Bonjour,
La dernière version de l'outil Agat (0.9.2) que je viens d'installer via Institut Français de Bioinformatique · GitLab retourne l'erreur ci-dessous, alors que la même commande fonctionne en chargeant le module en version 0.8.1. Probablement une histoire de version de Perl. Je ne sais pas comment résoudre cela.
[lgueguen@clust-slurm-client ~]$ agat_sq_add_attributes_from_tsv.pl --help
Can't locate Sort/Naturally.pm in @INC (you may need to install the Sort::Naturally module) (@INC contains: /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/5.32/site_perl /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/site_perl /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/5.32/vendor_perl /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/vendor_perl /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/5.32/core_perl /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/core_perl .) at /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/site_perl/AGAT/OmniscientI.pm line 12.
BEGIN failed--compilation aborted at /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/site_perl/AGAT/OmniscientI.pm line 12.
Compilation failed in require at /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/site_perl/AGAT/Omniscient.pm line 9.
BEGIN failed--compilation aborted at /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/site_perl/AGAT/Omniscient.pm line 9.
Compilation failed in require at /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/agat_sq_add_attributes_from_tsv.pl line 12.
BEGIN failed--compilation aborted at /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/agat_sq_add_attributes_from_tsv.pl line 12.
Le module en question est pourtant bien présent dans l'env conda :
[lgueguen@clust-slurm-client ~]$ conda list -n agat-0.9.2
# packages in environment at /shared/ifbstor1/software/miniconda/envs/agat-0.9.2:
#
# Name Version Build Channel
[...]
perl-sort-naturally 1.03 0 bioconda
[...]
J'ajoute ici les infos de Perl obtenues avec la version 0.9.2 :
[lgueguen@clust-slurm-client ~]$ module list
Currently Loaded Modulefiles:
1) agat/0.9.2
[lgueguen@clust-slurm-client ~]$ perl -V
Summary of my perl5 (revision 5 version 32 subversion 1) configuration:
Platform:
osname=linux
osvers=5.11.0-1028-azure
archname=x86_64-linux-thread-multi
uname='linux 92653537ccf0 5.11.0-1028-azure #31~20.04.2-ubuntu smp tue jan 18 08:46:15 utc 2022 x86_64 x86_64 x86_64 gnulinux '
config_args='-de -Dprefix=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2 -Dvendorprefix=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2 -Dscriptdir=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin -Dsitescript=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin -Dvendorscript=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin -Duserelocatableinc -Duseshrplib -Dinc_version_list=none -Dprivlib=.../../lib/perl5/core_perl -Dsitelib=.../../lib/perl5/site_perl -Dvendorlib=.../../lib/perl5/vendor_perl -Darchlib=.../../lib/perl5/5.32/core_perl -Dsitearch=.../../lib/perl5/5.32/site_perl -Dvendorarch=.../../lib/perl5/5.32/vendor_perl -Dinstallusrbinperl=n -Dusethreads -Dcccdlflags=-fPIC -Dldflags=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib -Wl,-rpath-link,/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib -L/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib -Ddefault_inc_excludes_dot=n -Dccflags=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/perl_1645063083032/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2=/usr/local/src/conda-prefix -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -Dcc=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/..//bin/x86_64-conda-linux-gnu-gcc -Dar=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/..//bin/x86_64-conda-linux-gnu-ar -Dlddlflags=-shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib -Wl,-rpath-link,/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib -L/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib -Dsysroot=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/..//x86_64-conda-linux-gnu/sysroot -Dmyhostname=conda -Dmydomain=.conda -Dperladmin=conda -Dcf_by=conda -Dcf_email=conda -Dsysman=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/man/man1 -Dman1dir=.../../man/man1 -Dman3dir=.../../man/man3'
