Closed xiyasong closed 1 month ago
HI @xiyasong
Sorry to hear you've been having trouble with the install. It can be tricky to debug these issues, but there are possibly a couple of simple workarounds.
1) If you run in offline mode, using a cache and fasta file, VEP shouldn't try to use that module, so you can bypass the issue that way. So use --offline
, --cache
, --dir_cache
and --fasta
(see here for more details).
2) Failing that, you can try using the containerised docker image of Ensembl VEP - available here, with instructions here. It comes with all dependencies and plugins packaged already.
Do let me know how you get on!
Hi, thanks for your kind reply and suggestions, I tried --offline --cache --dir_cache seems still not solved, but luckily: I solved the problem by creating a brand new conda environment and redo everything and it magically works. :)).
Describe the issue
A clear and concise description of what the bug is. Hi My VEP installaztion work fine with the --NO_HTSLIB, but when I try to use it for my real sample it gives error: -------------------- EXCEPTION -------------------- MSG: ERROR: Cannot use format vcf without Bio::DB::HTS::Tabix module installed
STACK Bio::EnsEMBL::VEP::AnnotationSource::File::new /sza_data/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm:178 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_custom /sza_data/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:328 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /sza_data/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:94 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /sza_data/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:170 STACK Bio::EnsEMBL::VEP::Runner::init /sza_data/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:128 STACK Bio::EnsEMBL::VEP::Runner::run /sza_data/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:200 STACK toplevel ./vep:46 Date (localtime) = Thu Jul 25 17:49:56 2024 Ensembl API version = 112
So, I tried to install Bio::DB::HTS module, by running perl INSTALL.pl, then it gives error: .... gcc -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread
Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-DB-HTS' version '2.11' Building Bio-DB-HTS Error: no compiler detected to compile 'lib/Bio/DB/HTS.c'. Aborting ERROR: Shared Bio::DB:HTS library not found
Additional information
Please fill in the following sections to help us find the source of your issue as quickly as possible.
System
Full VEP command line
Full error message
Checking for installed versions of the Ensembl API...done
Setting up directories
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 switching back to a branch.
If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example:
git switch -c
Or undo this operation with:
git switch -
Turn off this advice by setting config variable advice.detachedHead to false
~~~~~~~~~96 | glibc_objsize (dest)); |~~~~~In function ‘strncpy’, inlined from ‘full_path’ at cram/cram_io.c:3748:13, inlined from ‘cram_write_SAM_hdr’ at cram/cram_io.c:3823:17: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 95 | return builtin___strncpy_chk (dest, src, len, | ^~~~~~~~~~96 | glibc_objsize (dest)); |~~~~~In function ‘strncpy’, inlined from ‘cram_dopen’ at cram/cram_io.c:4126:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘builtin_strncpy’ specified bound 20 equals destination size [-Wstringop-truncation] 95 | return builtin_strncpy_chk (dest, src, len, | ^~~~~~~~~~96 | glibc_objsize (dest)); |~~~~~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 hts.c: In function ‘hts_idx_init’: hts.c:1386:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow] 1386 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; | ^~~ 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 In file included from /usr/include/string.h:535, from cram/cram_io.c:53: In function ‘strncpy’, inlined from ‘cram_populate_ref’ at cram/cram_io.c:2095:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 95 | return builtin_strncpy_chk (dest, src, len, | ^~~~~~~~~~96 | glibc_objsize (dest)); |~~~~~In function ‘strncpy’, inlined from ‘full_path’ at cram/cram_io.c:3748:13, inlined from ‘cram_write_SAM_hdr’ at cram/cram_io.c:3823:17: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 95 | return builtin_strncpy_chk (dest, src, len, | ^~~~~~~~~~96 | glibc_objsize (dest)); |~~~~~In function ‘strncpy’, inlined from ‘cram_dopen’ at cram/cram_io.c:4126:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘builtin_strncpy’ specified bound 20 equals destination size [-Wstringop-truncation] 95 | return builtin_strncpy_chk (dest, src, len, | ^~~~~~~~~~96 | __glibc_objsize (__dest)); |~~~~~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 -lpthreadCreated MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-DB-HTS' version '2.11' Building Bio-DB-HTS Error: no compiler detected to compile 'lib/Bio/DB/HTS.c'. Aborting ERROR: Shared Bio::DB:HTS library not found
Data files (if applicable)
They include: