Started by upstream project "hpo.annotations" build number 1262 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/hpo_mysqldb A tools/hpo_mysqldb/schemabackup_2010-06-18.sql At revision 5341 no change for https://github.com/monarch-initiative/hpo-annotation-data/trunk/util since the previous build [workspace] $ /bin/sh -xe /tmp/jenkins6338778846881773892.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* mkdir -p jar wget -N -P jar https://github.com/Phenomics/hpo-build-jars/raw/master/createGene2Phenotype.jar --2018-10-09 10:03:01-- https://github.com/Phenomics/hpo-build-jars/raw/master/createGene2Phenotype.jar 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... 302 Found Location: https://raw.githubusercontent.com/Phenomics/hpo-build-jars/master/createGene2Phenotype.jar [following] --2018-10-09 10:03:01-- https://raw.githubusercontent.com/Phenomics/hpo-build-jars/master/createGene2Phenotype.jar Connecting to proxy.charite.de (proxy.charite.de)|141.42.1.215|:8080... connected. Proxy request sent, awaiting response... 200 OK Length: 13418626 (13M) [application/octet-stream] Saving to: ‘jar/createGene2Phenotype.jar’ 0K .......... .......... .......... .......... .......... 0% 1.67M 8s 50K .......... .......... .......... .......... .......... 0% 4.84M 5s 100K .......... .......... .......... .......... .......... 1% 10.2M 4s 150K .......... .......... .......... .......... .......... 1% 6.00M 3s 200K .......... .......... .......... .......... .......... 1% 7.80M 3s 250K .......... .......... .......... .......... .......... 2% 6.72M 3s 300K .......... .......... .......... .......... .......... 2% 6.98M 3s 350K .......... .......... .......... .......... .......... 3% 7.27M 3s 400K .......... .......... .......... .......... .......... 3% 9.99M 2s 450K .......... .......... .......... .......... .......... 3% 7.39M 2s 500K .......... .......... .......... .......... .......... 4% 8.11M 2s 550K .......... .......... .......... .......... .......... 4% 10.2M 2s 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.......... .......... .......... 97% 84.8M 0s 12750K .......... .......... .......... .......... .......... 97% 48.9M 0s 12800K .......... .......... .......... .......... .......... 98% 64.7M 0s 12850K .......... .......... .......... .......... .......... 98% 69.1M 0s 12900K .......... .......... .......... .......... .......... 98% 24.5M 0s 12950K .......... .......... .......... .......... .......... 99% 47.1M 0s 13000K .......... .......... .......... .......... .......... 99% 16.8M 0s 13050K .......... .......... .......... .......... .......... 99% 136M 0s 13100K .... 100% 131M=0.6s Last-modified header missing -- time-stamps turned off. 2018-10-09 10:03:02 (21.2 MB/s) - ‘jar/createGene2Phenotype.jar’ saved [13418626/13418626] # 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 - --2018-10-09 10:03:02-- 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: 767875 (750K) [text/plain] Saving to: ‘mim2gene_medgen’ 0K .......... .......... .......... .......... .......... 6% 24.9M 0s 50K .......... .......... .......... .......... .......... 13% 22.1M 0s 100K .......... .......... .......... .......... .......... 20% 30.6M 0s 150K .......... .......... .......... .......... .......... 26% 43.4M 0s 200K .......... .......... .......... .......... .......... 33% 29.8M 0s 250K .......... .......... .......... .......... .......... 40% 52.2M 0s 300K .......... .......... .......... .......... .......... 46% 37.1M 0s 350K .......... .......... .......... .......... .......... 53% 42.4M 0s 400K .......... .......... .......... .......... .......... 60% 50.9M 0s 450K .......... .......... .......... .......... .......... 66% 33.2M 0s 500K .......... .......... .......... .......... .......... 73% 57.2M 0s 550K .......... .......... .......... .......... .......... 80% 60.1M 0s 600K .......... .......... .......... .......... .......... 