SuccessConsole Output

Started by upstream project "hpo.annotations" build number 1246
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 4739
no change for https://github.com/monarch-initiative/hpo-annotation-data/trunk/util since the previous build
[workspace] $ /bin/sh -xe /tmp/hudson6752032968805964468.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 -
--2017-10-09 10:48:19--  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: 754593 (737K) [text/plain]
Saving to: ‘mim2gene_medgen’

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2017-10-09 10:48:22 (28.2 MB/s) - ‘mim2gene_medgen’ saved [754593/754593]

--2017-10-09 10:48:22--  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: 2878788 (2.7M) [text/plain]
Saving to: ‘Homo_sapiens.gene_info.gz’

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2017-10-09 10:48:26 (10.4 MB/s) - ‘Homo_sapiens.gene_info.gz’ saved [2878788/2878788]

--2017-10-09 10:48:26--  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: 18429919 (18M) [text/xml]
Saving to: ‘en_product6.xml’

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2017-10-09 10:48:28 (11.5 MB/s) - ‘en_product6.xml’ saved [18429919/18429919]

--2017-10-09 10:48:28--  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: 18502124 (18M) [application/octet-stream]
Saving to: ‘phenotype_annotation.tab’

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2017-10-09 10:48:28 (76.7 MB/s) - ‘phenotype_annotation.tab’ saved [18502124/18502124]

--2017-10-09 10:48:28--  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]
--2017-10-09 10:48:28--  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: 5685945 (5.4M) [text/plain]
Saving to: ‘hp.obo’

