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Created May 28, 2021 00:08
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Example of meltdown on neo-wb.obo in NEO pipeline
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log.txt
11:33:31
11:33:31 2021-05-24 11:33:31 (41.9 MB/s) - ‘mirror/goa_sars-cov-2.gpi’ saved [13554/13554]
11:33:31
11:33:31 gzip -dc mirror/goa_sars-cov-2.gpi.gz | ./gpi2obo.pl -s Scov2 -n sars-cov-2 > target/neo-goa_sars-cov-2.obo.tmp && mv target/neo-goa_sars-cov-2.obo.tmp target/neo-goa_sars-cov-2.obo
11:33:31 owltools --create-ontology http://purl.obolibrary.org/obo/go/noctua/neo.owl target/neo-sgd.obo target/neo-pombase.obo target/neo-mgi.obo target/neo-zfin.obo target/neo-rgd.obo target/neo-dictybase.obo target/neo-fb.obo target/neo-tair.obo target/neo-wb.obo target/neo-goa_human.obo target/neo-goa_human_complex.obo target/neo-goa_human_rna.obo target/neo-goa_human_isoform.obo target/neo-goa_pig.obo target/neo-xenbase.obo target/neo-ecocyc.obo target/neo-pseudocap.obo target/neo-goa_sars-cov-2.obo imports/pr_import.obo --merge-support-ontologies -o -f obo neo.obo.tmp && grep -v ^owl-axioms neo.obo.tmp > neo.obo
11:33:35 adding support ont Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/go/noctua/sgd.owl>) VersionIRI(<null>))) [Axioms: 58029 Logical Axioms: 12892] First 20 axioms: {Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000001532>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000000982>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000005380>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000001389>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000001208>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000006336>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000003951>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000005957>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000002353>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000006701>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000006597>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000004692>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000004143>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000003267>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000005886>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000001807>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000003001>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000005848>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000001531>)) Declaration(Class(<http://purl.obolibrary.org/obo/SGD_S000001934>)) }
11:33:35 adding support ont Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/go/noctua/pombase.owl>) VersionIRI(<null>))) [Axioms: 48579 Logical Axioms: 10792] First 20 axioms: {SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPAPB17E12.11> <http://purl.obolibrary.org/obo/CHEBI_33695>) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPCC736.06> <http://purl.obolibrary.org/obo/CHEBI_33695>) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPBC8D2.01> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_4896>)) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPAC637.06> <http://purl.obolibrary.org/obo/CHEBI_33695>) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPBC16E9.09c> <http://purl.obolibrary.org/obo/CHEBI_33695>) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPAC1F7.10> <http://purl.obolibrary.org/obo/CHEBI_33695>) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPBC25B2.10> <http://purl.obolibrary.org/obo/CHEBI_33695>) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPBC2A9.11c> <http://purl.obolibrary.org/obo/CHEBI_33695>) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPBP4G3.02> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_4896>)) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPBP8B7.31> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_4896>)) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPBC1773.16c> <http://purl.obolibrary.org/obo/CHEBI_33695>) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPAC6B12.18> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_4896>)) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPAC10F6.11c> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_4896>)) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPAC4G8.06c> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_4896>)) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPAC688.03c> <http://purl.obolibrary.org/obo/CHEBI_33695>) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPBC1778.07> <http://purl.obolibrary.org/obo/CHEBI_33695>) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPCC965.09> <http://purl.obolibrary.org/obo/CHEBI_33695>) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPAC57A10.12c> <http://purl.obolibrary.org/obo/CHEBI_33695>) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPAC688.06c> <http://purl.obolibrary.org/obo/CHEBI_33695>) SubClassOf(<http://purl.obolibrary.org/obo/PomBase_SPAC212.02> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_4896>)) }
11:33:45 adding support ont Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/go/noctua/mgi.owl>) VersionIRI(<null>))) [Axioms: 1131303 Logical Axioms: 287731] First 20 axioms: {Declaration(Class(<http://purl.obolibrary.org/obo/RefSeq#_NM_019786>)) Declaration(Class(<http://purl.obolibrary.org/obo/RefSeq#_NM_177887>)) Declaration(Class(<http://purl.obolibrary.org/obo/MGI_MGI%3A1350917>)) Declaration(Class(<http://purl.obolibrary.org/obo/RefSeq#_NR_046016>)) Declaration(Class(<http://purl.obolibrary.org/obo/PR_A3KMN5>)) Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8R4G0>)) Declaration(Class(<http://purl.obolibrary.org/obo/MGI_MGI%3A1344387>)) Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q9CPW9-2>)) Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8R037>)) Declaration(Class(<http://purl.obolibrary.org/obo/MGI_MGI%3A5531112>)) Declaration(Class(<http://purl.obolibrary.org/obo/RefSeq#_NM_181345>)) Declaration(Class(<http://purl.obolibrary.org/obo/RefSeq#_NM_001244762>)) Declaration(Class(<http://purl.obolibrary.org/obo/MGI_MGI%3A5590800>)) Declaration(Class(<http://purl.obolibrary.org/obo/RefSeq#_NM_139140>)) Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8K1S6>)) Declaration(Class(<http://purl.obolibrary.org/obo/MGI_MGI%3A1925308>)) Declaration(Class(<http://purl.obolibrary.org/obo/MGI_MGI%3A97765>)) Declaration(Class(<http://purl.obolibrary.org/obo/RefSeq#_NM_001379481>)) Declaration(Class(<http://purl.obolibrary.org/obo/PR_Q8VHX2>)) Declaration(Class(<http://purl.obolibrary.org/obo/MGI_MGI%3A105490>)) }
11:33:55 adding support ont Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/go/noctua/zfin.owl>) VersionIRI(<null>))) [Axioms: 1519613 Logical Axioms: 74806] First 20 axioms: {AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-041111-310> "sich211-212o1.2"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-030131-2843> "GDQH01002251"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-061212-2> "MF118581"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-030131-3758> "IPR000242"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-030131-3869> "ENSDARG00000074691"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-040426-1264> "PTHR14085"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-080204-87> "XM_005166173"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-091118-23> "PROSITE:PS50003"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-081031-107> "InterPro:IPR003599"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-030616-129> "ENSDARG00000024964"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-090313-86> "ZFIN:ZDB-GENE-090313-86"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-131121-265> "ZFIN:ZDB-GENE-131121-265"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-061103-553> "IPR017441"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-140106-251> "GenBank:EB925622"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-110411-28> "PF00059"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-061201-8> "RefSeq:XP_017212791"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-030131-2891> "Pfam:PF00076"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-050320-109> "PANTHER:PTHR24273"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-090313-277> "PF15911"^^xsd:string) AnnotationAssertion(<https://w3id.org/biolink/vocab/category> <http://purl.obolibrary.org/obo/ZFIN_ZDB-GENE-040426-1305> <https://w3id.org/biolink/vocab/GeneProduct>) }
11:33:57 adding support ont Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/go/noctua/rgd.owl>) VersionIRI(<null>))) [Axioms: 182641 Logical Axioms: 40828] First 20 axioms: {AnnotationAssertion(<https://w3id.org/biolink/vocab/category> <http://purl.obolibrary.org/obo/RGD_15004026> <https://w3id.org/biolink/vocab/MacromolecularMachine>) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/RGD_1332792> "RGD:1332792"^^xsd:string) AnnotationAssertion(<https://w3id.org/biolink/vocab/category> <http://purl.obolibrary.org/obo/RGD_69424> <https://w3id.org/biolink/vocab/MacromolecularMachine>) AnnotationAssertion(<https://w3id.org/biolink/vocab/category> <http://purl.obolibrary.org/obo/RGD_1308784> <https://w3id.org/biolink/vocab/GeneProduct>) AnnotationAssertion(<https://w3id.org/biolink/vocab/category> <http://purl.obolibrary.org/obo/RGD_1333370> <https://w3id.org/biolink/vocab/MacromolecularMachine>) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/RGD_1311751> "RGD:1311751"^^xsd:string) AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RGD_1305301> "Abce1 Rnor"^^xsd:string) AnnotationAssertion(<https://w3id.org/biolink/vocab/category> <http://purl.obolibrary.org/obo/RGD_620257> <https://w3id.org/biolink/vocab/MacromolecularMachine>) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/RGD_15003922> "RGD:15003922"^^xsd:string) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/RGD_1310427> "RGD:1310427"^^xsd:string) AnnotationAssertion(<https://w3id.org/biolink/vocab/category> <http://purl.obolibrary.org/obo/RGD_1595850> <https://w3id.org/biolink/vocab/GeneProduct>) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/RGD_1310207> "transmembrane protein 63c Rnor"^^xsd:string) AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "NCBITaxon:10116"^^xsd:string) <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/RGD_2319165> "Vps51"^^xsd:string) AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RGD_1306446> "Tmprss11g Rnor"^^xsd:string) AnnotationAssertion(<https://w3id.org/biolink/vocab/category> <http://purl.obolibrary.org/obo/UniProtKB_Q9JK11-1> <https://w3id.org/biolink/vocab/GeneProductIsoform>) AnnotationAssertion(<https://w3id.org/biolink/vocab/category> <http://purl.obolibrary.org/obo/RGD_1334155> <https://w3id.org/biolink/vocab/MacromolecularMachine>) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/RGD_1549742> "RGD:1549742"^^xsd:string) AnnotationAssertion(<https://w3id.org/biolink/vocab/category> <http://purl.obolibrary.org/obo/RGD_735182> <https://w3id.org/biolink/vocab/GeneProduct>) AnnotationAssertion(<https://w3id.org/biolink/vocab/category> <http://purl.obolibrary.org/obo/RGD_620696> <https://w3id.org/biolink/vocab/MacromolecularMachine>) AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/RGD_1560339> "leucine-rich repeat-containing G protein-coupled receptor 6 Rnor"^^xsd:string) }