86% 50.3M 0s 650K .......... .......... .......... .......... .......... 93% 57.7M 0s 700K .......... .......... .......... .......... ......... 100% 54.5M=0.02s 2018-10-09 10:03:04 (39.1 MB/s) - ‘mim2gene_medgen’ saved [767875/767875] --2018-10-09 10:03:04-- 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: 2922915 (2.8M) [text/plain] Saving to: ‘Homo_sapiens.gene_info.gz’ 0K .......... .......... .......... .......... .......... 1% 20.0M 0s 50K .......... .......... .......... .......... .......... 3% 53.4M 0s 100K .......... .......... .......... .......... .......... 5% 449K 2s 150K .......... .......... .......... .......... .......... 7% 9.88M 2s 200K .......... .......... .......... .......... .......... 8% 49.0M 1s 250K .......... .......... .......... .......... .......... 10% 40.8M 1s 300K .......... .......... .......... .......... .......... 12% 52.0M 1s 350K .......... .......... .......... .......... .......... 14% 43.9M 1s 400K .......... .......... .......... .......... .......... 15% 62.8M 1s 450K .......... .......... .......... .......... .......... 17% 62.6M 1s 500K .......... .......... .......... .......... .......... 19% 51.4M 1s 550K .......... .......... .......... .......... .......... 21% 57.7M 0s 600K .......... .......... .......... .......... .......... 22% 54.1M 0s 650K .......... .......... .......... .......... .......... 24% 66.2M 0s 700K .......... .......... .......... .......... .......... 26% 59.6M 0s 750K .......... .......... .......... .......... .......... 28% 65.9M 0s 800K .......... .......... .......... .......... .......... 29% 67.0M 0s 850K .......... .......... .......... .......... .......... 31% 45.7M 0s 900K .......... .......... .......... .......... .......... 33% 106M 0s 950K .......... .......... .......... .......... .......... 35% 58.8M 0s 1000K .......... .......... .......... .......... .......... 36% 92.0M 0s 1050K .......... .......... .......... .......... .......... 38% 65.5M 0s 1100K .......... .......... .......... .......... .......... 40% 105M 0s 1150K .......... .......... .......... .......... .......... 42% 64.3M 0s 1200K .......... .......... .......... .......... .......... 43% 57.4M 0s 1250K .......... .......... .......... .......... .......... 45% 99.4M 0s 1300K .......... .......... .......... .......... .......... 47% 60.7M 0s 1350K .......... .......... .......... .......... .......... 49% 86.1M 0s 1400K .......... .......... .......... .......... .......... 50% 113M 0s 1450K .......... .......... .......... .......... .......... 52% 74.7M 0s 1500K .......... .......... .......... .......... .......... 54% 102M 0s 1550K .......... .......... .......... .......... .......... 56% 75.6M 0s 1600K .......... .......... .......... .......... .......... 57% 110M 0s 1650K .......... .......... .......... .......... .......... 59% 92.0M 0s 1700K .......... .......... .......... .......... .......... 61% 68.7M 0s 1750K .......... .......... .......... .......... .......... 63% 102M 0s 1800K .......... .......... .......... .......... .......... 64% 60.8M 0s 1850K .......... .......... .......... .......... .......... 66% 112M 0s 1900K .......... .......... .......... .......... .......... 68% 115M 0s 1950K .......... .......... .......... .......... .......... 70% 91.8M 0s 2000K .......... .......... .......... .......... .......... 71% 117M 0s 2050K .......... .......... .......... .......... .......... 73% 113M 0s 2100K .......... .......... .......... .......... .......... 75% 113M 0s 2150K .......... .......... .......... .......... .......... 77% 85.9M 0s 2200K .......... .......... .......... .......... .......... 78% 111M 0s 2250K .......... .......... .......... .......... .......... 80% 96.9M 0s 2300K .......... .......... .......... .......... .......... 82% 83.5M 0s 2350K .......... .......... .......... .......... .......... 84% 103M 0s 2400K .......... .......... .......... .......... .......... 