Open dariober opened 2 years ago
Thank you! This worked for me and saved me hours of pain. If our paths ever cross, I owe you a beer.
Hi, thanks for this, super useful! :)
I followed all your instructions but I got an error on: $ augustus --version augustus: error while loading shared libraries: libboost_iostreams.so.1.71.0: cannot open shared object file: No such file or directory
I do not have libboost_iostreams.so.1.71.0, I have these instead: $ ls libboost_iostreams.* libboost_iostreams.a libboost_iostreams.so.1.73 libboost_iostreams.so libboost_iostreams.so.1.73.0 libboost_iostreams.so.1
any advice on how to fix this?
You could try a softlink with the required file name. However, it might produce a segmentation fault. But it’s worth a try.
AnneJRomero @.***> schrieb am Do. 8. Sept. 2022 um 10:48:
Hi, thanks for this, super useful! :)
I followed all your instructions but I got an error on: $ augustus --version augustus: error while loading shared libraries: libboost_iostreams.so.1.71.0: cannot open shared object file: No such file or directory
I do not have libboost_iostreams.so.1.71.0, I have these instead: $ ls libboost_iostreams.* libboost_iostreams.a libboost_iostreams.so.1.73 libboost_iostreams.so libboost_iostreams.so.1.73.0 libboost_iostreams.so.1
any advice on how to fix this?
— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/Augustus/issues/358#issuecomment-1240418418, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JG4NDSH4YJC3VAP4NTV5GR47ANCNFSM57DTKYAA . You are receiving this because you are subscribed to this thread.Message ID: @.***>
You could try a softlink with the required file name. However, it might produce a segmentation fault. But it’s worth a try. AnneJRomero @.> schrieb am Do. 8. Sept. 2022 um 10:48: … Hi, thanks for this, super useful! :) I followed all your instructions but I got an error on: $ augustus --version augustus: error while loading shared libraries: libboost_iostreams.so.1.71.0: cannot open shared object file: No such file or directory I do not have libboost_iostreams.so.1.71.0, I have these instead: $ ls libboost_iostreams. libboost_iostreams.a libboost_iostreams.so.1.73 libboost_iostreams.so libboost_iostreams.so.1.73.0 libboost_iostreams.so.1 any advice on how to fix this? — Reply to this email directly, view it on GitHub <#358 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JG4NDSH4YJC3VAP4NTV5GR47ANCNFSM57DTKYAA . You are receiving this because you are subscribed to this thread.Message ID: **@.***>
Hi, I tried that and I'm still getting the same error message.
That’s weird. If the links are in the correct place, C++ programs usually try to use the files.
AnneJRomero @.***> schrieb am Do. 8. Sept. 2022 um 11:13:
You could try a softlink with the required file name. However, it might produce a segmentation fault. But it’s worth a try. AnneJRomero @.
*> schrieb am Do. 8. Sept. 2022 um 10:48: … <#m-7890995221488165899> Hi, thanks for this, super useful! :) I followed all your instructions but I got an error on: $ augustus --version augustus: error while loading shared libraries: libboost_iostreams.so.1.71.0: cannot open shared object file: No such file or directory I do not have libboost_iostreams.so.1.71.0, I have these instead: $ ls libboost_iostreams. libboost_iostreams.a libboost_iostreams.so.1.73 libboost_iostreams.so libboost_iostreams.so.1.73.0 libboost_iostreams.so.1 any advice on how to fix this? — Reply to this email directly, view it on GitHub <#358 (comment) https://github.com/Gaius-Augustus/Augustus/issues/358#issuecomment-1240418418>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JG4NDSH4YJC3VAP4NTV5GR47ANCNFSM57DTKYAA https://github.com/notifications/unsubscribe-auth/AJMC6JG4NDSH4YJC3VAP4NTV5GR47ANCNFSM57DTKYAA . You are receiving this because you are subscribed to this thread.Message ID: @.**>
Hi, I tried that and I'm still getting the same error message.
— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/Augustus/issues/358#issuecomment-1240446697, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JCYWRMEZAGBULWGYGTV5GU3TANCNFSM57DTKYAA . You are receiving this because you commented.Message ID: @.***>
Hi, I'm retrying again.
