Started by upstream project "hpo.annotations" build number 1248 originally caused by: Started by upstream project "hpo" build number 1706 originally caused by: Started by user koehler Building in workspace /var/lib/jenkins/jobs/hpo.annotations.monthly/workspace Cleaning local Directory . Checking out https://github.com/monarch-initiative/hpo-annotation-data/trunk/util@HEAD at revision HEAD A annotation A annotation/.gitignore A annotation/external_data.txt A annotation/makefile A tools A tools/annotationupdate A tools/annotationupdate/external_data.txt A tools/annotationupdate/jar A tools/annotationupdate/jar/SuggestAnnotations.jar A tools/annotationupdate/makefile A tools/gene2phenotype A tools/gene2phenotype/createGene2Phenotype.jar A tools/hpo_mysqldb A tools/hpo_mysqldb/createMysqlHPODbVersion.jar A tools/hpo_mysqldb/schemabackup_2010-06-18.sql At revision 4748 no change for https://github.com/monarch-initiative/hpo-annotation-data/trunk/util since the previous build [workspace] $ /bin/sh -xe /tmp/jenkins7367094617012013136.sh + make -C annotation make: Entering directory '/var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation' mkdir -p data #some cleanup beforehand rm -f data/hp.obo rm -f data/phenotype_annotation.tab rm -f data/mim2* # Employ wget to retrieve data from NCBI/OMIM, Orphanet, HPO stuff. # File are listed in external_data.txt. We also ignore lines starting with "#" cd data ; cat ../external_data.txt | sed "/^#.*$/d" | wget --retry-connrefused -N -i - --2017-12-12 13:55:50-- ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/mim2gene_medgen Resolving proxy.charite.de (proxy.charite.de)... 141.42.1.215 Connecting to proxy.charite.de (proxy.charite.de)|141.42.1.215|:8080... connected. Proxy request sent, awaiting response... 200 OK Length: 754939 (737K) [text/plain] Saving to: ‘mim2gene_medgen’ 0K .......... .......... .......... .......... .......... 6% 20.7M 0s 50K .......... .......... .......... .......... .......... 13% 21.7M 0s 100K .......... .......... .......... .......... .......... 20% 23.3M 0s 150K .......... .......... .......... .......... .......... 27% 38.1M 0s 200K .......... .......... .......... .......... .......... 33% 23.3M 0s 250K .......... .......... .......... .......... .......... 40% 36.7M 0s 300K .......... .......... .......... .......... .......... 47% 30.0M 0s 350K .......... .......... .......... .......... .......... 54% 26.5M 0s 400K .......... .......... .......... .......... .......... 61% 37.4M 0s 450K .......... .......... .......... .......... .......... 67% 41.2M 0s 500K .......... .......... .......... .......... .......... 74% 26.3M 0s 550K .......... .......... .......... .......... .......... 81% 47.3M 0s 600K .......... .......... .......... .......... .......... 88% 35.3M 0s 650K .......... .......... .......... .......... .......... 94% 43.9M 0s 700K .......... .......... .......... ....... 100% 120M=0.02s 2017-12-12 13:55:53 (31.2 MB/s) - ‘mim2gene_medgen’ saved [754939/754939] --2017-12-12 13:55:53-- ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz Reusing existing connection to proxy.charite.de:8080. Proxy request sent, awaiting response... 200 OK Length: 2883761 (2.8M) [text/plain] Saving to: ‘Homo_sapiens.gene_info.gz’ 0K .......... .......... .......... .......... .......... 1% 21.5M 0s 50K .......... .......... .......... .......... .......... 3% 41.4M 0s 100K .......... .......... .......... .......... .......... 5% 209K 4s 150K .......... .......... .......... .......... .......... 7% 42.0M 3s 200K .......... .......... .......... .......... .......... 8% 44.9M 3s 250K .......... .......... .......... .......... .......... 10% 36.1M 2s 300K .......... .......... .......... .......... .......... 