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RAREMETAL FAQ

617 bytes added, 11:46, 20 March 2018
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[[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====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 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===
==GENERAL QUESTIONS==
 '''Q: ===What is rareMetalWorkerRAREMETALWORKER? How is it related to rareMetalRAREMETAL?'''===
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.
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