85% 111M 0s 2450K .......... .......... .......... .......... .......... 87% 107M 0s 2500K .......... .......... .......... .......... .......... 89% 80.5M 0s 2550K .......... .......... .......... .......... .......... 91% 102M 0s 2600K .......... .......... .......... .......... .......... 92% 118M 0s 2650K .......... .......... .......... .......... .......... 94% 104M 0s 2700K .......... .......... .......... .......... .......... 96% 97.3M 0s 2750K .......... .......... .......... .......... .......... 98% 124M 0s 2800K .......... .......... .......... .......... .......... 99% 96.5M 0s 2850K .... 100% 8410G=0.2s 2018-10-09 10:03:07 (18.2 MB/s) - ‘Homo_sapiens.gene_info.gz’ saved [2922915/2922915] --2018-10-09 10:03:07-- http://www.orphadata.org/data/xml/en_product6.xml Reusing existing connection to proxy.charite.de:8080. Proxy request sent, awaiting response... 200 OK Length: 19213951 (18M) [text/xml] Saving to: ‘en_product6.xml’ 0K .......... .......... .......... .......... .......... 0% 548K 34s 50K .......... .......... .......... .......... .......... 0% 1.54M 23s 100K .......... .......... .......... .......... .......... 0% 1.56M 19s 150K .......... .......... .......... .......... .......... 1% 1.38M 18s 200K .......... .......... .......... .......... .......... 1% 1.82M 16s 250K .......... .......... .......... .......... .......... 1% 1.51M 15s 300K .......... .......... .......... .......... .......... 1% 1.64M 15s 350K .......... .......... .......... .......... .......... 2% 1.59M 14s 400K .......... .......... .......... .......... .......... 2% 1.59M 14s 450K .......... .......... .......... .......... .......... 2% 1.58M 14s 500K .......... .......... .......... .......... .......... 2% 66.0M 12s 550K .......... .......... .......... .......... .......... 3% 1.58M 12s 600K .......... 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35.7M 0s 18750K .......... ... 100% 7.44M=1.4s 2018-10-09 10:03:08 (13.0 MB/s) - ‘en_product6.xml’ saved [19213951/19213951] --2018-10-09 10:03:08-- 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: 19128987 (18M) [application/octet-stream] Saving to: ‘phenotype_annotation.tab’ 0K .......... .......... .......... .......... .......... 0% 98.1M 0s 50K .......... .......... .......... .......... .......... 0% 32.3M 0s 100K .......... .......... .......... .......... .......... 0% 28.8M 0s 150K .......... .......... .......... .......... .......... 1% 42.5M 0s 200K .......... .......... .......... .......... .......... 1% 16.8M 1s 250K .......... .......... .......... .......... .......... 1% 82.4M 1s 300K .......... .......... .......... .......... .......... 1% 11.5M 1s 350K .......... .......... .......... .......... .......... 2% 71.9M 1s 400K .......... .......... .......... .......... .......... 2% 82.7M 1s 450K .......... .......... .......... .......... .......... 2% 41.1M 1s 500K .......... .......... .......... .......... .......... 2% 86.2M 1s 550K .......... .......... .......... .......... .......... 3% 30.6M 1s 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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] --2018-10-09 10:03:09-- 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: 6192170 (5.9M) [text/plain] Saving to: ‘hp.obo’ 0K .......... .......... .......... .......... .......... 0% 1.42M 4s 50K .......... .......... .......... .......... .......... 1% 3.95M 3s 100K .......... .......... .......... .......... .......... 2% 8.61M 2s 150K .......... .......... .......... .......... .......... 3% 4.50M 2s 200K .......... .......... .......... .......... .......... 4% 7.37M 2s 250K .......... .......... .......... .......... .......... 4% 6.44M 1s 300K .......... .......... .......... .......... .......... 5% 6.77M 1s 350K .......... .......... .......... .......... .......... 6% 6.76M 1s 400K .......... .......... .......... .......... .......... 7% 4.71M 1s 450K .......... .......... .......... .......... .......... 8% 8.13M 1s 500K .......... .......... .......... .......... .......... 9% 7.70M 1s 550K .......... .......... .......... .......... .......... 9% 7.96M 1s 600K .......... .......... 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.......... ....... 100% 9.45M=0.5s Last-modified header missing -- time-stamps turned off. 2018-10-09 10:03:10 (11.7 MB/s) - ‘hp.obo’ saved [6192170/6192170] FINISHED --2018-10-09 10:03:10-- Total wall clock time: 7.7s Downloaded: 5 files, 46M in 2.4s (19.2 MB/s) java -Xmx1G -jar jar/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 Oct 09, 2018 10:03:10 AM ontologizer.go.OBOParser doParse INFO: Got 13941 terms and 17594 relations in 294 ms Details of parsed obo file: data-version: releases/2018-10-09 format: 1.2 term definitions: 13941 Oct 09, 2018 10:03:10 AM ontologizer.go.Ontology assignLevel1TermsAndFixRoot INFO: Ontology contains a single level-one term (All (HP:0000001) Oct 09, 2018 10:03:11 AM ontologizer.go.Ontology assignLevel1TermsAndFixRoot INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118) WARN: Frequency of 4281 terms was zero!! Set IC of these to : 9.27706400401909 = -1 * (log(1 / 10690) mims:10763 with inh: 6840 parse NCBI summary of gene_info-file other: 855 tRNA: 599 rRNA: 59 scRNA: 4 biological-region: 3309 protein-coding: 20216 ncRNA: 17267 pseudo: 16434 snRNA: 64 snoRNA: 541 unknown: 1771 entrez2symbol size: 42914 there were 2 unidentified gene-IDs: [107305681, 2439] diseaseid-to-entrezid: 4848 ORPHANETPARSING: orphadisease2HGNCgenes:3748 ORPHANETPARSING: hgncid2entrez:27506 there were 31 unmappable HGNC-IDs: [3082, 14252, 37475, 21340, 3101, 33472, 30161, 22993, 34382, 22433, 35416, 31376, 32780, 39436, 32944, 17204, 3777, 12599, 26071, 20684, 14260, 33240, 43726, 25855, 8141, 43724, 32314, 33445, 16706, 33485, 13730] diseaseId2entry.size(): 10763 omim: 7470 orphanet: 3246 others: 47 Disease entries with at least one known disease gene: 6404 Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 10690 generating files for source-filter: OMIM and frequency-filter: FREQUENT_FEATURES debug disease = AnnotatedItem [itemId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0] annotations did not contain debug disease generating files for source-filter: OMIM and frequency-filter: ALL_FREQUENCIES debug disease = AnnotatedItem [itemId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0] annotations did not contain debug disease generating files for source-filter: ORPHA and frequency-filter: FREQUENT_FEATURES annotation: Sensorineural hearing impairment (HP:0000407) HPO 0.12 filters: true/false annotation: Conjunctivitis (HP:0000509) HPO 0.12 filters: true/false annotation: Hyperhidrosis (HP:0000975) HPO 0.9 filters: true/true annotation: Pruritus (HP:0000989) HPO 0.9 filters: true/true annotation: Urticaria (HP:0001025) HPO 0.9 filters: true/true annotation: Arthritis (HP:0001369) HPO 0.9 filters: true/true annotation: Dehydration (HP:0001944) HPO 0.12 filters: true/false annotation: Fever (HP:0001945) HPO 0.9 filters: true/true annotation: Polydipsia (HP:0001959) HPO 0.12 filters: true/false annotation: Nausea and vomiting (HP:0002017) HPO 0.5 filters: true/true annotation: Abdominal pain (HP:0002027) HPO 0.12 filters: true/false annotation: Headache (HP:0002315) HPO 0.5 filters: true/true annotation: Arthralgia (HP:0002829) HPO 0.12 filters: true/false annotation: Myalgia (HP:0003326) HPO 0.9 filters: true/true annotation: Erythema (HP:0010783) HPO 0.9 filters: true/true annotation: Fatigue (HP:0012378) HPO 0.9 filters: true/true annotation: Dysesthesia (HP:0012534) HPO 0.9 filters: true/true debug disease = AnnotatedItem [itemId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0] annotations did not contain debug disease generating files for source-filter: ORPHA and frequency-filter: ALL_FREQUENCIES annotation: Sensorineural hearing impairment (HP:0000407) HPO 0.12 filters: true/true annotation: Conjunctivitis (HP:0000509) HPO 0.12 filters: true/true annotation: Hyperhidrosis (HP:0000975) HPO 0.9 filters: true/true annotation: Pruritus (HP:0000989) HPO 0.9 filters: true/true annotation: Urticaria (HP:0001025) HPO 0.9 filters: true/true annotation: Arthritis (HP:0001369) HPO 0.9 filters: true/true annotation: Dehydration (HP:0001944) HPO 0.12 filters: true/true annotation: Fever (HP:0001945) HPO 0.9 filters: true/true annotation: Polydipsia (HP:0001959) HPO 0.12 filters: true/true annotation: Nausea and vomiting (HP:0002017) HPO 0.5 filters: true/true annotation: Abdominal pain (HP:0002027) HPO 0.12 filters: true/true annotation: Headache (HP:0002315) HPO 0.5 filters: true/true annotation: Arthralgia (HP:0002829) HPO 0.12 filters: true/true annotation: Myalgia (HP:0003326) HPO 0.9 filters: true/true annotation: Erythema (HP:0010783) HPO 0.9 filters: true/true annotation: Fatigue (HP:0012378) HPO 0.9 filters: true/true annotation: Dysesthesia (HP:0012534) HPO 0.9 filters: true/true debug disease = AnnotatedItem [itemId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0] annotations did not contain debug disease generating files for source-filter: ALL_SOURCES and frequency-filter: FREQUENT_FEATURES annotation: Sensorineural hearing impairment (HP:0000407) HPO 0.12 filters: true/false annotation: Conjunctivitis (HP:0000509) HPO 0.12 filters: true/false annotation: Hyperhidrosis (HP:0000975) HPO 0.9 filters: true/true annotation: Pruritus (HP:0000989) HPO 0.9 filters: true/true annotation: Urticaria (HP:0001025) HPO 0.9 filters: true/true annotation: Arthritis (HP:0001369) HPO 0.9 filters: true/true annotation: Dehydration (HP:0001944) HPO 0.12 filters: true/false annotation: Fever (HP:0001945) HPO 0.9 filters: true/true annotation: Polydipsia (HP:0001959) HPO 0.12 filters: true/false annotation: Nausea and vomiting (HP:0002017) HPO 0.5 filters: true/true annotation: Abdominal pain (HP:0002027) HPO 0.12 filters: true/false annotation: Headache (HP:0002315) HPO 0.5 filters: true/true annotation: Arthralgia (HP:0002829) HPO 0.12 filters: true/false annotation: Myalgia (HP:0003326) HPO 0.9 filters: true/true annotation: Erythema (HP:0010783) HPO 0.9 filters: true/true annotation: Fatigue (HP:0012378) HPO 0.9 filters: true/true annotation: Dysesthesia (HP:0012534) HPO 0.9 filters: true/true debug disease = AnnotatedItem [itemId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0] annotations did not contain debug disease generating files for source-filter: ALL_SOURCES and frequency-filter: ALL_FREQUENCIES annotation: Sensorineural hearing impairment (HP:0000407) HPO 0.12 filters: true/true annotation: Conjunctivitis (HP:0000509) HPO 0.12 filters: true/true annotation: Hyperhidrosis (HP:0000975) HPO 0.9 filters: true/true annotation: Pruritus (HP:0000989) HPO 0.9 filters: true/true annotation: Urticaria (HP:0001025) HPO 0.9 filters: true/true annotation: Arthritis (HP:0001369) HPO 0.9 filters: true/true annotation: Dehydration (HP:0001944) HPO 0.12 filters: true/true annotation: Fever (HP:0001945) HPO 0.9 filters: true/true annotation: Polydipsia (HP:0001959) HPO 0.12 filters: true/true annotation: Nausea and vomiting (HP:0002017) HPO 0.5 filters: true/true annotation: Abdominal pain (HP:0002027) HPO 0.12 filters: true/true annotation: Headache (HP:0002315) HPO 0.5 filters: true/true annotation: Arthralgia (HP:0002829) HPO 0.12 filters: true/true annotation: Myalgia (HP:0003326) HPO 0.9 filters: true/true annotation: Erythema (HP:0010783) HPO 0.9 filters: true/true annotation: Fatigue (HP:0012378) HPO 0.9 filters: true/true annotation: Dysesthesia (HP:0012534) HPO 0.9 filters: true/true debug disease = AnnotatedItem [itemId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0] annotations did not contain debug disease make: Leaving directory '/var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation' Archiving artifacts Finished: SUCCESS