12% 45.4M 2s 350K .......... .......... .......... .......... .......... 14% 89.4M 1s 400K .......... .......... .......... .......... .......... 15% 45.4M 1s 450K .......... .......... .......... .......... .......... 17% 47.5M 1s 500K .......... .......... .......... .......... .......... 19% 47.0M 1s 550K .......... .......... .......... .......... .......... 21% 99.4M 1s 600K .......... .......... .......... .......... .......... 23% 47.3M 1s 650K .......... .......... .......... .......... .......... 24% 48.1M 1s 700K .......... .......... .......... .......... .......... 26% 58.8M 1s 750K .......... .......... .......... .......... .......... 28% 62.6M 1s 800K .......... .......... .......... .......... .......... 30% 54.8M 1s 850K .......... .......... .......... .......... .......... 31% 55.4M 1s 900K .......... .......... .......... .......... .......... 33% 84.4M 1s 950K .......... .......... .......... .......... .......... 35% 62.4M 0s 1000K .......... .......... .......... .......... .......... 37% 77.6M 0s 1050K .......... .......... .......... .......... .......... 39% 51.2M 0s 1100K .......... .......... .......... .......... .......... 40% 52.5M 0s 1150K .......... .......... .......... .......... .......... 42% 111M 0s 1200K .......... .......... .......... .......... .......... 44% 56.3M 0s 1250K .......... .......... .......... .......... .......... 46% 89.5M 0s 1300K .......... .......... .......... .......... .......... 47% 68.2M 0s 1350K .......... .......... .......... .......... .......... 49% 73.5M 0s 1400K .......... .......... .......... .......... .......... 51% 71.5M 0s 1450K .......... .......... .......... .......... .......... 53% 88.3M 0s 1500K .......... .......... .......... .......... .......... 55% 65.5M 0s 1550K .......... .......... .......... .......... .......... 56% 95.3M 0s 1600K .......... .......... .......... .......... .......... 58% 91.1M 0s 1650K .......... .......... .......... .......... .......... 60% 78.5M 0s 1700K .......... .......... .......... .......... .......... 62% 76.5M 0s 1750K .......... .......... .......... .......... .......... 63% 75.3M 0s 1800K .......... .......... .......... .......... .......... 65% 74.3M 0s 1850K .......... .......... .......... .......... .......... 67% 113M 0s 1900K .......... .......... .......... .......... .......... 69% 85.9M 0s 1950K .......... .......... .......... .......... .......... 71% 85.8M 0s 2000K .......... .......... .......... .......... .......... 72% 90.6M 0s 2050K .......... .......... .......... .......... .......... 74% 112M 0s 2100K .......... .......... .......... .......... .......... 76% 72.7M 0s 2150K .......... .......... .......... .......... .......... 78% 113M 0s 2200K .......... .......... .......... .......... .......... 79% 64.6M 0s 2250K .......... .......... .......... .......... .......... 81% 100M 0s 2300K .......... .......... .......... .......... .......... 83% 103M 0s 2350K .......... .......... .......... .......... .......... 85% 81.2M 0s 2400K .......... .......... .......... .......... .......... 86% 115M 0s 2450K .......... .......... .......... .......... .......... 88% 79.9M 0s 2500K .......... .......... .......... .......... .......... 90% 115M 0s 2550K .......... .......... .......... .......... .......... 92% 95.0M 0s 2600K .......... .......... .......... .......... .......... 94% 88.1M 0s 2650K .......... .......... .......... .......... .......... 95% 115M 0s 2700K .......... .......... .......... .......... .......... 97% 88.6M 0s 2750K .......... .......... .......... .......... .......... 99% 111M 0s 2800K .......... ...... 