SuccessConsole Output

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 4598
[workspace] $ /bin/sh -xe /tmp/hudson9198532480986237728.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
# Employ wget to retrieve data from NCBI/OMIM, Orphanet, HPO stuff. 
# File are listed in data.txt. We also ignore lines starting with "#"
cd data ; cat ../external_data.txt | sed "/^#.*$/d" | wget --retry-connrefused -N -i -
--2017-04-13 13:20:21--  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: 745114 (728K) [text/plain]
Saving to: ‘mim2gene_medgen’

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   700K .......... .......... .......                         100% 87.2M=0.02s

2017-04-13 13:20:24 (30.2 MB/s) - ‘mim2gene_medgen’ saved [745114/745114]

--2017-04-13 13:20:24--  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: 2818955 (2.7M) [text/plain]
Saving to: ‘Homo_sapiens.gene_info.gz’

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  2750K ..                                                    100% 70.6M=2.8s

2017-04-13 13:20:30 (986 KB/s) - ‘Homo_sapiens.gene_info.gz’ saved [2818955/2818955]

--2017-04-13 13:20:30--  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: 17661923 (17M) [text/xml]
Saving to: ‘en_product6.xml’

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2017-04-13 13:20:32 (12.4 MB/s) - ‘en_product6.xml’ saved [17661923/17661923]

--2017-04-13 13:20:32--  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: 18654900 (18M) [application/octet-stream]
Saving to: ‘phenotype_annotation.tab’

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2017-04-13 13:20:32 (50.2 MB/s) - ‘phenotype_annotation.tab’ saved [18654900/18654900]

--2017-04-13 13:20:32--  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]
--2017-04-13 13:20:33--  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: 5233103 (5.0M) [text/plain]
Saving to: ‘hp.obo’