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  1150K .......... .......... .......... .......... .......... 21% 11.7M 1s
  1200K .......... .......... .......... .......... .......... 22% 3.83M 1s
  1250K .......... .......... .......... .......... .......... 23% 6.04M 1s
  1300K .......... .......... .......... .......... .......... 24% 19.4M 1s
  1350K .......... .......... .......... .......... .......... 25% 11.2M 1s
  1400K .......... .......... .......... .......... .......... 26% 9.68M 1s
  1450K .......... .......... .......... .......... .......... 27% 11.6M 0s
  1500K .......... .......... .......... .......... .......... 27% 18.8M 0s
  1550K .......... .......... .......... .......... .......... 28% 14.8M 0s
  1600K .......... .......... .......... .......... .......... 29% 11.4M 0s
  1650K .......... .......... .......... .......... .......... 30% 15.6M 0s
  1700K .......... .......... .......... .......... .......... 31% 14.9M 0s
  1750K .......... .......... .......... .......... .......... 32% 15.4M 0s
  1800K .......... .......... .......... .......... .......... 33% 14.2M 0s
  1850K .......... .......... .......... .......... .......... 34% 19.2M 0s
  1900K .......... .......... .......... .......... .......... 35% 13.8M 0s
  1950K .......... .......... .......... .......... .......... 36% 18.1M 0s
  2000K .......... .......... .......... .......... .......... 36% 12.8M 0s
  2050K .......... .......... .......... .......... .......... 37% 16.0M 0s
  2100K .......... .......... .......... .......... .......... 38% 14.0M 0s
  2150K .......... .......... .......... .......... .......... 39% 16.5M 0s
  2200K .......... .......... .......... .......... .......... 40% 17.1M 0s
  2250K .......... .......... .......... .......... .......... 41% 31.6M 0s
  2300K .......... .......... .......... .......... .......... 42% 13.3M 0s
  2350K .......... .......... .......... .......... .......... 43% 17.6M 0s
  2400K .......... .......... .......... .......... .......... 44% 14.6M 0s
  2450K .......... .......... .......... .......... .......... 45% 23.0M 0s
  2500K .......... .......... .......... .......... .......... 45% 21.1M 0s
  2550K .......... .......... .......... .......... .......... 46% 12.5M 0s
  2600K .......... .......... .......... .......... .......... 47% 12.3M 0s
  2650K .......... .......... .......... .......... .......... 48% 21.7M 0s
  2700K .......... .......... .......... .......... .......... 49% 13.8M 0s
  2750K .......... .......... .......... .......... .......... 50% 26.2M 0s
  2800K .......... .......... .......... .......... .......... 51% 27.9M 0s
  2850K .......... .......... .......... .......... .......... 52% 25.3M 0s
  2900K .......... .......... .......... .......... .......... 53% 29.1M 0s
  2950K .......... .......... .......... .......... .......... 54% 11.8M 0s
  3000K .......... .......... .......... .......... .......... 54% 22.5M 0s
  3050K .......... .......... .......... .......... .......... 55% 34.5M 0s
  3100K .......... .......... .......... .......... .......... 56% 21.0M 0s
  3150K .......... .......... .......... .......... .......... 57% 15.1M 0s
  3200K .......... .......... .......... .......... .......... 58% 18.8M 0s
  3250K .......... .......... .......... .......... .......... 59% 23.7M 0s
  3300K .......... .......... .......... .......... .......... 60% 27.9M 0s
  3350K .......... .......... .......... .......... .......... 61% 24.7M 0s
  3400K .......... .......... .......... .......... .......... 62% 12.3M 0s
  3450K .......... .......... .......... .......... .......... 63% 35.2M 0s
  3500K .......... .......... .......... .......... .......... 63% 29.2M 0s
  3550K .......... .......... .......... .......... .......... 64% 27.6M 0s
  3600K .......... .......... .......... .......... .......... 65% 20.0M 0s
  3650K .......... .......... .......... .......... .......... 66% 13.6M 0s
  3700K .......... .......... .......... .......... .......... 67% 34.9M 0s
  3750K .......... .......... .......... .......... .......... 68% 26.4M 0s
  3800K .......... .......... .......... .......... .......... 69% 18.0M 0s
  3850K .......... .......... .......... .......... .......... 70% 17.9M 0s
  3900K .......... .......... .......... .......... .......... 71% 34.8M 0s
  3950K .......... .......... .......... .......... .......... 72% 25.9M 0s
  4000K .......... .......... .......... .......... .......... 72% 28.7M 0s
  4050K .......... .......... .......... .......... .......... 73% 26.0M 0s
  4100K .......... .......... .......... .......... .......... 74% 12.5M 0s
  4150K .......... .......... .......... .......... .......... 75% 27.6M 0s
  4200K .......... .......... .......... .......... .......... 76% 41.0M 0s
  4250K .......... .......... .......... .......... .......... 77% 40.6M 0s
  4300K .......... .......... .......... .......... .......... 78% 26.2M 0s
  4350K .......... .......... .......... .......... .......... 79% 41.1M 0s
  4400K .......... .......... .......... .......... .......... 80% 12.4M 0s
  4450K .......... .......... .......... .......... .......... 81% 34.5M 0s
  4500K .......... .......... .......... .......... .......... 81% 24.3M 0s
  4550K .......... .......... .......... .......... .......... 82% 42.4M 0s
  4600K .......... .......... .......... .......... .......... 83% 39.4M 0s
  4650K .......... .......... .......... .......... .......... 84% 18.8M 0s
  4700K .......... .......... .......... .......... .......... 85% 19.4M 0s
  4750K .......... .......... .......... .......... .......... 86% 40.9M 0s
  4800K .......... .......... .......... .......... .......... 87% 25.5M 0s
  4850K .......... .......... .......... .......... .......... 88% 33.3M 0s
  4900K .......... .......... .......... .......... .......... 89% 26.5M 0s
  4950K .......... .......... .......... .......... .......... 90% 47.0M 0s
  5000K .......... .......... .......... .......... .......... 90% 13.2M 0s
  5050K .......... .......... .......... .......... .......... 91% 45.8M 0s
  5100K .......... .......... .......... .......... .......... 92% 50.9M 0s
  5150K .......... .......... .......... .......... .......... 93% 31.4M 0s
  5200K .......... .......... .......... .......... .......... 94% 29.7M 0s
  5250K .......... .......... .......... .......... .......... 95% 36.5M 0s
  5300K .......... .......... .......... .......... .......... 96% 12.7M 0s
  5350K .......... .......... .......... .......... .......... 97% 66.4M 0s
  5400K .......... .......... .......... .......... .......... 98% 32.3M 0s
  5450K .......... .......... .......... .......... .......... 99% 33.5M 0s
  5500K .......... .......... .......... .......... .......... 99% 33.4M 0s
  5550K ..                                                    100% 71.9M=0.4s

