augustus PPX error (Mac Homebrew install)

Discussions about compiler errors and installation problems

Moderator: bioinf

jonpalmer
Posts: 3
Joined: Mon Apr 25, 2016 4:20 pm

augustus PPX error (Mac Homebrew install)

Postby jonpalmer » Mon Apr 25, 2016 4:25 pm

I'm getting an error when trying to use a protein profile in Augustus. I've tried several different versions, Augustus 3.2.1, 3.2.2 and get the same error in all of the distributions. The error does not exist when I run on Linux, so seems like it must be some sort of compilation error. I've installed Augustus using HomeBrew - which works well for everything else, i.e. 95% of the program seems to run correctly. Here's the error I'm seeing when I try to pass in a --proteinprofile= option to augustus.

Code: Select all

jon@Jons-MacBook-Pro:/usr/local/opt/augustus/libexec/examples$ augustus --proteinprofile=profile/PF00995.16.prfl --species=generic example.fa
# This output was generated with AUGUSTUS (version 3.2.1).
# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
# O. Keller, S. König, L. Gerischer and L. Romoth.
# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters using config directory /usr/local/opt/augustus/libexec/config/ ...

augustus: ERROR
   PP::Profile: Error parsing pattern file"profile/PF00995.16.prfl", line 9.


Here's I'm using a profile shipped with Augustus, so it seems like the part of the code that parses the prfl file is not running correctly. Any ideas on why this is happening or how to fix?

jonpalmer
Posts: 3
Joined: Mon Apr 25, 2016 4:20 pm

Re: augustus PPX error (Mac Homebrew install)

Postby jonpalmer » Tue May 03, 2016 3:24 pm

I have also tried to compile on CentOS 7 the newest version of Augustus 3.2.2. However, now I'm getting a segmentation fault when trying to run PPX. Please help. Here is what I did for compilation.

Code: Select all

#compile filterBam, adding BAMTOOLS variable with path to bamtools
[augustus-3.2.2]$ make -C auxprogs/filterBam/src/ BAMTOOLS=/home/ngs/.linuxbrew/opt/bamtools/include/bamtools LIBZIP=true
make: Entering directory `/home/ngs/augustus-3.2.2/auxprogs/filterBam/src'
g++     -std=c++0x  -c filterBam.cc -o filterBam.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++     -std=c++0x  -c functions/MatePairs.cc -o MatePairs.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++     -std=c++0x  -c functions/getReferenceName.cc -o getReferenceName.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++     -std=c++0x  -c functions/initOptions.cc -o initOptions.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++     -std=c++0x  -c functions/SingleAlignment.cc -o SingleAlignment.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++     -std=c++0x  -c functions/printElapsedTime.cc -o printElapsedTime.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++     -std=c++0x  -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++     -std=c++0x  -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++     -std=c++0x  -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools -Iheaders -I./bamtools
g++     -std=c++0x  filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz
filterBam compiled with BAMTOOLS=/home/ngs/.linuxbrew/opt/bamtools/include/bamtools
cp filterBam ../../../bin/filterBam
make: Leaving directory `/home/ngs/augustus-3.2.2/auxprogs/filterBam/src'

