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calling de novo mutations in trios

well...I try to learn so much as possible the utils we have on internet for study vcf files :)

I found pretty interesting Polymutt and triodenovo programs, sadly I cant install them on my pc because core.

says something like this

Makefile:23: recipe for target 'MemoryMapArray.o' failed
make[1]: *** [MemoryMapArray.o] Error 1
make[1]: Leaving directory '/home/cri/Desktop/polymutt.0.18/core'
Makefile:9: recipe for target 'all' failed
make: *** [all] Error 2

Is another similar program I could use? Thanks!!

de novo
• 3,440 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by cristina_sabiers cristina_sabiers

what are the lines before Makefile:23: recipe for target 'MemoryMapArray.o' failed ??

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum 
MemoryMapArray.h:230:47: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the   use of an undeclared name is deprecated)

with polymutt appear that

with triodenovo this

cc1plus: all warnings being treated as errors
Makefile:23: recipe for target 'Input.o' failed
make[1]: *** [Input.o] Error 1
make[1]: Leaving directory '/home/cri/Desktop/triodenovo.0.05/core'
Makefile:8: recipe for target 'all' failed
make: *** [all] Error 2
• 1 views • link
written by cristina_sabiers cristina_sabiers

this is still not useful. Add more lineSSSS please.

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

ohhh sorry! Ok thanks! hope is ok with this now. Triodenovo

make[1]: Entering directory '/home/cri/Desktop/triodenovo.0.05/core'
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result StringArray.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result MathLu.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result Genetics.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result MathMatrix.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result Kinship.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result IntHash.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result Random.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result WindowsHelper.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result PedigreeGlobals.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result FastaLike.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result CustomSettings.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result MathSVD.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result LongLongCounter.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result Parameters.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result KinshipX.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result MathMiser.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result MathSobol.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result Matings.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result StringHash.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result MathFloatVector.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result Sort.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result PedigreePerson.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result IntegerInfo.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result PedigreeDescription.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result PedigreeAlleleFreq.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result MathCholesky.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result GeneticCode.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result Input.cpp
In file included from Input.cpp:1:0:
Input.h:7:63: error: deprecated conversion from string constant to ‘char*’ [-Werror=write-strings]
 void Input(const char * prompt, char * s, char * _default = "");
                                                               ^
cc1plus: all warnings being treated as errors
Makefile:23: recipe for target 'Input.o' failed
make[1]: *** [Input.o] Error 1
make[1]: Leaving directory '/home/cri/Desktop/triodenovo.0.05/core'
Makefile:8: recipe for target 'all' failed
make: *** [all] Error 2
• 1 views • link
updated by GenoMax GenoMax • written by cristina_sabiers cristina_sabiers

polymutt

bix  -I../third/pcre/include VCFInputFile.cpp
g++ -c -O4 -DNDEBUG -std=c++0x -D__STDC_LIMIT_MACROS -I. -I../base -I../third/tabix  -I../third/pcre/include VCFIndividual.cpp
g++ -c -O4 -DNDEBUG -std=c++0x -D__STDC_LIMIT_MACROS -I. -I../base -I../third/tabix  -I../third/pcre/include SiteSet.cpp
g++ -c -O4 -DNDEBUG -std=c++0x -D__STDC_LIMIT_MACROS -I. -I../base -I../third/tabix  -I../third/pcre/include VCFHeader.cpp
ar rcs lib-vcf.a PeopleSet.o VCFUtil.o PlinkInputFile.o PlinkOutputFile.o VCFInfo.o VCFInputFile.o VCFIndividual.o SiteSet.o VCFHeader.o
make[1]: Leaving directory '/home/cri/Desktop/polymutt.0.18/libVcf'
(cd core; make)
make[1]: Entering directory '/home/cri/Desktop/polymutt.0.18/core'
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result MathLu.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result PedigreeTwin.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result MathMatrix.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result Kinship.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result IntHash.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result Random.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result WindowsHelper.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result Hash.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result PedigreeGlobals.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result Genetics.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result FastaLike.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result CustomSettings.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result MathSVD.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result LongLongCounter.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result Parameters.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result KinshipX.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result MemoryMapArray.cpp
In file included from MemoryMapArray.cpp:19:0:
MemoryMapArray.h: In member function ‘int MemoryMapArray<elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass>::create(const char*, indexT, int)’:
MemoryMapArray.h:230:47: error: there are no arguments to ‘gethostname’ that depend on a template parameter, so a declaration of ‘gethostname’ must be available [-fpermissive]
         gethostname(hostname, sizeof(hostname));
                                               ^
MemoryMapArray.h:230:47: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
Makefile:23: recipe for target 'MemoryMapArray.o' failed
make[1]: *** [MemoryMapArray.o] Error 1
make[1]: Leaving directory '/home/cri/Desktop/polymutt.0.18/core'
Makefile:9: recipe for target 'all' failed
make: *** [all] Error 2
• 1 views • link
updated by GenoMax GenoMax • written by cristina_sabiers cristina_sabiers

Hello cristina_sabiers!

We believe that this post does not fit the main topic of this site.