11:33:58 adding support ont Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/go/noctua/dictybase.owl>) VersionIRI(<null>))) [Axioms: 152187 Logical Axioms: 25370] First 20 axioms: {SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0291972> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_44689>)) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0274845> <http://purl.obolibrary.org/obo/CHEBI_36080>) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0278063> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_44689>)) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0292640> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_44689>)) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0288921> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_44689>)) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0275179> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_44689>)) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0270994> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_44689>)) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0276285> <http://purl.obolibrary.org/obo/CHEBI_36080>) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0284991> <http://purl.obolibrary.org/obo/CHEBI_36080>) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0283517> <http://purl.obolibrary.org/obo/CHEBI_36080>) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0283701> <http://purl.obolibrary.org/obo/CHEBI_36080>) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0273281> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_44689>)) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0295077> <http://purl.obolibrary.org/obo/CHEBI_33695>) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0291452> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_44689>)) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0276829> <http://purl.obolibrary.org/obo/CHEBI_36080>) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0293184> <http://purl.obolibrary.org/obo/CHEBI_36080>) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0273955> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_44689>)) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0272436> <http://purl.obolibrary.org/obo/CHEBI_36080>) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0281877> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_44689>)) SubClassOf(<http://purl.obolibrary.org/obo/dictyBase#_DDB_G0294673> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_44689>)) }
11:33:59 adding support ont Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/go/noctua/fb.owl>) VersionIRI(<null>))) [Axioms: 122729 Logical Axioms: 28704] First 20 axioms: {Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0011656>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0031730>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0004106>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0028990>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0024229>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0037670>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0000114>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0038983>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0000668>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0033736>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0039765>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0050163>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0035073>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0259734>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0033348>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0033246>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0028965>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0264492>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0037305>)) Declaration(Class(<http://purl.obolibrary.org/obo/FB_FBgn0026089>)) }
11:34:01 adding support ont Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/go/noctua/tair.owl>) VersionIRI(<null>))) [Axioms: 261088 Logical Axioms: 61728] First 20 axioms: {Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2024316>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2082817>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2169253>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2103391>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2041076>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A6532566278>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2222637>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2051299>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2033163>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2044330>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2056936>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2153311>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2201861>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2019983>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2036992>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2145274>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2084420>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2140025>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2127378>)) Declaration(Class(<http://purl.obolibrary.org/obo/TAIR_locus%3A2061006>)) }
11:34:02 [Fatal Error] :1:1: Content is not allowed in prolog.
11:34:02 2021-05-24 11:34:02,183 ERROR (CommandRunner:4815) could not parse:target/neo-wb.obo
11:34:02 org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/var/lib/jenkins/workspace/ology_pipeline_issue-35-neo-test/neo/target/neo-wb.obo
11:34:02 Could not parse ontology. Either a suitable parser could not be found, or parsing failed. See parser logs below for explanation.
