likhitha-surapaneni
commented
3 months ago Hi @ethankreuzer ,
Sorry to hear that you are facing issues.
Can you please let us what is returned when you run perl -e "use Bio::DB::HTS::Tabix"?
An option is to uninstall the tabix, download the ensembl-vep and run an installation from scratch with --NO_HTSLIB
Describe the issue
I am trying to download the cache file for humans on build hg38 with theinstaller, but it is not doing it and I do not know why
Additional information
I ran the following line:
$ perl INSTALL.pl --AUTO ac --species homo_sapiens --assembly GRCh38 --NO_HTSLIB
Also I did not load the DBD:mysql Perl module becasue I was having issues
System
Versions: ensembl : 112.3add379 ensembl-funcgen : 112.be19ffa ensembl-io : 112.2851b6f ensembl-variation : 112.4113356 ensembl-vep : 112.0
Last part of terminal output
-------------------- EXCEPTION -------------------- MSG: ERROR: Cannot use format gff without Bio::DB::HTS::Tabix module installed
STACK Bio::EnsEMBL::VEP::AnnotationSource::File::new /project/richards/ethan.kreuzer/EXWAS/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm:178 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_custom /project/richards/ethan.kreuzer/EXWAS/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:328 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /project/richards/ethan.kreuzer/EXWAS/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:94 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /project/richards/ethan.kreuzer/EXWAS/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:170 STACK Bio::EnsEMBL::VEP::Runner::init /project/richards/ethan.kreuzer/EXWAS/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:128 STACK Bio::EnsEMBL::VEP::Runner::next_output_line /project/richards/ethan.kreuzer/EXWAS/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:362 STACK toplevel ./t/Runner.t:833 Date (localtime) = Mon Jun 3 12:25:06 2024 Ensembl API version = 112
Tests were run but no plan was declared and done_testing() was not seen.
Looks like your test exited with 255 just after 81.
./t/Runner.t ......................................... Dubious, test returned 255 (wstat 65280, 0xff00) All 81 subtests passed ./t/Stats.t .......................................... Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 791. ./t/Stats.t .......................................... ok
./t/TranscriptTree.t ................................. Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 791. ./t/TranscriptTree.t ................................. ok
./t/Utils.t .......................................... ok
./t/VariantRecoder.t ................................. Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 791. ./t/VariantRecoder.t ................................. ok
./t/bam_edit.t ....................................... Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 791. ./t/bam_edit.t ....................................... ok
./t/version.t ........................................ ok
Test Summary Report
./t/Runner.t (Wstat: 65280 Tests: 81 Failed: 0) Non-zero exit status: 255 Parse errors: No plan found in TAP output Files=49, Tests=1927, 109 wallclock secs ( 0.45 usr 0.21 sys + 95.95 cusr 9.95 csys = 106.56 CPU) Result: FAIL Failed 1/49 test programs. 0/1927 subtests failed.
Proof no cache files (if applicable)
" [-----.-------@---- ensembl-vep]$ ls ~/.vep Plugins tmp "
The cache files are not here