100% 97.8M=0.3s 2017-12-12 13:55:57 (9.82 MB/s) - ‘Homo_sapiens.gene_info.gz’ saved [2883761/2883761] --2017-12-12 13:55:57-- http://www.orphadata.org/data/xml/en_product6.xml Reusing existing connection to proxy.charite.de:8080. 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99% 113M 0s 18100K .......... .......... .......... .......... .......... 99% 113M 0s 18150K .......... .......... .......... ...... 100% 72.7M=1.2s 2017-12-12 13:55:58 (14.6 MB/s) - ‘en_product6.xml’ saved [18623277/18623277] --2017-12-12 13:55:58-- http://compbio.charite.de/jenkins/job/hpo.annotations/lastSuccessfulBuild/artifact/misc/phenotype_annotation.tab Reusing existing connection to proxy.charite.de:8080. Proxy request sent, awaiting response... 200 OK Length: 18896952 (18M) [application/octet-stream] Saving to: ‘phenotype_annotation.tab’ 0K .......... .......... .......... .......... .......... 0% 23.6M 1s 50K .......... .......... .......... .......... .......... 0% 28.8M 1s 100K .......... .......... .......... .......... .......... 0% 11.4M 1s 150K .......... .......... .......... .......... .......... 1% 7.84M 1s 200K .......... .......... .......... .......... .......... 1% 66.6M 1s 250K .......... .......... .......... .......... .......... 1% 77.3M 1s 300K .......... .......... .......... .......... .......... 1% 88.6M 1s 350K .......... .......... .......... .......... .......... 2% 14.6M 1s 400K .......... .......... .......... .......... .......... 2% 90.3M 1s 450K .......... .......... .......... .......... .......... 2% 63.9M 1s 500K .......... .......... .......... .......... .......... 2% 44.3M 1s 550K .......... .......... .......... .......... .......... 3% 10.5M 1s 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18100K .......... .......... .......... .......... .......... 98% 91.5M 0s 18150K .......... .......... .......... .......... .......... 98% 116M 0s 18200K .......... .......... .......... .......... .......... 98% 113M 0s 18250K .......... .......... .......... .......... .......... 99% 99.1M 0s 18300K .......... .......... .......... .......... .......... 99% 113M 0s 18350K .......... .......... .......... .......... .......... 99% 119M 0s 18400K .......... .......... .......... .......... .......... 99% 89.7M 0s 18450K .... 100% 98.8M=0.4s 2017-12-12 13:55:59 (48.4 MB/s) - ‘phenotype_annotation.tab’ saved [18896952/18896952] --2017-12-12 13:55:59-- http://purl.obolibrary.org/obo/hp.obo Reusing existing connection to proxy.charite.de:8080. Proxy request sent, awaiting response... 302 Found Location: https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo [following] --2017-12-12 13:55:59-- https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo Connecting to proxy.charite.de (proxy.charite.de)|141.42.1.215|:8080... connected. Proxy request sent, awaiting response... 200 OK Length: 5738327 (5.5M) [text/plain] Saving to: ‘hp.obo’ 0K .......... .......... .......... .......... .......... 0% 2.05M 3s 50K .......... .......... .......... .......... .......... 1% 4.68M 2s 100K .......... .......... .......... .......... .......... 2% 12.4M 1s 150K .......... .......... .......... .......... .......... 3% 7.08M 1s 200K .......... .......... .......... .......... .......... 4% 11.2M 1s 250K .......... .......... .......... .......... .......... 5% 8.43M 1s 300K .......... .......... .......... .......... .......... 6% 10.3M 1s 350K .......... .......... .......... .......... .......... 7% 7.65M 1s 400K .......... .......... .......... .......... .......... 8% 9.10M 1s 450K .......... .......... .......... .......... .......... 8% 12.2M 1s 500K .......... .......... .......... .......... .......... 9% 7.83M 1s 550K .......... .......... .......... .......... .......... 