For the step, 'Compile augustus and the auxiliary programs':
make MYSQL=false augustus auxprogs echo $? # Check 0 exit code
I get the error:
mkdir -p bin
cd src && make
make[1]: Entering directory /mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/src' echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_SQLITE" > cxxflags make[1]: Leaving directory
/mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/src'
mkdir -p bin
cd auxprogs && make
make[1]: Entering directory /mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs' cd aln2wig; make; make[2]: Entering directory
/mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs/aln2wig'
make[2]: aln2wig' is up to date. make[2]: Leaving directory
/mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs/aln2wig'
cd bam2hints; make;
make[2]: Entering directory /mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs/bam2hints' g++ -Wall -O3 -L/scratch/ar14g12/.conda/envs/augustus/lib -Wl,-rpath,/scratch/ar14g12/.conda/envs/augustus/lib -L/scratch/ar14g12/.conda/envs/augustus/lib -Wl,-rpath,/scratch/ar14g12/.conda/envs/augustus/lib -I/scratch/ar14g12/.conda/envs/augustus/include/bamtools -I/scratch/ar14g12/.conda/envs/augustus/include -o bam2hints bam2hints.o -lbamtools -lz bam2hints.o: In function
main':
bam2hints.cc:(.text.startup+0x73e): undefined reference to BamTools::BamReader::Open(std::string const&)' collect2: error: ld returned 1 exit status make[2]: *** [bam2hints] Error 1 make[2]: Leaving directory
/mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs/bam2hints'
make[1]: [all] Error 2
make[1]: Leaving directory `/mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs'
make: [auxprogs] Error 2
2
What am I doing wrong?
@AnneJRomero Can you start from a fresh conda environment, show the commands you execute with their output?
If it helps, on my setup libboost_iostreams.so
is a symlink to libboost_iostreams.so.1.80.0
:
conda activate augustus
ls -l ${CONDA_PREFIX}/lib/libboost_iostreams.so
lrwxrwxrwx 1 db291g db291g 28 Aug 20 18:42 /export/projects/III-data/wcmp_bioinformatics/db291g/miniconda3/envs/augustus/lib/libboost_iostreams.so -> libboost_iostreams.so.1.80.0
and this is my conda environment:
conda list
# packages in environment at /export/projects/III-data/wcmp_bioinformatics/db291g/miniconda3/envs/augustus:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bamtools 2.5.2 hd03093a_0 bioconda
biopython 1.79 py310h5764c6d_2 conda-forge
boost-cpp 1.80.0 h75c5d50_0 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.6.15 ha878542_0 conda-forge
cdbtools 0.99 hd03093a_7 bioconda
diamond 0.9.19 h2e03b76_5 bioconda
gmp 6.2.1 h58526e2_0 conda-forge
gsl 2.7 he838d99_0 conda-forge
htslib 1.15.1 h9753748_0 bioconda
icu 70.1 h27087fc_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
libblas 3.9.0 16_linux64_openblas conda-forge
libcblas 3.9.0 16_linux64_openblas conda-forge
libcurl 7.83.1 h7bff187_0 conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgfortran-ng 12.1.0 h69a702a_16 conda-forge
libgfortran5 12.1.0 hdcd56e2_16 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 16_linux64_openblas conda-forge
libnghttp2 1.47.0 hdcd2b5c_1 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.21 pthreads_h78a6416_1 conda-forge
libpng 1.6.37 h753d276_4 conda-forge
libsqlite 3.39.2 h753d276_1 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libzlib 1.2.12 h166bdaf_2 conda-forge
lp_solve 5.5.2.5 h14c3975_1001 conda-forge
metis 5.1.0 h58526e2_1006 conda-forge
mpfr 4.1.0 h9202a9a_1 conda-forge
mysql-connector-c 6.1.11 h6eb9d5d_1007 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
numpy 1.23.2 py310h53a5b5f_0 conda-forge
openssl 1.1.1q h166bdaf_0 conda-forge
perl 5.32.1 2_h7f98852_perl5 conda-forge
perl-apache-test 1.43 pl5321hd8ed1ab_0 conda-forge
perl-app-cpanminus 1.7046 pl5321hd8ed1ab_0 conda-forge
perl-base 2.23 pl5321hdfd78af_2 bioconda
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-class-load 0.25 pl5321hdfd78af_1 bioconda
