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Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
Apache License 2.0
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Install issue: BaseVEP.t #Failed test 'get_slice - fasta_db' #623

Closed redmanln closed 4 years ago

redmanln commented 4 years ago

Hi,

I am running on Ubuntu 18.04.2. I have been trying to install the ensemble-vep 98 release and keep getting the following error: ./t/BaseVEP.t ........................................ 1/? Failed test 'get_slice - fasta_db' at ./t/BaseVEP.t line 131. Structures begin differing at: $got->{coord_system}{version} = '' $expected->{coord_system}{version} = undef ./t/BaseVEP.t ........................................ 31/? # Looks like you failed 1 test of 46. ./t/BaseVEP.t ........................................ Dubious, test returned 1 (wstat 256, 0x100) Any help I can get would be greatly appreciated! The full installation code is below. 



lindsay:~/ensembl-vep$ perl INSTALL.pl

Hello! This installer is configured to install v98 of the Ensembl API for use by the VEP.
It will not affect any existing installations of the Ensembl API that you may have.

It will also download and install cache files from Ensembl's FTP server.

Checking for installed versions of the Ensembl API...done
It looks like you already have the following API modules installed:

ensembl

The VEP requires the ensembl, ensembl-io, ensembl-variation and ensembl-funcgen modules

Skip to the next step (n) to install cache files

Do you want to continue installing the API (y/n)? y

Setting up directories
 - fetching BioPerl
 - unpacking ./Bio/tmp/release-1-6-924.zip
 - moving files
Attempting to install Bio::DB::HTS and htslib.

>>> If this fails, try re-running with --NO_HTSLIB

 - checking out HTSLib
Cloning into 'htslib'...
remote: Enumerating objects: 9, done.
remote: Counting objects: 100% (9/9), done.
remote: Compressing objects: 100% (7/7), done.
remote: Total 12213 (delta 4), reused 5 (delta 2), pack-reused 12204
Receiving objects: 100% (12213/12213), 8.90 MiB | 6.81 MiB/s, done.
Resolving deltas: 100% (8697/8697), done.
Note: checking out '1832d3a1b75133e55fb6abffc3f50f8a6ed5ceae'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

 - building HTSLIB in ./htslib
In /home/lindsay/ensembl-vep/htslib
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
echo '#define HAVE_LZMA_H 1' >> config.h
echo '#define HAVE_FSEEKO 1' >> config.h
echo '#define HAVE_DRAND48 1' >> config.h
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o kstring.o kstring.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o errmod.o errmod.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o faidx.o faidx.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o hfile.o hfile.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.9-dirty"' > version.h
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o hts.o hts.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o hts_os.o hts_os.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o md5.o md5.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o multipart.o multipart.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o probaln.o probaln.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o realn.o realn.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o regidx.o regidx.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o sam.o sam.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o tbx.o tbx.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o textutils.o textutils.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o thread_pool.o thread_pool.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o vcf.o vcf.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/files.o cram/files.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/sam_header.o cram/sam_header.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/string_alloc.o cram/string_alloc.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
ranlib libhts.a
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o kfunc.pico kfunc.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o knetfile.pico knetfile.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o kstring.pico kstring.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o bgzf.pico bgzf.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o errmod.pico errmod.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o faidx.pico faidx.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o hfile.pico hfile.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o hfile_net.pico hfile_net.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o hts.pico hts.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o hts_os.pico hts_os.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o md5.pico md5.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o multipart.pico multipart.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o probaln.pico probaln.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o realn.pico realn.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o regidx.pico regidx.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o sam.pico sam.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o tbx.pico tbx.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o textutils.pico textutils.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o thread_pool.pico thread_pool.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o vcf.pico vcf.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o vcfutils.pico vcfutils.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/files.pico cram/files.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -shared -Wl,-soname,libhts.so.2  -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico -lz -lm -lbz2 -llzma -lpthread
ln -sf libhts.so libhts.so.2
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o bgzip.o bgzip.c
gcc  -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o htsfile.o htsfile.c
gcc  -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o tabix.o tabix.c
gcc  -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/hts_endian.o test/hts_endian.c
gcc  -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/fieldarith.o test/fieldarith.c
gcc  -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/hfile.o test/hfile.c
gcc  -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/sam.o test/sam.c
gcc  -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/test_bgzf.o test/test_bgzf.c
gcc  -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/test_realn.o test/test_realn.c
gcc  -o test/test_realn test/test_realn.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/test-regidx.o test/test-regidx.c
gcc  -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/test_view.o test/test_view.c
gcc  -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc  -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc  -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc  -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc  -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread
 - unpacking ./Bio/tmp/biodbhts.zip to ./Bio/tmp/
./Bio/tmp/Bio-DB-HTS-2.11 - moving files to ./biodbhts
 - making Bio::DB:HTS
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-DB-HTS' version '2.11'
Building Bio-DB-HTS
x86_64-linux-gnu-gcc -I/home/lindsay/ensembl-vep/htslib -I/usr/lib/x86_64-linux-gnu/perl/5.26/CORE -DVERSION="2.11" -DXS_VERSION="2.11" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -o lib/Bio/DB/HTS.o lib/Bio/DB/HTS.c
lib/Bio/DB/HTS.xs: In function ‘XS_Bio__DB__HTS__VCF__Header_fmt_text’:
lib/Bio/DB/HTS.xs:1770:5: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
     RETVAL = newSVpv(bcf_hdr_fmt_text(header, is_bcf, &len), 0);
     ^~~~~~
In file included from lib/Bio/DB/HTS.xs:59:0:
/home/lindsay/ensembl-vep/htslib/htslib/vcf.h:439:11: note: declared here
     char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
           ^~~~~~~~~~~~~~~~
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/HTS.bs')
x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/HTS.so lib/Bio/DB/HTS.o -L/home/lindsay/ensembl-vep/htslib -Wl,-rpath,/home/lindsay/ensembl-vep/htslib -lhts -lpthread -lz
x86_64-linux-gnu-gcc -I/home/lindsay/ensembl-vep/htslib -I/usr/lib/x86_64-linux-gnu/perl/5.26/CORE -DVERSION="2.11" -DXS_VERSION="2.11" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -o lib/Bio/DB/HTS/Faidx.o lib/Bio/DB/HTS/Faidx.c
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bs')
x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so lib/Bio/DB/HTS/Faidx.o -L/home/lindsay/ensembl-vep/htslib -Wl,-rpath,/home/lindsay/ensembl-vep/htslib -lhts -lpthread -lz