Last-modified header missing -- time-stamps turned off.
2017-10-09 10:48:29 (14.5 MB/s) - ‘hp.obo’ saved [5685945/5685945]

FINISHED --2017-10-09 10:48:29--
Total wall clock time: 9.6s
Downloaded: 5 files, 44M in 2.4s (18.3 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
Oct 09, 2017 10:48:29 AM ontologizer.go.OBOParser doParse
INFO: Got 13156 terms and 16794 relations in 148 ms
Details of parsed obo file:
  data-version:		releases/2017-10-05
  format:		1.2
  term definitions:	13156
Oct 09, 2017 10:48:29 AM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
Oct 09, 2017 10:48:30 AM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118)
WARN: Frequency of 3952 terms was zero!!
Set IC of these to : 9.221774749601845
mims:10209 with inh: 6910
parse NCBI
summary of gene_info-file
  other: 864
  tRNA: 599
  rRNA: 59
  scRNA: 4
  biological-region: 1643
  protein-coding: 20451
  ncRNA: 17707
  pseudo: 16399
  snRNA: 64
  snoRNA: 541
  unknown: 1763
entrez2symbol size: 41932
there were 1 unidentified gene-IDs: [2439]
diseaseid-to-entrezid: 4546
ORPHANETPARSING: orphadisease2HGNCgenes:3625
ORPHANETPARSING: hgncid2entrez:27313
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(): 10209
 omim: 7322
 orphanet: 2840
 others: 47
Disease entries with at least one known disease gene: 5785
Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 10115
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
Oct 09, 2017 10:48:44 AM ontologizer.go.OBOParser doParse
INFO: Got 13156 terms and 16794 relations in 184 ms
Details of parsed obo file:
  data-version:		releases/2017-10-05
  format:		1.2
  term definitions:	13156
Oct 09, 2017 10:48:44 AM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
Oct 09, 2017 10:48:45 AM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118)
WARN: Frequency of 3952 terms was zero!!
Set IC of these to : 9.221774749601845
mims:10209 with inh: 6910
parse NCBI
summary of gene_info-file
  other: 864
  tRNA: 599
  rRNA: 59
  scRNA: 4
  biological-region: 1643
  protein-coding: 20451
  ncRNA: 17707
  pseudo: 16399
  snRNA: 64
  snoRNA: 541
  unknown: 1763
entrez2symbol size: 41932
there were 1 unidentified gene-IDs: [2439]
diseaseid-to-entrezid: 4546
ORPHANETPARSING: orphadisease2HGNCgenes:3625
ORPHANETPARSING: hgncid2entrez:27313
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(): 10209
 omim: 7322
 orphanet: 2840
 others: 47
Disease entries with at least one known disease gene: 5785
Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 10115
10_2017
make connection / created db
connecting to jdbc:mysql://localhost:3306/mysql
dropping database: MYHPO_10_2017 (if exists)
creating database: MYHPO_10_2017
create schema (tables, relations)
Execute: [mysql, --user=hudson_mysql, --password=hpo_hudson, --host=localhost, --port=3306, MYHPO_10_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() = 201072
insert term2term
Insert annotations:
dumping to file: ./MYHPO_10_2017.sql
  calling: [mysqldump, --user=hudson_mysql, --password=hpo_hudson, --host=localhost, --port=3306, MYHPO_10_2017]
Done dumping to file.
exiting...
make: Leaving directory '/var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation'
Archiving artifacts
Finished: SUCCESS