11:34:02 The following parsers were tried:
11:34:02 1) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@44dcf709
11:34:02 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@7da4aade
11:34:02 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@2c105677
11:34:02 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
11:34:02 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@1d1d30c0
11:34:02 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad
11:34:02 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3
11:34:02 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c
11:34:02 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36
11:34:02 10) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d
11:34:02 11) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493
11:34:02 12) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc
11:34:02 13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5
11:34:02 14) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@663bbc4
11:34:02 15) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d
11:34:02 16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@371cc546
11:34:02 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@5db1f375
11:34:02 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d
11:34:02
11:34:02
11:34:02 Detailed logs:
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@44dcf709
11:34:02 Stack trace:
11:34:02 org.xml.sax.SAXParseException; systemId: file:/var/lib/jenkins/workspace/ology_pipeline_issue-35-neo-test/neo/target/neo-wb.obo; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:78)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 Content is not allowed in prolog. com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:203)
11:34:02 com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:177)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:400)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1473)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:994)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
11:34:02 com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@7da4aade
11:34:02 Stack trace:
11:34:02 org.xml.sax.SAXParseException; systemId: file:/var/lib/jenkins/workspace/ology_pipeline_issue-35-neo-test/neo/target/neo-wb.obo; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:70)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 Content is not allowed in prolog. com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:203)
11:34:02 com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:177)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:400)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1473)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:994)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
11:34:02 com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@2c105677
11:34:02 Stack trace:
11:34:02 Encountered " <PNAME_NS> "ontology: "" at line 1, column 1.
11:34:02 Was expecting one of:
11:34:02 "Ontology" ...
11:34:02 "Prefix" ...
11:34:02 (Line 0) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:94)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 Encountered " <PNAME_NS> "ontology: "" at line 1, column 1.
11:34:02 Was expecting one of:
11:34:02 "Ontology" ...
11:34:02 "Prefix" ...
11:34:02 org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.generateParseException(OWLFunctionalSyntaxParser.java:3443)
11:34:02 org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.jj_consume_token(OWLFunctionalSyntaxParser.java:3363)
11:34:02 org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.Ontology(OWLFunctionalSyntaxParser.java:192)
11:34:02 org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.parse(OWLFunctionalSyntaxParser.java:171)
11:34:02 org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:92)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
11:34:02 Stack trace:
11:34:02 org.openrdf.rio.RDFParseException: Namespace prefix 'ontology' used but not defined [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 Namespace prefix 'ontology' used but not defined [line 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
11:34:02 org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
11:34:02 org.openrdf.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1366)
11:34:02 org.openrdf.rio.helpers.RDFParserBase.getNamespace(RDFParserBase.java:369)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parseQNameOrBoolean(TurtleParser.java:1039)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:617)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parseSubject(TurtleParser.java:448)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:382)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:260)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@1d1d30c0
11:34:02 Stack trace:
11:34:02 Encountered 'ontology: go/noctua/wb' at line 1 column 1. Expected either 'Ontology:' or 'Prefix:' (Line 1) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser.parse(ManchesterOWLSyntaxOntologyParser.java:120)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad
11:34:02 Stack trace:
11:34:02 org.openrdf.rio.RDFParseException: Expected '<' or '_', found: o [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 Expected '<' or '_', found: o [line 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
11:34:02 org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
11:34:02 org.openrdf.rio.ntriples.NTriplesParser.reportFatalError(NTriplesParser.java:648)
11:34:02 org.openrdf.rio.ntriples.NTriplesParser.parseSubject(NTriplesParser.java:348)
11:34:02 org.openrdf.rio.nquads.NQuadsParser.parseQuad(NQuadsParser.java:123)
11:34:02 org.openrdf.rio.nquads.NQuadsParser.parse(NQuadsParser.java:102)
11:34:02 org.openrdf.rio.nquads.NQuadsParser.parse(NQuadsParser.java:60)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3
11:34:02 Stack trace:
11:34:02 org.openrdf.rio.RDFParseException: Found IOException during parsing [line 1, column 9] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 Found IOException during parsing [line 1, column 9] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