10% 17.4M 1s 600K .......... .......... 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4000K .......... .......... .......... .......... .......... 72% 10.9M 0s 4050K .......... .......... .......... .......... .......... 73% 101M 0s 4100K .......... .......... .......... .......... .......... 74% 16.4M 0s 4150K .......... .......... .......... .......... .......... 74% 38.4M 0s 4200K .......... .......... .......... .......... .......... 75% 101M 0s 4250K .......... .......... .......... .......... .......... 76% 24.2M 0s 4300K .......... .......... .......... .......... .......... 77% 17.7M 0s 4350K .......... .......... .......... .......... .......... 78% 39.3M 0s 4400K .......... .......... .......... .......... .......... 79% 24.9M 0s 4450K .......... .......... .......... .......... .......... 80% 33.4M 0s 4500K .......... .......... .......... .......... .......... 81% 28.6M 0s 4550K .......... .......... .......... .......... .......... 82% 31.0M 0s 4600K .......... .......... .......... .......... .......... 82% 14.4M 0s 4650K .......... .......... .......... .......... .......... 83% 67.9M 0s 4700K .......... .......... .......... .......... .......... 84% 27.1M 0s 4750K .......... .......... .......... .......... .......... 85% 29.6M 0s 4800K .......... .......... .......... .......... .......... 86% 25.9M 0s 4850K .......... .......... .......... .......... .......... 87% 37.2M 0s 4900K .......... .......... .......... .......... .......... 88% 20.3M 0s 4950K .......... .......... .......... .......... .......... 89% 16.6M 0s 5000K .......... .......... .......... .......... .......... 90% 22.8M 0s 5050K .......... .......... .......... .......... .......... 91% 28.0M 0s 5100K .......... .......... .......... .......... .......... 91% 31.3M 0s 5150K .......... .......... .......... .......... .......... 92% 76.7M 0s 5200K .......... .......... .......... .......... .......... 93% 49.0M 0s 5250K .......... .......... .......... .......... .......... 94% 30.0M 0s 5300K .......... .......... .......... .......... .......... 95% 11.7M 0s 5350K .......... .......... .......... .......... .......... 96% 37.4M 0s 5400K .......... .......... .......... .......... .......... 97% 52.0M 0s 5450K .......... .......... .......... .......... .......... 98% 77.0M 0s 5500K .......... .......... .......... .......... .......... 99% 36.7M 0s 5550K .......... .......... .......... .......... .......... 99% 52.4M 0s 5600K ... 100% 7315G=0.3s Last-modified header missing -- time-stamps turned off. 2017-12-12 13:55:59 (15.7 MB/s) - ‘hp.obo’ saved [5738327/5738327] FINISHED --2017-12-12 13:55:59-- Total wall clock time: 9.2s Downloaded: 5 files, 45M in 2.2s (20.0 MB/s) java -Xmx1G -jar ../tools/gene2phenotype/createGene2Phenotype.jar --data "data" --out-folder "." User defined parameters set to: hpo path: /var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation/data/hp.obo (exists: true) out path: /var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation/. (exists: true) data path: /var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation/data (exists: true) parse: /var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation/data/hp.obo Dec 12, 2017 1:56:00 PM ontologizer.go.OBOParser doParse INFO: Got 13201 terms and 16835 relations in 166 ms Details of parsed obo file: data-version: releases/2017-12-12 format: 1.2 term definitions: 13201 Dec 12, 2017 1:56:00 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot INFO: Ontology contains a single level-one term (All (HP:0000001) Dec 12, 2017 1:56:00 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118) WARN: Frequency of 3913 terms was zero!! Set IC of these to : 9.230535079261703 mims:10298 with inh: 6910 parse NCBI summary of gene_info-file other: 864 tRNA: 599 rRNA: 59 scRNA: 4 biological-region: 1867 protein-coding: 20463 ncRNA: 17702 pseudo: 16390 snRNA: 64 snoRNA: 541 unknown: 1762 entrez2symbol size: 42163 there were 2 unidentified gene-IDs: [107305681, 2439] diseaseid-to-entrezid: 4596 ORPHANETPARSING: orphadisease2HGNCgenes:3658 ORPHANETPARSING: hgncid2entrez:27342 there were 30 unmappable HGNC-IDs: [3082, 14252, 37475, 21340, 3101, 33472, 30161, 22993, 34382, 22433, 35416, 31376, 39436, 32944, 17204, 3777, 12599, 26071, 20684, 14260, 33240, 43726, 25855, 8141, 43724, 32314, 33445, 16706, 33485, 13730] diseaseId2entry.size(): 10298 omim: 7323 orphanet: 2928 others: 47 Disease entries with at least one known disease gene: 5825 Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 10204 generating files for source-filter: OMIM and frequency-filter: FREQUENT_FEATURES debug disease = DiseaseEntry [diseaseId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0] annotations was null generating files for source-filter: OMIM and frequency-filter: ALL_FREQUENCIES debug disease = DiseaseEntry [diseaseId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0] annotations was null generating files for source-filter: ORPHA and frequency-filter: FREQUENT_FEATURES annotation: Sensorineural hearing impairment (HP:0000407) orphadata 0.12 filters: true/false annotation: Conjunctivitis (HP:0000509) orphadata 0.12 filters: true/false annotation: Hyperhidrosis (HP:0000975) orphadata 0.9 filters: true/true annotation: Pruritus (HP:0000989) orphadata 0.9 filters: true/true annotation: Urticaria (HP:0001025) orphadata 0.9 filters: true/true annotation: Arthritis (HP:0001369) orphadata 0.9 filters: true/true annotation: Dehydration (HP:0001944) orphadata 0.12 filters: true/false annotation: Fever (HP:0001945) orphadata 0.9 filters: true/true annotation: Polydipsia (HP:0001959) orphadata 0.12 filters: true/false annotation: Nausea and vomiting (HP:0002017) orphadata 0.5 filters: true/true annotation: Abdominal pain (HP:0002027) orphadata 0.12 filters: true/false annotation: Headache (HP:0002315) orphadata 0.5 filters: true/true annotation: Arthralgia (HP:0002829) orphadata 0.12 filters: true/false annotation: Myalgia (HP:0003326) orphadata 0.9 filters: true/true annotation: Erythema (HP:0010783) orphadata 0.9 filters: true/true annotation: Fatigue (HP:0012378) orphadata 0.9 filters: true/true annotation: Dysesthesia (HP:0012534) orphadata 0.9 filters: true/true debug disease = DiseaseEntry [diseaseId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0] annotations was null generating files for source-filter: ORPHA and frequency-filter: ALL_FREQUENCIES annotation: Sensorineural hearing impairment (HP:0000407) orphadata 0.12 filters: true/true annotation: Conjunctivitis (HP:0000509) orphadata 0.12 filters: true/true annotation: Hyperhidrosis (HP:0000975) orphadata 0.9 filters: true/true annotation: Pruritus (HP:0000989) orphadata 0.9 filters: true/true annotation: Urticaria (HP:0001025) orphadata 0.9 filters: true/true annotation: Arthritis (HP:0001369) orphadata 0.9 filters: true/true annotation: Dehydration (HP:0001944) orphadata 0.12 filters: true/true annotation: Fever (HP:0001945) orphadata 0.9 filters: true/true annotation: Polydipsia (HP:0001959) orphadata 0.12 filters: true/true annotation: Nausea and vomiting (HP:0002017) orphadata 0.5 filters: true/true annotation: Abdominal pain (HP:0002027) orphadata 0.12 filters: true/true annotation: Headache (HP:0002315) orphadata 0.5 filters: true/true annotation: Arthralgia (HP:0002829) orphadata 0.12 filters: true/true annotation: Myalgia (HP:0003326) orphadata 0.9 filters: true/true annotation: Erythema (HP:0010783) orphadata 0.9 filters: true/true annotation: Fatigue (HP:0012378) orphadata 0.9 filters: true/true annotation: Dysesthesia (HP:0012534) orphadata 0.9 filters: true/true debug disease = DiseaseEntry [diseaseId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0] annotations was null generating files for source-filter: ALL_SOURCES and frequency-filter: FREQUENT_FEATURES annotation: Sensorineural hearing impairment (HP:0000407) orphadata 0.12 filters: true/false annotation: Conjunctivitis (HP:0000509) orphadata 0.12 filters: true/false annotation: Hyperhidrosis (HP:0000975) orphadata 0.9 filters: true/true annotation: Pruritus (HP:0000989) orphadata 0.9 filters: true/true annotation: Urticaria (HP:0001025) orphadata 0.9 filters: true/true annotation: Arthritis (HP:0001369) orphadata 0.9 filters: true/true annotation: Dehydration (HP:0001944) orphadata 0.12 filters: true/false annotation: Fever (HP:0001945) orphadata 0.9 filters: true/true annotation: Polydipsia (HP:0001959) orphadata 0.12 filters: true/false annotation: Nausea and vomiting (HP:0002017) orphadata 0.5 filters: true/true annotation: Abdominal pain (HP:0002027) orphadata 0.12 filters: true/false annotation: Headache (HP:0002315) orphadata 0.5 filters: true/true annotation: Arthralgia (HP:0002829) orphadata 0.12 filters: true/false annotation: Myalgia (HP:0003326) orphadata 0.9 filters: true/true annotation: Erythema (HP:0010783) orphadata 0.9 filters: true/true annotation: Fatigue (HP:0012378) orphadata 0.9 filters: true/true annotation: Dysesthesia (HP:0012534) orphadata 0.9 filters: true/true debug disease = DiseaseEntry [diseaseId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0] annotations was null generating files for source-filter: ALL_SOURCES and frequency-filter: ALL_FREQUENCIES annotation: Sensorineural hearing impairment (HP:0000407) orphadata 0.12 filters: true/true annotation: Conjunctivitis (HP:0000509) orphadata 0.12 filters: true/true annotation: Hyperhidrosis (HP:0000975) orphadata 0.9 filters: true/true annotation: Pruritus (HP:0000989) orphadata 0.9 filters: true/true annotation: Urticaria (HP:0001025) orphadata 0.9 filters: true/true annotation: Arthritis (HP:0001369) orphadata 0.9 filters: true/true annotation: Dehydration (HP:0001944) orphadata 0.12 filters: true/true annotation: Fever (HP:0001945) orphadata 0.9 filters: true/true annotation: Polydipsia (HP:0001959) orphadata 0.12 filters: true/true annotation: Nausea and vomiting (HP:0002017) orphadata 0.5 filters: true/true annotation: Abdominal pain (HP:0002027) orphadata 0.12 filters: true/true annotation: Headache (HP:0002315) orphadata 0.5 filters: true/true annotation: Arthralgia (HP:0002829) orphadata 0.12 filters: true/true annotation: Myalgia (HP:0003326) orphadata 0.9 filters: true/true annotation: Erythema (HP:0010783) orphadata 0.9 filters: true/true annotation: Fatigue (HP:0012378) orphadata 0.9 filters: true/true annotation: Dysesthesia (HP:0012534) orphadata 0.9 filters: true/true debug disease = DiseaseEntry [diseaseId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0] annotations was null java -Xmx1G -jar ../tools/hpo_mysqldb/createMysqlHPODbVersion.jar --data "data" --out-folder "." --database-schema "../tools/hpo_mysqldb/schemabackup_2010-06-18.sql" --mysql-user "hudson_mysql" --mysql-password "hpo_hudson" --mysql-host "localhost" --mysql-port "3306" loading ontology and annotations loading: data/hp.obo parse: data/hp.obo Dec 12, 2017 1:56:14 PM ontologizer.go.OBOParser doParse INFO: Got 13201 terms and 16835 relations in 134 ms Details of parsed obo file: data-version: releases/2017-12-12 format: 1.2 term definitions: 13201 Dec 12, 2017 1:56:14 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot INFO: Ontology contains a single level-one term (All (HP:0000001) Dec 12, 2017 1:56:15 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118) WARN: Frequency of 3913 terms was zero!! Set IC of these to : 9.230535079261703 mims:10298 with inh: 6910 parse NCBI summary of gene_info-file other: 864 tRNA: 599 rRNA: 59 scRNA: 4 biological-region: 1867 protein-coding: 20463 ncRNA: 17702 pseudo: 16390 snRNA: 64 snoRNA: 541 unknown: 1762 entrez2symbol size: 42163 there were 2 unidentified gene-IDs: [107305681, 2439] diseaseid-to-entrezid: 4596 ORPHANETPARSING: orphadisease2HGNCgenes:3658 ORPHANETPARSING: hgncid2entrez:27342 there were 30 unmappable HGNC-IDs: [3082, 14252, 37475, 21340, 3101, 33472, 30161, 22993, 34382, 22433, 35416, 31376, 39436, 32944, 17204, 3777, 12599, 26071, 20684, 14260, 33240, 43726, 25855, 8141, 43724, 32314, 33445, 16706, 33485, 13730] diseaseId2entry.size(): 10298 omim: 7323 orphanet: 2928 others: 47 Disease entries with at least one known disease gene: 5825 Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 10204 12_2017 make connection / created db connecting to jdbc:mysql://localhost:3306/mysql dropping database: MYHPO_12_2017 (if exists) creating database: MYHPO_12_2017 create schema (tables, relations) Execute: [mysql, --user=hudson_mysql, --password=hpo_hudson, --host=localhost, --port=3306, MYHPO_12_2017, -e, source ../tools/hpo_mysqldb/schemabackup_2010-06-18.sql] Done restore. insert terms WARN: invalid external object: 10.1007/978-0-387-79948-3_2046 / DOI WARN: invalid external object: 0005291 / MP WARN: invalid external object: 0005555 / MP WARN: invalid external object: 0010210 / MP WARN: invalid external object: 0003009 / MP WARN: invalid external object: 0008556 / MP WARN: invalid external object: 0004947 / MP WARN: invalid external object: 0011478 / MP WARN: invalid external object: 0008271 / MP WARN: invalid external object: 3632007 / PMID WARN: invalid external object: 0001764 / MP WARN: invalid external object: 26079824 / PMID WARN: invalid external object: 0005257 / MP WARN: invalid external object: 20590416 / pmid WARN: invalid external object: 16671223 / pmid WARN: invalid external object: 24618488 / pmid WARN: invalid external object: 24467750 / pmid WARN: invalid external object: 24808988 / pmid WARN: invalid external object: 15961866 / pmid WARN: invalid external object: 17490914 / pmid WARN: invalid external object: 20643692 / pmid WARN: invalid external object: 24046799 / pmid WARN: invalid external object: 24822139 / pmid WARN: invalid external object: 20573927 / pmid WARN: invalid external object: 16391543 / pmid WARN: invalid external object: 10199473 / pmid WARN: invalid external object: 12089752 / pmid WARN: invalid external object: 23513084 / pmid WARN: invalid external object: 22544358 / pmid WARN: invalid external object: 21712856 / pmid WARN: invalid external object: 3409932 / pmid WARN: invalid external object: 18691338 / pmid WARN: invalid external object: 4058748 / pmid WARN: invalid external object: 21931493 / pmid WARN: invalid external object: //emedicine.medscape.com/article/281484-overview / http WARN: invalid external object: 26379327 / PMID WARN: invalid external object: 18616733 / PMID WARN: invalid external object: 18809899 / PMID WARN: invalid external object: sjwang / RGD insert graph-path allpathes.size() = 201376 insert term2term Insert annotations: dumping to file: ./MYHPO_12_2017.sql calling: [mysqldump, --user=hudson_mysql, --password=hpo_hudson, --host=localhost, --port=3306, MYHPO_12_2017] Done dumping to file. exiting... make: Leaving directory '/var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation' Archiving artifacts Finished: SUCCESS