SuccessConsole Output

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’

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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’

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  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.
Proxy request sent, awaiting response... 200 OK
Length: 18623277 (18M) [text/xml]
Saving to: ‘en_product6.xml’

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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’

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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’

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   350K .......... .......... .......... .......... ..........  7% 7.65M 1s
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   450K .......... .......... .......... .......... ..........  8% 12.2M 1s
   500K .......... .......... .......... .......... ..........  9% 7.83M 1s
   550K .......... .......... .......... .......... .......... 10% 17.4M 1s
   600K .......... .......... .......... .......... .......... 11% 10.1M 1s
   650K .......... .......... .......... .......... .......... 12% 10.1M 1s
   700K .......... .......... .......... .......... .......... 13% 12.6M 1s
   750K .......... .......... .......... .......... .......... 14% 6.25M 1s
   800K .......... .......... .......... .......... .......... 15% 25.8M 1s
   850K .......... .......... .......... .......... .......... 16% 11.6M 1s
   900K .......... .......... .......... .......... .......... 16% 9.83M 1s
   950K .......... .......... .......... .......... .......... 17% 12.7M 1s
  1000K .......... .......... .......... .......... .......... 18% 15.8M 1s
  1050K .......... .......... .......... .......... .......... 19% 9.58M 1s
  1100K .......... .......... .......... .......... .......... 20% 9.48M 1s
  1150K .......... .......... .......... .......... .......... 21% 12.1M 1s
  1200K .......... .......... .......... .......... .......... 22% 16.7M 0s
  1250K .......... .......... .......... .......... .......... 23% 12.5M 0s
  1300K .......... .......... .......... .......... .......... 24% 18.1M 0s
  1350K .......... .......... .......... .......... .......... 24% 12.5M 0s
  1400K .......... .......... .......... .......... .......... 25% 14.0M 0s
  1450K .......... .......... .......... .......... .......... 26% 17.0M 0s
  1500K .......... .......... .......... .......... .......... 27% 13.0M 0s
  1550K .......... .......... .......... .......... .......... 28% 10.8M 0s
  1600K .......... .......... .......... .......... .......... 29% 16.5M 0s
  1650K .......... .......... .......... .......... .......... 30% 14.9M 0s
  1700K .......... .......... .......... .......... .......... 31% 13.9M 0s
  1750K .......... .......... .......... .......... .......... 32% 18.9M 0s
  1800K .......... .......... .......... .......... .......... 33% 14.2M 0s
  1850K .......... .......... .......... .......... .......... 33% 17.9M 0s
  1900K .......... .......... .......... .......... .......... 34% 14.7M 0s
  1950K .......... .......... .......... .......... .......... 35% 12.1M 0s
  2000K .......... .......... .......... .......... .......... 36% 23.0M 0s
  2050K .......... .......... .......... .......... .......... 37% 9.59M 0s
  2100K .......... .......... .......... .......... .......... 38% 39.4M 0s
  2150K .......... .......... .......... .......... .......... 39% 13.3M 0s
  2200K .......... .......... .......... .......... .......... 40% 39.1M 0s
  2250K .......... .......... .......... .......... .......... 41% 10.8M 0s
  2300K .......... .......... .......... .......... .......... 41% 32.2M 0s
  2350K .......... .......... .......... .......... .......... 42% 12.1M 0s
  2400K .......... .......... .......... .......... .......... 43% 24.0M 0s
  2450K .......... .......... .......... .......... .......... 44% 14.1M 0s
  2500K .......... .......... .......... .......... .......... 45% 21.2M 0s
  2550K .......... .......... .......... .......... .......... 46% 18.8M 0s
  2600K .......... .......... .......... .......... .......... 47% 18.5M 0s
  2650K .......... .......... .......... .......... .......... 48% 44.1M 0s
  2700K .......... .......... .......... .......... .......... 49% 14.8M 0s
  2750K .......... .......... .......... .......... .......... 49% 13.4M 0s
  2800K .......... .......... .......... .......... .......... 50% 27.4M 0s
  2850K .......... .......... .......... .......... .......... 51% 28.0M 0s
  2900K .......... .......... .......... .......... .......... 52% 16.1M 0s
  2950K .......... .......... .......... .......... .......... 53% 15.7M 0s
  3000K .......... .......... .......... .......... .......... 54% 14.3M 0s
  3050K .......... .......... .......... .......... .......... 55% 20.1M 0s
  3100K .......... .......... .......... .......... .......... 56% 9.37M 0s
  3150K .......... .......... .......... .......... .......... 57% 34.5M 0s
  3200K .......... .......... .......... .......... .......... 57% 13.3M 0s
  3250K .......... .......... .......... .......... .......... 58% 27.4M 0s
  3300K .......... .......... .......... .......... .......... 59% 18.1M 0s
  3350K .......... .......... .......... .......... .......... 60% 37.7M 0s
  3400K .......... .......... .......... .......... .......... 61% 49.7M 0s
  3450K .......... .......... .......... .......... .......... 62% 34.3M 0s
  3500K .......... .......... .......... .......... .......... 63% 25.5M 0s
  3550K .......... .......... .......... .......... .......... 64% 17.7M 0s
  3600K .......... .......... .......... .......... .......... 65% 27.3M 0s
  3650K .......... .......... .......... .......... .......... 66% 27.3M 0s
  3700K .......... .......... .......... .......... .......... 66% 17.8M 0s
  3750K .......... .......... .......... .......... .......... 67% 30.4M 0s
  3800K .......... .......... .......... .......... .......... 68% 23.7M 0s
  3850K .......... .......... .......... .......... .......... 69% 29.3M 0s
  3900K .......... .......... .......... .......... .......... 70% 17.1M 0s
  3950K .......... .......... .......... .......... .......... 71% 25.3M 0s
  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