Question asnwered by pierre lindenbaum

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 1 views • link
written by cristina_sabiers cristina_sabiers

That is the right way!

• 1 views • link
written by GenoMax GenoMax

1 answer

Try to find the file: core/MemoryMapArray.h

at the top of the file, add the following line:

#include <unistd.h>

and try to compile again.

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

thanks pierre,

Didnt work, but now my message is shorter. Polymutt

    make[1]: Entering directory '/home/cri/Desktop/polymutt.0.18/third'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/cri/Desktop/polymutt.0.18/third'
(cd base; make)
make[1]: Entering directory '/home/cri/Desktop/polymutt.0.18/base'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/cri/Desktop/polymutt.0.18/base'
(cd libVcf; make)
make[1]: Entering directory '/home/cri/Desktop/polymutt.0.18/libVcf'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/cri/Desktop/polymutt.0.18/libVcf'
(cd core; make)
make[1]: Entering directory '/home/cri/Desktop/polymutt.0.18/core'
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result PatternMatcher.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result PeelerNodes.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result MemoryAllocators.cpp
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result Input.cpp
In file included from Input.cpp:1:0:
Input.h:7:63: error: deprecated conversion from string constant to ‘char*’ [-Werror=write-strings]
 void Input(const char * prompt, char * s, char * _default = "");
                                                               ^
cc1plus: all warnings being treated as errors
Makefile:23: recipe for target 'Input.o' failed
make[1]: *** [Input.o] Error 1
make[1]: Leaving directory '/home/cri/Desktop/polymutt.0.18/core'
Makefile:9: recipe for target 'all' failed
make: *** [all] Error 2

triodenovo

make[1]: Entering directory '/home/cri/Desktop/triodenovo.0.05/third'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/cri/Desktop/triodenovo.0.05/third'
(cd base; make)
make[1]: Entering directory '/home/cri/Desktop/triodenovo.0.05/base'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/cri/Desktop/triodenovo.0.05/base'
(cd libVcf; make)
make[1]: Entering directory '/home/cri/Desktop/triodenovo.0.05/libVcf'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/cri/Desktop/triodenovo.0.05/libVcf'
(cd core; make)
make[1]: Entering directory '/home/cri/Desktop/triodenovo.0.05/core'
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result Input.cpp
In file included from Input.cpp:1:0:
Input.h:7:63: error: deprecated conversion from string constant to ‘char*’ [-Werror=write-strings]
 void Input(const char * prompt, char * s, char * _default = "");
                                                               ^
cc1plus: all warnings being treated as errors
Makefile:23: recipe for target 'Input.o' failed
make[1]: *** [Input.o] Error 1
make[1]: Leaving directory '/home/cri/Desktop/triodenovo.0.05/core'
Makefile:8: recipe for target 'all' failed
make: *** [all] Error 2
• 1 views • link
updated by GenoMax GenoMax • written by cristina_sabiers cristina_sabiers

your version of the C++ compiler is too old and doesn't support the default arguments.

You might try to find in the Makefile(s) the argument -Werror

`` -Werror Make all warnings into errors. ```

and remove all the occurences of -Werror

of course, the best would be to use a linux instead of this micro$oft thing.

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

@cristina is using some flavor of linux (ubuntu?) if memory serves me right.

• 1 views • link
written by GenoMax GenoMax

@cristina: Is your system patched with all latest updates?

• 1 views • link
written by GenoMax GenoMax

Sorry couldnt answer before bc my post limits in this forum...yes I use ubuntu 16, I have updated and i had installed g++5.1 but still get this error

make[1]: Entering directory '/home/cri/Desktop/polymutt.0.18/third'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/cri/Desktop/polymutt.0.18/third'
(cd base; make)
make[1]: Entering directory '/home/cri/Desktop/polymutt.0.18/base'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/cri/Desktop/polymutt.0.18/base'
(cd libVcf; make)
make[1]: Entering directory '/home/cri/Desktop/polymutt.0.18/libVcf'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/cri/Desktop/polymutt.0.18/libVcf'
(cd core; make)
make[1]: Entering directory '/home/cri/Desktop/polymutt.0.18/core'
g++ -c -O4 -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -Werror -Wno-unused-variable -Wno-unused-result Input.cpp
In file included from Input.cpp:1:0:
Input.h:7:63: error: deprecated conversion from string constant to ‘char*’ [-Werror=write-strings]
 void Input(const char * prompt, char * s, char * _default = "");
                                                               ^
cc1plus: all warnings being treated as errors
Makefile:23: recipe for target 'Input.o' failed
make[1]: *** [Input.o] Error 1
make[1]: Leaving directory '/home/cri/Desktop/polymutt.0.18/core'
Makefile:9: recipe for target 'all' failed
make: *** [all] Error 2

I deleted the -Werror on make file and the install worked!!!! I must say I really dont understand why works like that XD

thanks a lot for the help!!! :)))

• 1 views • link
updated by GenoMax GenoMax • written by cristina_sabiers cristina_sabiers

nice, close the question by flagging my answer. Thxs.

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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