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[[Category:RAREMETAL]]
[[Category:RAREMETALWORKER]]
==COMPILE PROBLEMS==
==COMPILE PROBLEMS==
===error: zlib.h: No such file or directory===
===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):
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)
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)
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)
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.)
2) raremetal/src/Makefile, add: (I added it on the line right after USER_LIBS is defined.)
OTHER_LIBS = -lgfortran
OTHER_LIBS = -lgfortran
NOTE: this has been fixed by identifying a bug in makefile. If you still see the same error message, please try the above solutions.
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===
===error while loading shared libraries===
make[1]: *** [samtools] Error 2
make[1]: *** [samtools] Error 2
make: *** [../../libStatGen/libStatGen. a] Error 2
make: *** [../../libStatGen/libStatGen. a] Error 2
====SOLUTION====
====SOLUTION====
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.
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 ===
===error: BGZF EOF marker is missing in reffhsexome_v2.vcf.gz===
../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====
This is most likely that you are having an older version of Make. To compile, you have to use Make version 3.80 and older. To get updated version of make, please go to [http://ftp.gnu.org/gnu/make '''make download'''].
==RUNTIME ERRORS==
===error: BGZF EOF marker is missing in xxx.vcf.gz===
Loading input files...
Loading input files...
Loading DAT files ... done.
Loading DAT files ... done.
Loading PED files ... done.
Loading PED files ... done.
BGZF EOF marker is missing in reffhsexome_v2.vcf.gz
BGZF EOF marker is missing in xxx.vcf.gz
Exiting, exception thrown: FAIL_IO: Failed to open reffhsexome_v2.vcf.gz
Exiting, exception thrown: FAIL_IO: Failed to open xxx.vcf.gz
====SOLUTION====
====SOLUTION====
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.
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.
===recommended strategies for debugging===
===recommended strategies for debugging===
==GENERAL QUESTIONS==
==GENERAL QUESTIONS==
===What is RAREMETALWORKER? How is it related to RAREMETAL?===
A: [[Rare-Metal-Worker|'''RAREMETALWORKER''']] is the program that generates summary statistics for individual studies to share. It generates both single variant association results and covariance matrices of score statistics together with QC statistics. It enables analysis of familial data, population data, unrelated individuals and samples with cryptic relatedness and population stratification. [[RareMETAL|'''RAREMETAL''']] takes the summary statistics generated by RAREMETALWORKER to perform both single variant and gene-level association analysis.
A: [[Rare-Metal-Worker|'''rareMetalWorker''']] is the program that generates summary statistics for individual studies to share. It generates both single variant association results and covariance matrices of score statistics together with QC statistics. It enables analysis of familial data, population data, unrelated individuals and samples with cryptic relatedness and population stratification. [[RareMETAL|'''rareMETAL''']] takes the summary statistics generated by raerMetalWorker to perform both single variant and gene-level association analysis.