perl-class-load-xs 0.10 pl5321h9f5acd7_6 bioconda
perl-class-method-modifiers 2.13 pl5321hdfd78af_0 bioconda
perl-constant 1.33 pl5321hd8ed1ab_0 conda-forge
perl-cpan-meta 2.150010 pl5321hdfd78af_1 bioconda
perl-cpan-meta-requirements 2.140 pl5321hdfd78af_1 bioconda
perl-cpan-meta-yaml 0.018 pl5321hdfd78af_1 bioconda
perl-data-dumper 2.183 pl5321h166bdaf_0 conda-forge
perl-data-optlist 0.112 pl5321hdfd78af_0 bioconda
perl-dbi 1.643 pl5321hec16e2b_1 bioconda
perl-devel-globaldestruction 0.14 pl5321hdfd78af_1 bioconda
perl-devel-overloadinfo 0.007 pl5321hdfd78af_0 bioconda
perl-devel-stacktrace 2.04 pl5321hdfd78af_1 bioconda
perl-dist-checkconflicts 0.11 pl5321hdfd78af_3 bioconda
perl-encode 3.19 pl5321hec16e2b_1 bioconda
perl-eval-closure 0.14 pl5321h9f5acd7_6 bioconda
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-extutils-cbuilder 0.280230 pl5321hdfd78af_2 bioconda
perl-extutils-makemaker 7.64 pl5321hd8ed1ab_0 conda-forge
perl-extutils-manifest 1.73 pl5321hdfd78af_0 bioconda
perl-extutils-parsexs 3.44 pl5321hdfd78af_0 bioconda
perl-file-path 2.18 pl5321hd8ed1ab_0 conda-forge
perl-file-temp 0.2304 pl5321hd8ed1ab_0 conda-forge
perl-file-which 1.24 pl5321hd8ed1ab_0 conda-forge
perl-getopt-long 2.52 pl5321hdfd78af_0 bioconda
perl-ipc-cmd 1.04 pl5321hdfd78af_0 bioconda
perl-json-pp 4.11 pl5321hd8ed1ab_0 conda-forge
perl-locale-maketext-simple 0.21 pl5321hdfd78af_3 bioconda
perl-module-build 0.4231 pl5321hdfd78af_0 bioconda
perl-module-corelist 5.20220620 pl5321hdfd78af_0 bioconda
perl-module-implementation 0.09 pl5321hdfd78af_3 bioconda
perl-module-load 0.34 pl5321hdfd78af_0 bioconda
perl-module-load-conditional 0.68 pl5321hdfd78af_3 bioconda
perl-module-metadata 1.000037 pl5321hdfd78af_0 bioconda
perl-module-runtime 0.016 pl5321hdfd78af_2 bioconda
perl-module-runtime-conflicts 0.003 pl5321hdfd78af_1 bioconda
perl-moo 2.005004 pl5321hdfd78af_0 bioconda
perl-moose 2.2201 pl5321hec16e2b_2 bioconda
perl-mro-compat 0.15 pl5321hdfd78af_0 bioconda
perl-package-deprecationmanager 0.17 pl5321hdfd78af_1 bioconda
perl-package-stash 0.40 pl5321h87f3376_1 bioconda
perl-package-stash-xs 0.29 pl5321h87f3376_1 bioconda
perl-parallel-forkmanager 2.02 pl5321hdfd78af_1 bioconda
perl-params-check 0.38 pl5321hdfd78af_2 bioconda
perl-params-util 1.102 pl5321h9f5acd7_1 bioconda
perl-parent 0.238 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321h166bdaf_0 conda-forge
perl-perl-ostype 1.010 pl5321hd8ed1ab_0 conda-forge
perl-role-tiny 2.002004 pl5321hdfd78af_0 bioconda
perl-scalar-list-utils 1.63 pl5321h166bdaf_0 conda-forge
perl-storable 3.15 pl5321h166bdaf_0 conda-forge
perl-sub-exporter 0.988 pl5321hdfd78af_0 bioconda
perl-sub-exporter-progressive 0.001013 pl5321hdfd78af_1 bioconda
perl-sub-identify 0.14 pl5321hec16e2b_2 bioconda
perl-sub-install 0.928 pl5321hdfd78af_3 bioconda
perl-sub-name 0.21 pl5321hec16e2b_3 bioconda
perl-sub-quote 2.006006 pl5321hdfd78af_0 bioconda
perl-text-abbrev 1.02 pl5321hdfd78af_1 bioconda
perl-text-parsewords 3.31 pl5321hdfd78af_0 bioconda
perl-try-tiny 0.31 pl5321ha770c72_0 conda-forge
perl-version 0.9929 pl5321h166bdaf_0 conda-forge
perl-xsloader 0.24 pl5321hd8ed1ab_0 conda-forge
perl-yaml 1.30 pl5321hdfd78af_0 bioconda
pip 22.2.2 pyhd8ed1ab_0 conda-forge
python 3.10.5 h582c2e5_0_cpython conda-forge
python_abi 3.10 2_cp310 conda-forge
readline 8.1.2 h0f457ee_0 conda-forge
setuptools 65.1.0 py310hff52083_0 conda-forge
sqlite 3.39.2 h4ff8645_1 conda-forge
suitesparse 5.10.1 h9e50725_1 conda-forge
tar 1.34 ha1f6473_0 conda-forge
tbb 2021.5.0 h924138e_1 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tzdata 2022c h191b570_0 conda-forge
ucsc-fatotwobit 377 ha8a8165_5 bioconda
ucsc-twobitinfo 377 ha8a8165_3 bioconda
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.12 h166bdaf_2 conda-forge
zstd 1.5.2 h6239696_4 conda-forge
Hi,
I copied your list of packages, installed ones that I didn't have and updated the packages that were outdated.