#compile rest of augustus with include path to bamtools
[augustus-3.2.2]$ make INCLUDES=/home/ngs/.linuxbrew/opt/bamtools/include/bamtools LIBZIP=true
mkdir -p bin
cd src && make
make[1]: Entering directory `/home/ngs/augustus-3.2.2/src'
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o genbank.o genbank.cc -I../include
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
                 from ../include/genbank.hh:26,
                 from genbank.cc:15:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
 # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
                                                                               ^
In file included from /home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
                 from ../include/genbank.hh:26,
                 from genbank.cc:15:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
 # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
                                                                                    ^
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
                 from ../include/genbank.hh:26,
                 from genbank.cc:15:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
 # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
                                                                                    ^
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o properties.o properties.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o pp_profile.o pp_profile.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o pp_hitseq.o pp_hitseq.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o pp_scoring.o pp_scoring.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o statemodel.o statemodel.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o namgene.o namgene.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o types.o types.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o gene.o gene.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o evaluation.o evaluation.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o motif.o motif.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o geneticcode.o geneticcode.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o hints.o hints.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o extrinsicinfo.o extrinsicinfo.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o projectio.o projectio.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o intronmodel.o intronmodel.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o exonmodel.o exonmodel.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o igenicmodel.o igenicmodel.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o utrmodel.o utrmodel.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o merkmal.o merkmal.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o vitmatrix.o vitmatrix.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o lldouble.o lldouble.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o mea.o mea.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o graph.o graph.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o meaPath.o meaPath.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o exoncand.o exoncand.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o randseqaccess.o randseqaccess.cc -I../include
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
                 from ../include/genbank.hh:26,
                 from randseqaccess.cc:16:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
 # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
                                                                               ^
In file included from /home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
                 from ../include/genbank.hh:26,
                 from randseqaccess.cc:16:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
 # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
                                                                                    ^
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
                 from ../include/genbank.hh:26,
                 from randseqaccess.cc:16:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
 # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
                                                                                    ^
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o fasta.o fasta.cc -I../include
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
                 from ../include/fasta.hh:18,
                 from fasta.cc:14:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
 # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
                                                                               ^
In file included from /home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
                 from ../include/fasta.hh:18,
                 from fasta.cc:14:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
 # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
                                                                                    ^
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
                 from ../include/fasta.hh:18,
                 from fasta.cc:14:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
 # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
                                                                                    ^
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o ncmodel.o ncmodel.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o commontrain.o commontrain.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o igenictrain.o igenictrain.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o introntrain.o introntrain.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o exontrain.o exontrain.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o utrtrain.o utrtrain.cc -I../include
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o dummy.o dummy.cc -I../include
g++  -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT  -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o dummy.o -I../include -lboost_iostreams
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
                 from ../include/genbank.hh:26,
                 from augustus.cc:16:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
 # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
                                                                               ^
In file included from /home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
                 from ../include/genbank.hh:26,
                 from augustus.cc:16:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
 # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
                                                                                    ^
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
                 from ../include/genbank.hh:26,
                 from augustus.cc:16:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
 # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
                                                                                    ^
cp augustus ../bin/
g++  -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT  -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o -I../include -lboost_iostreams
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
                 from ../include/genbank.hh:26,
                 from etraining.cc:15:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
 # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
                                                                               ^
In file included from /home/ngs/.linuxbrew/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
                 from ../include/genbank.hh:26,
                 from etraining.cc:15:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
 # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
                                                                                    ^
In file included from /home/ngs/.linuxbrew/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/detail/push.hpp:24,
                 from /home/ngs/.linuxbrew/include/boost/iostreams/filtering_stream.hpp:19,
                 from ../include/genbank.hh:26,
                 from etraining.cc:15:
/home/ngs/.linuxbrew/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
 # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
                                                                                    ^
cp etraining ../bin/
g++  -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT  -o prepareAlign pp_prepare_align.cc
cp prepareAlign ../bin/
g++ -c -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include
g++  -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT  -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -lboost_iostreams
cp fastBlockSearch ../bin/
echo "-Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3   -DZIPINPUT" > cxxflags
make[1]: Leaving directory `/home/ngs/augustus-3.2.2/src'
cd auxprogs && make
make[1]: Entering directory `/home/ngs/augustus-3.2.2/auxprogs'
cd bam2hints; make;
make[2]: Entering directory `/home/ngs/augustus-3.2.2/auxprogs/bam2hints'
g++ -Wall -O2    -c bam2hints.cc -o bam2hints.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools
g++ -Wall -O2   -o bam2hints bam2hints.o -lbamtools -lz
cp bam2hints ../../bin
make[2]: Leaving directory `/home/ngs/augustus-3.2.2/auxprogs/bam2hints'
cd compileSpliceCands; make;
make[2]: Entering directory `/home/ngs/augustus-3.2.2/auxprogs/compileSpliceCands'
gcc -Wall -pedantic -ansi  -c compileSpliceCands.c
cc    -c -o list.o list.c
gcc  -o compileSpliceCands compileSpliceCands.o list.o;
make[2]: Leaving directory `/home/ngs/augustus-3.2.2/auxprogs/compileSpliceCands'
cd filterBam; make;
make[2]: Entering directory `/home/ngs/augustus-3.2.2/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory `/home/ngs/augustus-3.2.2/auxprogs/filterBam/src'
g++     -std=c++0x  -c filterBam.cc -o filterBam.o /home/ngs/.linuxbrew/opt/bamtools/include/bamtools
filterBam.cc:14:31: fatal error: api/BamReader.h: No such file or directory
compilation terminated.
make[3]: *** [filterBam.o] Error 1
make[3]: Leaving directory `/home/ngs/augustus-3.2.2/auxprogs/filterBam/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/ngs/augustus-3.2.2/auxprogs/filterBam'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/ngs/augustus-3.2.2/auxprogs'
make: *** [all] Error 2

#got error on bam2hints, move into folder and recompile and then it works?
[ngs@localhost augustus-3.2.2]$ cd auxprogs/bam2hints
[ngs@localhost bam2hints]$ make INCLUDES=/home/ngs/.linuxbrew/opt/bamtools/include/bamtools LIBZIP=true
make: `bam2hints' is up to date.
[ngs@localhost bam2hints]$ make clean
rm -f bam2hints.o bam2hints ../../bin/bam2hints
[ngs@localhost bam2hints]$ make INCLUDES=/home/ngs/.linuxbrew/opt/bamtools/include/bamtools LIBZIP=true
g++ -Wall -O2    -c bam2hints.cc -o bam2hints.o -I/home/ngs/.linuxbrew/opt/bamtools/include/bamtools
g++ -Wall -O2   -o bam2hints bam2hints.o -lbamtools -lz
cp bam2hints ../../bin


And then this is what I ran and I get a Segmentation Fault.

Code: Select all

#now try to use proteinprofile and I get segmentation fault
[augustus-3.2.2]$ cd examples
[examples]$ ../bin/augustus --species=generic --proteinprofile=profile/PF00012.13.prfl --AUGUSTUS_CONFIG_PATH=/home/ngs/augustus-3.2.2/config example.fa
Segmentation fault


My version of GCC:

Code: Select all

$ gcc --version
gcc (Homebrew gcc 5.3.0) 5.3.0

User avatar
katharina
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Re: augustus PPX error (Mac Homebrew install)

Postby katharina » Fri Mar 31, 2017 8:34 am

I am sorry that we currently do not have the resources to fix bugs for Mac OS :-(

We take this issue on our long list of bugs. Hopefully we will fix it one day.

I apologize for the long silence, I was on parental leave.

Best,

Katharina
Katharina


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