Failing tests t/Runner.t

[PetrKralCZ]

Describe the issue

One of my colleagues reports failing tests. Do you have any idea what could be the cause?

#   Failed test 'run - count up/downstream (default)'
#   at ./t/Runner.t line 534.
#          got: '2'
#     expected: '1'

#   Failed test 'run - count up/downstream (10000)'
#   at ./t/Runner.t line 551.
#          got: '3'
#     expected: '2'

#   Failed test 'run - count up/downstream (1000,2000)'
#   at ./t/Runner.t line 570.
#          got: '5'
#     expected: '4'
# Looks like you failed 3 tests of 110.

System

• VEP version: 113.0
• Perl version: 5.36.1
• OS: Rocky Linux 8.10
• tabix installed ? Yes

Full VEP command line

perl INSTALL.pl --NO_BIOPERL --NO_HTSLIB --AUTO af --SPECIES cyprinus_carpio_carpio --NO_UPDATE --DESTDIR /apps/eb/el8/upstream/software/VEP/113.0-GCC-12.3.0/modules/api

Full error message

./t/Haplo_AnnotationSource_Database_Transcript.t ..... ok
./t/AnnotationSource_Cache_Transcript.t .............. ok
./t/AnnotationSource_File_BED.t ...................... ok
./t/InputBuffer.t .................................... ok
./t/Parser_ID.t ...................................... ok
./t/AnnotationSource_Cache_Variation.t ............... ok
./t/BaseVEP.t ........................................ ok
./t/AnnotationSource_Cache_VariationTabix.t .......... ok

#   Failed test 'run - count up/downstream (default)'
#   at ./t/Runner.t line 534.
#          got: '2'
#     expected: '1'

#   Failed test 'run - count up/downstream (10000)'
#   at ./t/Runner.t line 551.
#          got: '3'
#     expected: '2'

#   Failed test 'run - count up/downstream (1000,2000)'
#   at ./t/Runner.t line 570.
#          got: '5'
#     expected: '4'
# Looks like you failed 3 tests of 110.
./t/Runner.t ......................................... 
Dubious, test returned 3 (wstat 768, 0x300)
Failed 3/110 subtests 
	(less 6 skipped subtests: 101 okay)
./t/Utils.t .......................................... ok
./t/OutputFactory_VCF.t .............................. ok
./t/AnnotationSource_File_GFF.t ...................... ok
WARNING: found tandem repeats with different references per alternative allele: SVLEN=5,10; only using reference with largest size
WARNING: found tandem repeats with different references per alternative allele: SVLEN=5,10; only using reference with largest size
./t/Parser_VCF.t ..................................... ok
./t/AnnotationSource_File_BigWig.t ................... ok
./t/Haplo_InputBuffer.t .............................. ok
./t/Parser_Region.t .................................. ok
./t/AnnotationSource.t ............................... ok
./t/AnnotationSource_Database_Variation.t ............ ok
./t/Config.t ......................................... ok
./t/Haplo_Runner.t ................................... ok
./t/Parser_HGVS.t .................................... ok
./t/Stats.t .......................................... ok
./t/OutputFactory_VEP_output.t ....................... ok
./t/Parser.t ......................................... ok
./t/FilterSet.t ...................................... ok
./t/Parser_CAID.t .................................... ok
./t/AnnotationSource_Database_Transcript.t ........... ok
WARNING: Ignoring 'cDNA_match' feature_type from /apps/eb/el8/upstream/software/VEP/113.0-GCC-12.3.0/t/testdata/custom/bam_edit.gff.gz GFF/GTF file. This feature_type is not supported in VEP.
./t/bam_edit.t ....................................... ok
./t/AnnotationSource_Cache_RegFeat.t ................. ok
./t/Parser_SPDI.t .................................... ok
./t/VariantRecoder.t ................................. ok
./t/AnnotationSourceAdaptor.t ........................ ok
./t/CacheDir.t ....................................... ok
./t/AnnotationSource_Database_RegFeat.t .............. ok
./t/version.t ........................................ ok
./t/OutputFactory_JSON.t ............................. ok
./t/AnnotationSource_File_VCF.t ...................... ok
./t/Haplo_AnnotationSource_Cache_Transcript.t ........ ok
./t/Haplo_Parser_VCF.t ............................... ok
./t/AnnotationSource_Database_StructuralVariation.t .. ok
./t/AnnotationSource_File_GTF.t ...................... ok
./t/TranscriptTree.t ................................. ok
./t/OutputFactory.t .................................. ok
./t/Parser_VEP_input.t ............................... ok
./t/OutputFactory_Tab.t .............................. ok
./t/AnnotationSource_File.t .......................... ok
WARNING: Ignoring 'chromosome' feature_type from /apps/eb/el8/upstream/software/VEP/113.0-GCC-12.3.0/t/testdata/custom/test.gff.gz GFF/GTF file. This feature_type is not supported in VEP.
WARNING: Ignoring 'biological_region' feature_type from /apps/eb/el8/upstream/software/VEP/113.0-GCC-12.3.0/t/testdata/custom/test.gff.gz GFF/GTF file. This feature_type is not supported in VEP.
WARNING: Ignoring 'three_prime_UTR' feature_type from /apps/eb/el8/upstream/software/VEP/113.0-GCC-12.3.0/t/testdata/custom/test.gff.gz GFF/GTF file. This feature_type is not supported in VEP.
WARNING: Ignoring 'five_prime_UTR' feature_type from /apps/eb/el8/upstream/software/VEP/113.0-GCC-12.3.0/t/testdata/custom/test.gff.gz GFF/GTF file. This feature_type is not supported in VEP.
./t/Haplo_AnnotationSource_File_GFF.t ................ ok
./t/AnnotationSource_Cache.t ......................... ok
WARNING: Ignoring 'three_prime_utr' feature_type from /apps/eb/el8/upstream/software/VEP/113.0-GCC-12.3.0/t/testdata/custom/test.gtf.gz GFF/GTF file. This feature_type is not supported in VEP.
WARNING: Ignoring 'start_codon' feature_type from /apps/eb/el8/upstream/software/VEP/113.0-GCC-12.3.0/t/testdata/custom/test.gtf.gz GFF/GTF file. This feature_type is not supported in VEP.
WARNING: Ignoring 'five_prime_utr' feature_type from /apps/eb/el8/upstream/software/VEP/113.0-GCC-12.3.0/t/testdata/custom/test.gtf.gz GFF/GTF file. This feature_type is not supported in VEP.
./t/Haplo_AnnotationSource_File_GTF.t ................ ok

[dglemos]

Hi @PetrKralCZ,
You can ignore the test while running the installation using the option --NO_TEST.
After the installation just to understand why it fails, can you run the command: perl ensembl-vep/t/Runner.t this should print more details.

[dglemos]

I'll close this now, but feel free to open a new issue if you encounter further issues.

Best wishes,
Diana