11:34:02 org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
11:34:02 org.openrdf.rio.rdfjson.RDFJSONParser.reportFatalError(RDFJSONParser.java:155)
11:34:02 org.openrdf.rio.rdfjson.RDFJSONParser.parse(RDFJSONParser.java:96)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c
11:34:02 Stack trace:
11:34:02 org.openrdf.rio.RDFParseException: Namespace prefix 'ontology' used but not defined [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 Namespace prefix 'ontology' used but not defined [line 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
11:34:02 org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
11:34:02 org.openrdf.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1366)
11:34:02 org.openrdf.rio.helpers.RDFParserBase.getNamespace(RDFParserBase.java:369)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parseQNameOrBoolean(TurtleParser.java:1039)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:617)
11:34:02 org.openrdf.rio.trig.TriGParser.parseGraph(TriGParser.java:132)
11:34:02 org.openrdf.rio.trig.TriGParser.parseStatement(TriGParser.java:119)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:159)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36
11:34:02 Stack trace:
11:34:02 org.openrdf.rio.RDFParseException: Expected '<' or '_', found: o [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 Expected '<' or '_', found: o [line 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
11:34:02 org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
11:34:02 org.openrdf.rio.ntriples.NTriplesParser.reportFatalError(NTriplesParser.java:648)
11:34:02 org.openrdf.rio.ntriples.NTriplesParser.parseSubject(NTriplesParser.java:348)
11:34:02 org.openrdf.rio.ntriples.NTriplesParser.parseTriple(NTriplesParser.java:280)
11:34:02 org.openrdf.rio.ntriples.NTriplesParser.parse(NTriplesParser.java:191)
11:34:02 org.openrdf.rio.ntriples.NTriplesParser.parse(NTriplesParser.java:130)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d
11:34:02 Stack trace:
11:34:02 org.openrdf.rio.RDFParseException: Could not parse JSONLD org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 Could not parse JSONLD com.github.jsonldjava.sesame.SesameJSONLDParser.parse(SesameJSONLDParser.java:69)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 Unrecognized token 'ontology': was expecting ('true', 'false' or 'null')
11:34:02 at [Source: java.io.BufferedReader@8c66097; line: 1, column: 9] com.fasterxml.jackson.core.JsonParser._constructError(JsonParser.java:1702)
11:34:02 com.fasterxml.jackson.core.base.ParserMinimalBase._reportError(ParserMinimalBase.java:558)
11:34:02 com.fasterxml.jackson.core.json.ReaderBasedJsonParser._reportInvalidToken(ReaderBasedJsonParser.java:2835)
11:34:02 com.fasterxml.jackson.core.json.ReaderBasedJsonParser._handleOddValue(ReaderBasedJsonParser.java:1903)
11:34:02 com.fasterxml.jackson.core.json.ReaderBasedJsonParser.nextToken(ReaderBasedJsonParser.java:749)
11:34:02 com.github.jsonldjava.utils.JsonUtils.fromReader(JsonUtils.java:123)
11:34:02 com.github.jsonldjava.utils.JsonUtils.fromInputStream(JsonUtils.java:103)
11:34:02 com.github.jsonldjava.utils.JsonUtils.fromInputStream(JsonUtils.java:81)
11:34:02 com.github.jsonldjava.sesame.SesameJSONLDParser.parse(SesameJSONLDParser.java:65)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493
11:34:02 Stack trace:
11:34:02 org.openrdf.rio.RDFParseException: File does not contain a binary RDF document org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 File does not contain a binary RDF document org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
11:34:02 org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:424)
11:34:02 org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:693)
11:34:02 org.openrdf.rio.binary.BinaryRDFParser.parse(BinaryRDFParser.java:87)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc
11:34:02 Stack trace:
11:34:02 org.openrdf.rio.RDFParseException: Content is not allowed in prolog. [line 1, column 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 Content is not allowed in prolog. [line 1, column 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
11:34:02 org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
11:34:02 org.openrdf.rio.rdfxml.RDFXMLParser.reportFatalError(RDFXMLParser.java:1286)
11:34:02 org.openrdf.rio.rdfxml.RDFXMLParser.fatalError(RDFXMLParser.java:1443)
11:34:02 com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:180)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:400)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1473)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:994)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5
11:34:02 Stack trace:
11:34:02 org.openrdf.rio.RDFParseException: Namespace prefix 'ontology' used but not defined [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 Namespace prefix 'ontology' used but not defined [line 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
11:34:02 org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
11:34:02 org.openrdf.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1366)
11:34:02 org.openrdf.rio.helpers.RDFParserBase.getNamespace(RDFParserBase.java:369)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parseQNameOrBoolean(TurtleParser.java:1039)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:617)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parseSubject(TurtleParser.java:448)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:382)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:260)
11:34:02 org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@663bbc4
11:34:02 Stack trace:
11:34:02 org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered "" at line 1, column 1.
11:34:02 Was expecting one of:
11:34:02 org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:105)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 Encountered "" at line 1, column 1.