hint=recommended
useposix=true
d_sigaction=define
useithreads=define
usemultiplicity=define
use64bitint=define
use64bitall=define
uselongdouble=undef
usemymalloc=n
default_inc_excludes_dot=undef
bincompat5005=undef
Compiler:
cc='/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/..//bin/x86_64-conda-linux-gnu-gcc'
ccflags ='-D_REENTRANT -D_GNU_SOURCE -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/perl_1645063083032/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2=/usr/local/src/conda-prefix -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'
optimize='-O2'
cppflags='--sysroot=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/..//x86_64-conda-linux-gnu/sysroot -D_REENTRANT -D_GNU_SOURCE -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/perl_1645063083032/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2=/usr/local/src/conda-prefix -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2'
ccversion=''
gccversion='9.4.0'
gccosandvers=''
intsize=4
longsize=8
ptrsize=8
doublesize=8
byteorder=12345678
doublekind=3
d_longlong=define
longlongsize=8
d_longdbl=define
longdblsize=16
longdblkind=3
ivtype='long'
ivsize=8
nvtype='double'
nvsize=8
Off_t='off_t'
lseeksize=8
alignbytes=8
prototype=define
Linker and Libraries:
ld='/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/..//bin/x86_64-conda-linux-gnu-gcc'
ldflags ='-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib -Wl,-rpath-link,/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib -L/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib -fstack-protector-strong'
libpth=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/..//bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/include-fixed /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/..//x86_64-conda-linux-gnu/sysroot/usr/lib /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/..//x86_64-conda-linux-gnu/sysroot/lib /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/..//x86_64-conda-linux-gnu/sysroot/lib64 /shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/..//x86_64-conda-linux-gnu/sysroot/usr/lib64
libs=-lpthread -ldl -lm -lcrypt -lutil -lc
perllibs=-lpthread -ldl -lm -lcrypt -lutil -lc
libc=
so=so
useshrplib=true
libperl=libperl.so
gnulibc_version='2.17'
Dynamic Linking:
dlsrc=dl_dlopen.xs
dlext=so
d_dlsymun=undef
ccdlflags='-Wl,-E -Wl,-rpath,/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/../lib/perl5/5.32/core_perl/CORE'
cccdlflags='-fPIC --sysroot=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/..//x86_64-conda-linux-gnu/sysroot'
lddlflags='-shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib -Wl,-rpath-link,/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib -L/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib --sysroot=/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/bin/..//x86_64-conda-linux-gnu/sysroot -fstack-protector-strong'
Characteristics of this binary (from libperl):
Compile-time options:
HAS_TIMES
MULTIPLICITY
PERLIO_LAYERS
PERL_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT
PERL_MALLOC_WRAP
PERL_OP_PARENT
PERL_PRESERVE_IVUV
USE_64_BIT_ALL
USE_64_BIT_INT
USE_ITHREADS
USE_LARGE_FILES
USE_LOCALE
USE_LOCALE_COLLATE
USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC
USE_LOCALE_TIME
USE_PERLIO
USE_PERL_ATOF
USE_REENTRANT_API
USE_THREAD_SAFE_LOCALE
Built under linux
Compiled at Feb 17 2022 02:01:35
@INC:
/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/5.32/site_perl
/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/site_perl
/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/5.32/vendor_perl
/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/vendor_perl
/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/5.32/core_perl
/shared/ifbstor1/software/miniconda/envs/agat-0.9.2/lib/perl5/core_perl
.
