input files...
Loading DAT files ... done.
Loading PED files ... done.
BGZF EOF marker is missing in reffhsexome_v2xxx.vcf.gzExiting, exception thrown: FAIL_IO: Failed to open reffhsexome_v2xxx.vcf.gz
====SOLUTION====
This problem has been solved. If you are using version 0.4.5 or older, please download the newest version [[[RAREMETALWORKER]#Where_to_Download |'''download 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. ==RUNTIME ERRORS==
===recommended strategies for debugging===