I'm not getting the error message anymore. : $ augustus --version AUGUSTUS (3.4.0) is a gene prediction tool. Sources and documentation at https://github.com/Gaius-Augustus/Augustus
Thank you! :)
I tried testing the installation with: $ augustus --species=human --UTR=on examples/example.fa Segmentation fault (core dumped)
Why am I getting 'Segmentation fault (core dumped)' error?
I had the same problem as AnneJRomero. For some reason I couldn't install the same package versions as listed by dario using conda. For me, the only way to make a compiled augustus and auxprogs to work was to follow the install.md instructions (install every dependencies manually and point them in common.mk). Mysql++-dev without root it seens nearly impossible to do it, so use MYSQL=false argument as pointed by Dario. It surprised me that such a popular predictor is this hard to install... I really appreciate Dario's initiative to make it easier.
We have several docker containers that have Augustus with all dependencies. For example, it's in the GALBA container (https://github.com/Gaius-Augustus/GALBA). These containers can be executed either with Docker, or Singularity (the latter for non-root scenarios).
I had the same problem as AnneJRomero. ( ´•̥̥̥ω•̥̥̥` )
g++ -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc In file included from ../include/genbank.hh:12:0, from genbank.cc:10: ../include/types.hh:16:43: fatal error: boost/archive/text_oarchive.hpp: No such file or directory
^
compilation terminated. make[1]: [genbank.o] Error 1 make[1]: Leaving directory `/home/u041175/workspace/jiakeli/rnaseq/software/new/Augustus-3.5.0/src' make: [augustus] Error 2 I need help
It exceeds my patience to compile AUGUSTUS without root permissions on our HPC. We have instructions, see https://github.com/Gaius-Augustus/Augustus/blob/master/docs/INSTALL.md , where also Troubleshooting sections are linked. I recommend running the Docker container in Singularity.
On Thu, Mar 14, 2024 at 6:04 AM jkl826 @.***> wrote:
g++ -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc In file included from ../include/genbank.hh:12:0, from genbank.cc:10: ../include/types.hh:16:43: fatal error: boost/archive/text_oarchive.hpp: No such file or directory
include <boost/archive/text_oarchive.hpp>
^ compilation terminated. make[1]: [genbank.o] Error 1 make[1]: Leaving directory `/home/u041175/workspace/jiakeli/rnaseq/software/new/Augustus-3.5.0/src' make: [augustus] Error 2 I need help
— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/Augustus/issues/358#issuecomment-1996496614, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JGLFPRSP2CW6N3QR2LYYEVWJAVCNFSM57DTKYAKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOJZGY2DSNRWGE2A . You are receiving this because you commented.Message ID: @.***>
Hi, I'm retrying again.
For the step, 'Compile augustus and the auxiliary programs':
make MYSQL=false augustus auxprogs echo $? # Check 0 exit code
I get the error:
mkdir -p bin cd src && make make[1]: Entering directory
/mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/src' echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_SQLITE" > cxxflags make[1]: Leaving directory
/mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/src' mkdir -p bin cd auxprogs && make make[1]: Entering directory/mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs' cd aln2wig; make; make[2]: Entering directory
/mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs/aln2wig' make[2]:aln2wig' is up to date. make[2]: Leaving directory
/mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs/aln2wig' cd bam2hints; make; make[2]: Entering directory/mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs/bam2hints' g++ -Wall -O3 -L/scratch/ar14g12/.conda/envs/augustus/lib -Wl,-rpath,/scratch/ar14g12/.conda/envs/augustus/lib -L/scratch/ar14g12/.conda/envs/augustus/lib -Wl,-rpath,/scratch/ar14g12/.conda/envs/augustus/lib -I/scratch/ar14g12/.conda/envs/augustus/include/bamtools -I/scratch/ar14g12/.conda/envs/augustus/include -o bam2hints bam2hints.o -lbamtools -lz bam2hints.o: In function
main': bam2hints.cc:(.text.startup+0x73e): undefined reference toBamTools::BamReader::Open(std::string const&)' collect2: error: ld returned 1 exit status make[2]: *** [bam2hints] Error 1 make[2]: Leaving directory
/mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs/bam2hints' make[1]: [all] Error 2 make[1]: Leaving directory `/mainfs/scratch/ar14g12/PIPS/annotation/genes/Augustus/auxprogs' make: [auxprogs] Error 2 2What am I doing wrong?
Maybe you have solved this problem? I met the same one.
Since installing augustus from source without root previleges wasn't easy for me, I thought posting here the commands I used for installation.
If not already done, install conda, bioconda, and, optional but recommended, mamba (these are useful anyway).
Create and activate a dedicated environment for augustus (or activate an existing one of your choice):
requirements.txt
and install them:common.mk
with the correct settings:Tested (not thoroughly) on Ubuntu 18 and CentOS 7 with augustus commit
d1fd097
. Note that augustus is also on bioconda but the version there may be outdated. Any feedback most welcome.