nuno-agostinho
commented
2 years ago Hi @dorkylever,
Have you tried to add the full BigFile.pm's lib path to PERL5LIB? Maybe one of these lines:
PERL5LIB=/root/.cpan/build/Bio-BigFile-1.07-3/lib:$PERL5LIB
PERL5LIB=/root/.cpanm/work/1649836297.7943/Bio-BigFile-1.07/lib:$PERL5LIB
PERL5LIB=/root/.cpanm/work/1649837172.8442/Bio-BigFile-1.07/lib:$PERL5LIBOtherwise, you can also try to run VEP Docker given that it has BigFile already installed.
Please update me after trying these options, thanks!
Best regards, Nuno
dorkylever
Hi Everyone,
This might not be the best place but I'm running into the following eror below when using Conservation. For full clarificaion, I'm using the Windows Ubuntu App (18.04) and EnsemblVEP was installed into /mnt/c/. I've installed BigFile using the instructions specified in the EnsemblVEP download page.
Kind Regards, Kyle
sudo /mnt/c/ensembl-vep/vep --format vcf --input_file C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf.gz --species mus_musculus --cache --dir_cache /root/.vep/ --output_file results_C57Bl6_v5.vcf --vcf --sift b --fork 64 --fasta GRCm38_68.fa --force_overwrite --cache_version 102 --assembly GRCm38 --pick --offline --compress_output bgzip --plugin Conservation WARNING: Failed to compile plugin Conservation: Can't locate Bio/DB/BigFile.pm in @INC (you may need to install the Bio::DB::BigFile module) (@INC contains: /root/.vep/Plugins /mnt/c/ensembl-vep/modules /mnt/c/ensembl-vep /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /mnt/c/ensembl-vep/Bio/EnsEMBL/IO/BigFileParser.pm line 34. BEGIN failed--compilation aborted at /mnt/c/ensembl-vep/Bio/EnsEMBL/IO/BigFileParser.pm line 34. Compilation failed in require at /usr/share/perl/5.30/parent.pm line 16. BEGIN failed--compilation aborted at /mnt/c/ensembl-vep/Bio/EnsEMBL/IO/Parser/BigWig.pm line 32. Compilation failed in require at /root/.vep/Plugins/Conservation.pm line 60. BEGIN failed--compilation aborted at /root/.vep/Plugins/Conservation.pm line 60. Compilation failed in require at (eval 37) line 2. BEGIN failed--compilation aborted at (eval 37) line 2.It looks like it's trying to find it in /mnt/c/ensembl-vep/Bio/DB/ but the file doesn't exist there:
root@JCSMR-050039WD:/mnt/c/ensembl-vep# locate BigFile.pm /root/.cpan/build/Bio-BigFile-1.07-0/blib/lib/Bio/DB/BigFile.pm /root/.cpan/build/Bio-BigFile-1.07-0/lib/Bio/DB/BigFile.pm /root/.cpan/build/Bio-BigFile-1.07-1/lib/Bio/DB/BigFile.pm /root/.cpan/build/Bio-BigFile-1.07-2/blib/lib/Bio/DB/BigFile.pm /root/.cpan/build/Bio-BigFile-1.07-2/lib/Bio/DB/BigFile.pm /root/.cpan/build/Bio-BigFile-1.07-3/blib/lib/Bio/DB/BigFile.pm /root/.cpan/build/Bio-BigFile-1.07-3/lib/Bio/DB/BigFile.pm /root/.cpanm/work/1649836297.7943/Bio-BigFile-1.07/lib/Bio/DB/BigFile.pm /root/.cpanm/work/1649837172.8442/Bio-BigFile-1.07/lib/Bio/DB/BigFile.pmI've added /root/.cpan/ and /root/cpanm/ to my PERL5LIB but it doesn't seem to help and '@INC' doesnt seem to have these paths when called despite them being configured in Perl:
`root@JCSMR-050039WD:/mnt/c/ensembl-vep# perl -V Summary of my perl5 (revision 5 version 30 subversion 0) configuration:
Platform: osname=linux osvers=4.19.0 archname=x86_64-linux-gnu-thread-multi uname='linux localhost 4.19.0 #1 smp debian 4.19.0 x86_64 gnulinux ' config_args='-Dmksymlinks -Dusethreads -Duselargefiles -Dcc=x86_64-linux-gnu-gcc -Dcpp=x86_64-linux-gnu-cpp -Dld=x86_64-linux-gnu-gcc -Dccflags=-DDEBIAN -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/perl-Wfb2Cd/perl-5.30.0=. -fstack-protector-strong -Wformat -Werror=format-security -Dldflags= -Wl,-Bsymbolic-functions -Wl,-z,relro -Dlddlflags=-shared -Wl,-Bsymbolic-functions -Wl,-z,relro -Dcccdlflags=-fPIC -Darchname=x86_64-linux-gnu -Dprefix=/usr -Dprivlib=/usr/share/perl/5.30 -Darchlib=/usr/lib/x86_64-linux-gnu/perl/5.30 -Dvendorprefix=/usr -Dvendorlib=/usr/share/perl5 -Dvendorarch=/usr/lib/x86_64-linux-gnu/perl5/5.30 -Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl/5.30.0 -Dsitearch=/usr/local/lib/x86_64-linux-gnu/perl/5.30.0 -Dman1dir=/usr/share/man/man1 -Dman3dir=/usr/share/man/man3 -Dsiteman1dir=/usr/local/man/man1 -Dsiteman3dir=/usr/local/man/man3 -Duse64bitint -Dman1ext=1 -Dman3ext=3perl -Dpager=/usr/bin/sensible-pager -Uafs -Ud_csh -Ud_ualarm -Uusesfio -Uusenm -Ui_libutil -Ui_xlocale -Uversiononly -DDEBUGGING=-g -Doptimize=-O2 -dEs -Duseshrplib -Dlibperl=libperl.so.5.30.0' hint=recommended useposix=true d_sigaction=define useithreads=define usemultiplicity=define use64bitint=define use64bitall=define uselongdouble=undef usemymalloc=n default_inc_excludes_dot=define bincompat5005=undef Compiler: cc='x86_64-linux-gnu-gcc' ccflags ='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64' optimize='-O2 -g' cppflags='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include' ccversion='' gccversion='9.3.0' 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='x86_64-linux-gnu-gcc' ldflags =' -fstack-protector-strong -L/usr/local/lib' libpth=/usr/local/lib /usr/include/x86_64-linux-gnu /usr/lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib libs=-lgdbm -lgdbm_compat -ldb -ldl -lm -lpthread -lc -lcrypt perllibs=-ldl -lm -lpthread -lc -lcrypt libc=libc-2.31.so so=so useshrplib=true libperl=libperl.so.5.30 gnulibc_version='2.31' Dynamic Linking: dlsrc=dl_dlopen.xs dlext=so d_dlsymun=undef ccdlflags='-Wl,-E' cccdlflags='-fPIC' lddlflags='-shared -L/usr/local/lib -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 Locally applied patches: DEBPKG:debian/cpan_definstalldirs - Provide a sensible INSTALLDIRS default for modules installed from CPAN. DEBPKG:debian/db_file_ver - https://bugs.debian.org/340047 Remove overly restrictive DB_File version check. DEBPKG:debian/doc_info - Replace generic man(1) instructions with Debian-specific information. DEBPKG:debian/enc2xs_inc - https://bugs.debian.org/290336 Tweak enc2xs to follow symlinks and ignore missing @INC directories. DEBPKG:debian/errno_ver - https://bugs.debian.org/343351 Remove Errno version check due to upgrade problems with long-running processes. DEBPKG:debian/libperl_embed_doc - https://bugs.debian.org/186778 Note that libperl-dev package is required for embedded linking DEBPKG:fixes/respect_umask - Respect umask during installation DEBPKG:debian/writable_site_dirs - Set umask approproately for site install directories DEBPKG:debian/extutils_set_libperl_path - EU:MM: set location of libperl.a under /usr/lib DEBPKG:debian/no_packlist_perllocal - Don't install .packlist or perllocal.pod for perl or vendor DEBPKG:debian/fakeroot - Postpone LD_LIBRARY_PATH evaluation to the binary targets. DEBPKG:debian/instmodsh_doc - Debian policy doesn't install .packlist files for core or vendor. DEBPKG:debian/ld_run_path - Remove standard libs from LD_RUN_PATH as per Debian policy. DEBPKG:debian/libnet_config_path - Set location of libnet.cfg to /etc/perl/Net as /usr may not be writable. DEBPKG:debian/perlivp - https://bugs.debian.org/510895 Make perlivp skip include directories in /usr/local DEBPKG:debian/squelch-locale-warnings - https://bugs.debian.org/508764 Squelch locale warnings in Debian package maintainer scripts DEBPKG:debian/patchlevel - https://bugs.debian.org/567489 List packaged patches for 5.30.0-9ubuntu0.2 in patchlevel.h DEBPKG:fixes/document_makemaker_ccflags - https://bugs.debian.org/628522 [rt.cpan.org #68613] Document that CCFLAGS should include $Config{ccflags} DEBPKG:debian/find_html2text - https://bugs.debian.org/640479 Configure CPAN::Distribution with correct name of html2text DEBPKG:debian/perl5db-x-terminal-emulator.patch - https://bugs.debian.org/668490 Invoke x-terminal-emulator rather than xterm in perl5db.pl DEBPKG:debian/cpan-missing-site-dirs - https://bugs.debian.org/688842 Fix CPAN::FirstTime defaults with nonexisting site dirs if a parent is writable DEBPKG:fixes/memoize_storable_nstore - [rt.cpan.org #77790] https://bugs.debian.org/587650 Memoize::Storable: respect 'nstore' option not respected DEBPKG:debian/makemaker-pasthru - https://bugs.debian.org/758471 Pass LD settings through to subdirectories DEBPKG:debian/makemaker-manext - https://bugs.debian.org/247370 Make EU::MakeMaker honour MANnEXT settings in generated manpage headers DEBPKG:debian/kfreebsd-softupdates - https://bugs.debian.org/796798 Work around Debian Bug#796798 DEBPKG:fixes/autodie-scope - https://bugs.debian.org/798096 Fix a scoping issue with "no autodie" and the "system" sub DEBPKG:fixes/memoize-pod - [rt.cpan.org #89441] Fix POD errors in Memoize DEBPKG:debian/hurd-softupdates - https://bugs.debian.org/822735 Fix t/op/stat.t failures on hurd DEBPKG:fixes/math_complex_doc_great_circle - https://bugs.debian.org/697567 [rt.cpan.org #114104] Math::Trig: clarify definition of great_circle_midpoint DEBPKG:fixes/math_complex_doc_see_also - https://bugs.debian.org/697568 [rt.cpan.org #114105] Math::Trig: add missing SEE ALSO DEBPKG:fixes/math_complex_doc_angle_units - https://bugs.debian.org/731505 [rt.cpan.org #114106] Math::Trig: document angle units DEBPKG:fixes/cpan_web_link - https://bugs.debian.org/367291 CPAN: Add link to main CPAN web site DEBPKG:debian/hppa_op_optimize_workaround - https://bugs.debian.org/838613 Temporarily lower the optimization of op.c on hppa due to gcc-6 problems DEBPKG:debian/installman-utf8 - https://bugs.debian.org/840211 Generate man pages with UTF-8 characters DEBPKG:fixes/getopt-long-4 - https://bugs.debian.org/864544 [rt.cpan.org #122068] Fix issue #122068. DEBPKG:debian/hppa_opmini_optimize_workaround - https://bugs.debian.org/869122 