Downloading required Ensembl API files
 - fetching ensembl
 - unpacking ./Bio/tmp/ensembl.zip
 - moving files
 - getting version information
 - fetching ensembl-variation
 - unpacking ./Bio/tmp/ensembl-variation.zip
 - moving files
 - getting version information
 - fetching ensembl-funcgen
 - unpacking ./Bio/tmp/ensembl-funcgen.zip
 - moving files
 - getting version information
 - fetching ensembl-io
 - unpacking ./Bio/tmp/ensembl-io.zip
 - moving files
 - getting version information

Testing VEP installation
./t/OutputFactory_Tab.t .............................. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/OutputFactory_Tab.t .............................. ok    
./t/bam_edit.t ....................................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/bam_edit.t ....................................... ok    
./t/AnnotationSource_File_GTF.t ...................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource_File_GTF.t ...................... ok    
./t/BaseVEP.t ........................................ Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/BaseVEP.t ........................................ 1/? 
#   Failed test 'get_slice - fasta_db'
#   at ./t/BaseVEP.t line 131.
#     Structures begin differing at:
#          $got->{coord_system}{version} = ''
#     $expected->{coord_system}{version} = undef
./t/BaseVEP.t ........................................ 31/? # Looks like you failed 1 test of 46.
./t/BaseVEP.t ........................................ Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/46 subtests 
    (less 8 skipped subtests: 37 okay)
./t/AnnotationSource_Database_Transcript.t ........... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource_Database_Transcript.t ........... ok    
./t/AnnotationSource_Cache_VariationTabix.t .......... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource_Cache_VariationTabix.t .......... ok    
./t/Stats.t .......................................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/Stats.t .......................................... ok    
./t/Parser_VEP_input.t ............................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/Parser_VEP_input.t ............................... ok    
./t/AnnotationSource_Cache_Variation.t ............... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource_Cache_Variation.t ............... ok    
./t/Parser.t ......................................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/Parser.t ......................................... ok     
./t/AnnotationSource_File_BigWig.t ................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource_File_BigWig.t ................... ok    
./t/Utils.t .......................................... ok    
./t/Parser_VCF.t ..................................... "my" variable $cnv_vf masks earlier declaration in same scope at ./t/Parser_VCF.t line 570.
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/Parser_VCF.t ..................................... 1/? WARNING: variant sv_dup on line 1 is too long to annotate: (10000)
WARNING: variant sv_dup on line 1 is too long to annotate: (10000)
./t/Parser_VCF.t ..................................... ok    
./t/AnnotationSource_Database_RegFeat.t .............. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource_Database_RegFeat.t .............. ok    
./t/Runner.t ......................................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/Runner.t ......................................... ok    
./t/AnnotationSource_File.t .......................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource_File.t .......................... ok    
./t/AnnotationSourceAdaptor.t ........................ Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSourceAdaptor.t ........................ ok    
./t/version.t ........................................ ok   
./t/OutputFactory_VCF.t .............................. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/OutputFactory_VCF.t .............................. ok    
./t/FilterSet.t ...................................... ok     
./t/TranscriptTree.t ................................. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/TranscriptTree.t ................................. ok    
./t/OutputFactory_JSON.t ............................. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/OutputFactory_JSON.t ............................. ok    
./t/Config.t ......................................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/Config.t ......................................... ok    