11:34:02 Was expecting one of:
11:34:02 org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.generateParseException(TurtleParser.java:1548)
11:34:02 org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.jj_consume_token(TurtleParser.java:1430)
11:34:02 org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.parseDocument(TurtleParser.java:153)
11:34:02 org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:98)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d
11:34:02 Stack trace:
11:34:02 org.openrdf.rio.RDFParseException: Content is not allowed in prolog. [line 1, column 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 Content is not allowed in prolog. [line 1, column 1] org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487)
11:34:02 org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737)
11:34:02 org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123)
11:34:02 org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90)
11:34:02 org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 Content is not allowed in prolog. com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:203)
11:34:02 com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:177)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:400)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1473)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:994)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112)
11:34:02 com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
11:34:02 com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:842)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@371cc546
11:34:02 Stack trace:
11:34:02 LINENO: 104844 -
11:34:02 LINE: relationship: in_taxon org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 LINENO: 104844 -
11:34:02 LINE: relationship: in_taxon org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1465)
11:34:02 org.obolibrary.oboformat.parser.OBOFormatParser.parseIdRef(OBOFormatParser.java:883)
11:34:02 org.obolibrary.oboformat.parser.OBOFormatParser.parseIdRef(OBOFormatParser.java:877)
11:34:02 org.obolibrary.oboformat.parser.OBOFormatParser.parseRelationship(OBOFormatParser.java:992)
11:34:02 org.obolibrary.oboformat.parser.OBOFormatParser.parseTermFrameClause(OBOFormatParser.java:667)
11:34:02 org.obolibrary.oboformat.parser.OBOFormatParser.parseTermFrameClauseEOL(OBOFormatParser.java:598)
11:34:02 org.obolibrary.oboformat.parser.OBOFormatParser.parseTermFrame(OBOFormatParser.java:572)
11:34:02 org.obolibrary.oboformat.parser.OBOFormatParser.parseEntityFrame(OBOFormatParser.java:539)
11:34:02 org.obolibrary.oboformat.parser.OBOFormatParser.parseOBODoc(OBOFormatParser.java:349)
11:34:02 org.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:307)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@5db1f375
11:34:02 Stack trace:
11:34:02 org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " <NAME> "ontology: "" at line 1, column 1.
11:34:02 Was expecting:
11:34:02 <EOF>
11:34:02 org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:289)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 Encountered " <NAME> "ontology: "" at line 1, column 1.
11:34:02 Was expecting:
11:34:02 <EOF>
11:34:02 org.semanticweb.owlapi.krss2.parser.KRSS2Parser.generateParseException(KRSS2Parser.java:3187)
11:34:02 org.semanticweb.owlapi.krss2.parser.KRSS2Parser.jj_consume_token(KRSS2Parser.java:3040)
11:34:02 org.semanticweb.owlapi.krss2.parser.KRSS2Parser.parse(KRSS2Parser.java:141)
11:34:02 org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:286)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02
11:34:02
11:34:02 --------------------------------------------------------------------------------
11:34:02 Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d
11:34:02 Stack trace:
11:34:02 org.openrdf.rio.RDFParseException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:111)
11:34:02 org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:95)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. org.semarglproject.rdf.rdfa.RdfaParser.processException(RdfaParser.java:1141)
11:34:02 org.semarglproject.source.XmlSource.process(XmlSource.java:50)
11:34:02 org.semarglproject.source.StreamProcessor.processInternal(StreamProcessor.java:87)
11:34:02 org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:167)
11:34:02 org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:154)
11:34:02 org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:109)
11:34:02 org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:95)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02 Content is not allowed in prolog. com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1239)
11:34:02 org.semarglproject.source.XmlSource.process(XmlSource.java:48)
11:34:02 org.semarglproject.source.StreamProcessor.processInternal(StreamProcessor.java:87)
11:34:02 org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:167)
11:34:02 org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:154)
11:34:02 org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:109)
11:34:02 org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:95)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
11:34:02 org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
11:34:02 uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
11:34:02
11:34:02
11:34:02
11:34:02 at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:257)
11:34:02 at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
11:34:02 at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
11:34:02 at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1108)
11:34:02 at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1064)
11:34:02 at owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:163)
11:34:02 at owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:150)
11:34:02 at owltools.io.ParserWrapper.parseOBO(ParserWrapper.java:136)
11:34:02 at owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4801)
11:34:02 at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:76)
11:34:02 at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:68)
11:34:02 at owltools.cli.CommandLineInterface.main(CommandLineInterface.java:12)
11:34:02 Makefile:27: recipe for target 'neo.obo' failed
11:34:02 make: *** [neo.obo] Error 1
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