Lower the optimization level of opmini.c on hppa DEBPKG:debian/sh4_op_optimize_workaround - https://bugs.debian.org/869373 Also lower the optimization level of op.c and opmini.c on sh4 DEBPKG:debian/perldoc-pager - https://bugs.debian.org/870340 [rt.cpan.org #120229] Fix perldoc terminal escapes when sensible-pager is less DEBPKG:debian/prune_libs - https://bugs.debian.org/128355 Prune the list of libraries wanted to what we actually need. DEBPKG:debian/mod_paths - Tweak @INC ordering for Debian DEBPKG:debian/configure-regen - https://bugs.debian.org/762638 Regenerate Configure et al. after probe unit changes DEBPKG:debian/deprecate-with-apt - https://bugs.debian.org/747628 Point users to Debian packages of deprecated core modules DEBPKG:debian/disable-stack-check - https://bugs.debian.org/902779 [perl #133327] Disable debugperl stack extension checks for binary compatibility with perl DEBPKG:fixes/eumm-usrmerge - https://bugs.debian.org/913637 Avoid mangling /bin non-perl shebangs on merged-/usr systems DEBPKG:debian/perlbug-editor - https://bugs.debian.org/922609 Use "editor" as the default perlbug editor, as per Debian policy DEBPKG:fixes/gid-parsing - [79e302e] https://bugs.debian.org/941985 [perl #134169] (perl #134169) mg.c reset endptr after use DEBPKG:fixes/CVE-2020-10543.patch - [PATCH v530 1/4] regcomp.c: Prevent integer overflow from nested regex quantifiers. DEBPKG:fixes/CVE-2020-10878-1.patch - [PATCH v530 2/4] study_chunk: extract rck_elide_nothing DEBPKG:fixes/CVE-2020-10878-2.patch - [PATCH v530 3/4] regcomp: use long jumps if there is any possibility of overflow DEBPKG:fixes/CVE-2020-12723.patch - [PATCH v530 4/4] study_chunk: avoid mutating regexp program within GOSUB Built under linux Compiled at Oct 19 2020 10:56:54 %ENV: PERL5LIB=":/mnt/c/ensembl-vep/:/root/cpanm/lib/perl5:/root/.cpan/:/root/cpanm/lib/perl5:/root/cpanm/lib/perl5:/root/cpanm/lib/perl5:/root/.cpanm/work/:/root/.cpan/:/root/cpanm/lib/perl5:/root/.cpanm/work/:/root/.cpan/:/root/cpanm/lib/perl5:/root/.cpanm/" @INC: /mnt/c/ensembl-vep/ /root/cpanm/lib/perl5/5.30.0/x86_64-linux-gnu-thread-multi /root/cpanm/lib/perl5/5.30.0 /root/cpanm/lib/perl5/x86_64-linux-gnu-thread-multi /root/cpanm/lib/perl5 /root/.cpan/ /root/cpanm/lib/perl5/5.30.0/x86_64-linux-gnu-thread-multi /root/cpanm/lib/perl5/5.30.0 /root/cpanm/lib/perl5/x86_64-linux-gnu-thread-multi /root/cpanm/lib/perl5 /root/cpanm/lib/perl5/5.30.0/x86_64-linux-gnu-thread-multi /root/cpanm/lib/perl5/5.30.0 /root/cpanm/lib/perl5/x86_64-linux-gnu-thread-multi /root/cpanm/lib/perl5 /root/cpanm/lib/perl5/5.30.0/x86_64-linux-gnu-thread-multi /root/cpanm/lib/perl5/5.30.0 /root/cpanm/lib/perl5/x86_64-linux-gnu-thread-multi /root/cpanm/lib/perl5 /root/.cpanm/work/ /root/.cpan/ /root/cpanm/lib/perl5/5.30.0/x86_64-linux-gnu-thread-multi /root/cpanm/lib/perl5/5.30.0 /root/cpanm/lib/perl5/x86_64-linux-gnu-thread-multi /root/cpanm/lib/perl5 /root/.cpanm/work/ /root/.cpan/ /root/cpanm/lib/perl5/5.30.0/x86_64-linux-gnu-thread-multi /root/cpanm/lib/perl5/5.30.0 /root/cpanm/lib/perl5/x86_64-linux-gnu-thread-multi /root/cpanm/lib/perl5 /root/.cpanm/ /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base`