et celles obtenues avec la version qui fonctionne 0.8.1 :
[lgueguen@clust-slurm-client ~]$ module purge
[lgueguen@clust-slurm-client ~]$ module load agat/0.8.1
[lgueguen@clust-slurm-client ~]$ perl -V
Summary of my perl5 (revision 5 version 26 subversion 2) configuration:
Platform:
osname=linux
osvers=4.15.0-1098-azure
archname=x86_64-linux-thread-multi
uname='linux 2f4e83381d95 4.15.0-1098-azure #109~16.04.1-ubuntu smp wed sep 30 18:53:14 utc 2020 x86_64 x86_64 x86_64 gnulinux '
config_args='-de -Dprefix=/shared/ifbstor1/software/miniconda/envs/agat-0.8.1 -Dusethreads -Duserelocatableinc -Dcccdlflags=-fPIC -Dldflags=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib -Wl,-rpath-link,/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib -L/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib -Ddefault_inc_excludes_dot=n -Dcc=/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/bin/..//bin/x86_64-conda-linux-gnu-gcc -Dar=/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/bin/..//bin/x86_64-conda-linux-gnu-ar -Dlddlflags=-shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib -Wl,-rpath-link,/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib -L/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib -Dsysroot=/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/bin/..//x86_64-conda-linux-gnu/sysroot'
hint=recommended
useposix=true
d_sigaction=define
useithreads=define
usemultiplicity=define
use64bitint=define
use64bitall=define
uselongdouble=undef
usemymalloc=n
default_inc_excludes_dot=undef
bincompat5005=undef
Compiler:
cc='/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/bin/..//bin/x86_64-conda-linux-gnu-gcc'
ccflags ='-D_REENTRANT -D_GNU_SOURCE --sysroot=/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/bin/..//x86_64-conda-linux-gnu/sysroot -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2'
optimize='-O2'
cppflags='--sysroot=/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/bin/..//x86_64-conda-linux-gnu/sysroot -D_REENTRANT -D_GNU_SOURCE --sysroot=/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/bin/..//x86_64-conda-linux-gnu/sysroot -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong'
ccversion=''
gccversion='7.5.0'
gccosandvers=''
intsize=4
longsize=8
ptrsize=8
doublesize=8
byteorder=12345678
doublekind=3
d_longlong=define
longlongsize=8
d_longdbl=define
longdblsize=16
longdblkind=3
ivtype='long'
ivsize=8
nvtype='double'
nvsize=8
Off_t='off_t'
lseeksize=8
alignbytes=8
prototype=define
Linker and Libraries:
ld='/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/bin/..//bin/x86_64-conda-linux-gnu-gcc'
ldflags ='-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib -Wl,-rpath-link,/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib -L/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib -fstack-protector-strong'
libpth=/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/bin/..//bin/../lib/gcc/x86_64-conda-linux-gnu/7.5.0/include-fixed /shared/ifbstor1/software/miniconda/envs/agat-0.8.1/bin/..//x86_64-conda-linux-gnu/sysroot/usr/lib /shared/ifbstor1/software/miniconda/envs/agat-0.8.1/bin/..//x86_64-conda-linux-gnu/sysroot/lib /shared/ifbstor1/software/miniconda/envs/agat-0.8.1/bin/..//x86_64-conda-linux-gnu/sysroot/lib64 /shared/ifbstor1/software/miniconda/envs/agat-0.8.1/bin/..//x86_64-conda-linux-gnu/sysroot/usr/lib64
libs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
libc=
so=so
useshrplib=false
libperl=libperl.a
gnulibc_version='2.12'
Dynamic Linking:
dlsrc=dl_dlopen.xs
dlext=so
d_dlsymun=undef
ccdlflags='-Wl,-E'
cccdlflags='-fPIC --sysroot=/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/bin/..//x86_64-conda-linux-gnu/sysroot'
lddlflags='-shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib -Wl,-rpath-link,/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib -L/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib --sysroot /shared/ifbstor1/software/miniconda/envs/agat-0.8.1/bin/..//x86_64-conda-linux-gnu/sysroot -fstack-protector-strong'
Characteristics of this binary (from libperl):
Compile-time options:
HAS_TIMES
MULTIPLICITY
PERLIO_LAYERS
PERL_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT
PERL_MALLOC_WRAP
PERL_OP_PARENT
PERL_PRESERVE_IVUV
USE_64_BIT_ALL
USE_64_BIT_INT
USE_ITHREADS
USE_LARGE_FILES
USE_LOCALE
USE_LOCALE_COLLATE
USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC
USE_LOCALE_TIME
USE_PERLIO
USE_PERL_ATOF
USE_REENTRANT_API
Built under linux
Compiled at Oct 28 2020 22:51:00
@INC:
/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib/site_perl/5.26.2/x86_64-linux-thread-multi
/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib/site_perl/5.26.2
/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib/5.26.2/x86_64-linux-thread-multi
/shared/ifbstor1/software/miniconda/envs/agat-0.8.1/lib/5.26.2
.