./t/Parser_ID.t ...................................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/Parser_ID.t ...................................... ok   
./t/InputBuffer.t .................................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/InputBuffer.t .................................... ok    
./t/AnnotationSource_Cache.t ......................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource_Cache.t ......................... ok   
./t/AnnotationSource_File_GFF.t ...................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource_File_GFF.t ...................... ok    
./t/Parser_HGVS.t .................................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/Parser_HGVS.t .................................... ok    
./t/OutputFactory_VEP_output.t ....................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/OutputFactory_VEP_output.t ....................... ok    
./t/CacheDir.t ....................................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/CacheDir.t ....................................... ok    
./t/Parser_SPDI.t .................................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/Parser_SPDI.t .................................... ok   
./t/AnnotationSource_Database_Variation.t ............ Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource_Database_Variation.t ............ ok    
./t/AnnotationSource_Cache_Transcript.t .............. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource_Cache_Transcript.t .............. ok    
./t/AnnotationSource_File_BED.t ...................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource_File_BED.t ...................... ok    
./t/AnnotationSource.t ............................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource.t ............................... ok    
./t/Parser_Region.t .................................. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/Parser_Region.t .................................. ok    
./t/AnnotationSource_Cache_RegFeat.t ................. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource_Cache_RegFeat.t ................. ok    
./t/OutputFactory.t .................................. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/OutputFactory.t .................................. ok     
./t/AnnotationSource_File_VCF.t ...................... Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource_File_VCF.t ...................... ok    
./t/AnnotationSource_Database_StructuralVariation.t .. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/AnnotationSource_Database_StructuralVariation.t .. ok    
./t/VariantRecoder.t ................................. Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
./t/VariantRecoder.t ................................. ok    

Test Summary Report
-------------------
./t/BaseVEP.t                                      (Wstat: 256 Tests: 46 Failed: 1)
  Failed test:  27
  Non-zero exit status: 1
Files=41, Tests=1714, 116 wallclock secs ( 0.23 usr  0.08 sys + 113.31 cusr  2.40 csys = 116.02 CPU)
Result: FAIL
Failed 1/41 test programs. 1/1714 subtests failed.
aparton commented 4 years ago

Hi,

Thanks for this report. The good news is, I don't think that it's serious and VEP should operate normally despite this failing test.

The issue looks like it's related to Bio::DB::HTS. To help us investigate this issue, I have a couple of questions:

1) Which perl version are you using? 2) Do you see any error message if you run: perl -e 'use Bio::DB::HTS::Faidx' ? 3) Have you previously installed HTSLib or Bio::DB::HTS on this machine?

Kind Regards, Andrew

redmanln commented 4 years ago

Thanks!

  1. v5.26.1
  2. Yes, I get the following error: Can't locate Bio/DB/HTS/Faidx.pm in @INC (you may need to install the Bio::DB::HTS::Faidx module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at -e line 1. BEGIN failed--compilation aborted at -e line 1.
  3. I think I did attempt to install HTSLib before. I was trying to install VEP following these instructions: https://gist.github.com/ckandoth/5390e3ae4ecf182fa92f6318cfa9fa97
aparton commented 4 years ago

Hi,

Apologies for the delay in getting back to you. This warning message seems to be due to the multiple HTSLib versions on your machine, however VEP should still work normally in this situation.

Removing your other version of HTSLib from your $PERL5LIB and rerunning the installer should remove this message, however it's not necessary for you to do so, VEP will still run as normal.

Kind Regards, Andrew

aparton commented 4 years ago

Hi,

I'm going to close this issue now. If you have any more questions, please feel free to reopen it or open a new one.

Kind Regards, Andrew