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  1500K .......... .......... .......... .......... .......... 30% 2.14M 1s
  1550K .......... .......... .......... .......... .......... 31% 3.10M 1s
  1600K .......... .......... .......... .......... .......... 32% 3.00M 1s
  1650K .......... .......... .......... .......... .......... 33% 3.16M 1s
  1700K .......... .......... .......... .......... .......... 34% 3.15M 1s
  1750K .......... .......... .......... .......... .......... 35% 3.15M 1s
  1800K .......... .......... .......... .......... .......... 36% 3.41M 1s
  1850K .......... .......... .......... .......... .......... 37% 3.43M 1s
  1900K .......... .......... .......... .......... .......... 38% 2.42M 1s
  1950K .......... .......... .......... .......... .......... 39% 3.62M 1s
  2000K .......... .......... .......... .......... .......... 40% 3.41M 1s
  2050K .......... .......... .......... .......... .......... 41% 3.62M 1s
  2100K .......... .......... .......... .......... .......... 42% 3.53M 1s
  2150K .......... .......... .......... .......... .......... 43% 3.57M 1s
  2200K .......... .......... .......... .......... .......... 44% 3.70M 1s
  2250K .......... .......... .......... .......... .......... 45% 3.65M 1s
  2300K .......... .......... .......... .......... .......... 45% 3.18M 1s
  2350K .......... .......... .......... .......... .......... 46% 3.64M 1s
  2400K .......... .......... .......... .......... .......... 47% 3.82M 1s
  2450K .......... .......... .......... .......... .......... 48% 3.79M 1s
  2500K .......... .......... .......... .......... .......... 49% 3.82M 1s
  2550K .......... .......... .......... .......... .......... 50% 1.75M 1s
  2600K .......... .......... .......... .......... .......... 51% 4.16M 1s
  2650K .......... .......... .......... .......... .......... 52% 4.89M 1s
  2700K .......... .......... .......... .......... .......... 53% 2.06M 1s
  2750K .......... .......... .......... .......... .......... 54% 2.90M 1s
  2800K .......... .......... .......... .......... .......... 55% 3.17M 1s
  2850K .......... .......... .......... .......... .......... 56% 3.05M 1s
  2900K .......... .......... .......... .......... .......... 57% 2.95M 1s
  2950K .......... .......... .......... .......... .......... 58% 3.33M 1s
  3000K .......... .......... .......... .......... .......... 59% 3.04M 1s
  3050K .......... .......... .......... .......... .......... 60% 3.38M 1s
  3100K .......... .......... .......... .......... .......... 61% 2.56M 1s
  3150K .......... .......... .......... .......... .......... 62% 3.37M 1s
  3200K .......... .......... .......... .......... .......... 63% 3.51M 1s
  3250K .......... .......... .......... .......... .......... 64% 3.39M 1s
  3300K .......... .......... .......... .......... .......... 65% 3.58M 1s
  3350K .......... .......... .......... .......... .......... 66% 3.80M 1s
  3400K .......... .......... .......... .......... .......... 67% 3.42M 1s
  3450K .......... .......... .......... .......... .......... 68% 3.86M 1s
  3500K .......... .......... .......... .......... .......... 69% 2.78M 0s
  3550K .......... .......... .......... .......... .......... 70% 4.11M 0s
  3600K .......... .......... .......... .......... .......... 71% 3.21M 0s
  3650K .......... .......... .......... .......... .......... 72% 5.02M 0s
  3700K .......... .......... .......... .......... .......... 73% 3.70M 0s
  3750K .......... .......... .......... .......... .......... 74% 4.49M 0s
  3800K .......... .......... .......... .......... .......... 75% 3.85M 0s
  3850K .......... .......... .......... .......... .......... 76% 4.34M 0s
  3900K .......... .......... .......... .......... .......... 77% 3.11M 0s
  3950K .......... .......... .......... .......... .......... 78% 4.39M 0s
  4000K .......... .......... .......... .......... .......... 79% 4.27M 0s
  4050K .......... .......... .......... .......... .......... 80% 3.71M 0s
  4100K .......... .......... .......... .......... .......... 81% 3.89M 0s
  4150K .......... .......... .......... .......... .......... 82% 4.51M 0s
  4200K .......... .......... .......... .......... .......... 83% 3.93M 0s
  4250K .......... .......... .......... .......... .......... 84% 4.70M 0s
  4300K .......... .......... .......... .......... .......... 85% 4.54M 0s
  4350K .......... .......... .......... .......... .......... 86% 4.67M 0s
  4400K .......... .......... .......... .......... .......... 87% 4.59M 0s
  4450K .......... .......... .......... .......... .......... 88% 3.98M 0s
  4500K .......... .......... .......... .......... .......... 89% 4.21M 0s
  4550K .......... .......... .......... .......... .......... 90% 5.84M 0s
  4600K .......... .......... .......... .......... .......... 90% 4.57M 0s
  4650K .......... .......... .......... .......... .......... 91% 4.79M 0s
  4700K .......... .......... .......... .......... .......... 92% 5.02M 0s
  4750K .......... .......... .......... .......... .......... 93% 4.92M 0s
  4800K .......... .......... .......... .......... .......... 94% 4.16M 0s
  4850K .......... .......... .......... .......... .......... 95% 4.23M 0s
  4900K .......... .......... .......... .......... .......... 96% 5.12M 0s
  4950K .......... .......... .......... .......... .......... 97% 4.65M 0s
  5000K .......... .......... .......... .......... .......... 98% 5.30M 0s
  5050K .......... .......... .......... .......... .......... 99% 5.70M 0s
  5100K ..........                                            100%  198M=1.5s

Last-modified header missing -- time-stamps turned off.
2017-04-13 13:20:35 (3.36 MB/s) - ‘hp.obo’ saved [5233103/5233103]

FINISHED --2017-04-13 13:20:35--
Total wall clock time: 14s
Downloaded: 5 files, 43M in 6.0s (7.16 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
Apr 13, 2017 1:20:36 PM ontologizer.go.OBOParser doParse
INFO: Got 12358 terms and 16044 relations in 181 ms
Details of parsed obo file:
  data-version:		releases/2017-04-13
  format:		1.2
  term definitions:	12358
Apr 13, 2017 1:20:36 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
Apr 13, 2017 1:20:36 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118)
WARN: Frequency of 3577 terms was zero!!
Set IC of these to : 9.160519676992227
mims:9557 with inh: 6392
parse NCBI
summary of gene_info-file
  other: 860
  tRNA: 599
  rRNA: 57
  scRNA: 4
  protein-coding: 20591
  ncRNA: 17775
  pseudo: 16380
  snRNA: 64
  snoRNA: 541
  unknown: 2126
entrez2symbol size: 40491
there were 1 unidentified gene-IDs: [2439]
diseaseid-to-entrezid: 4424
ORPHANETPARSING: orphadisease2HGNCgenes:3567
ORPHANETPARSING: hgncid2entrez:27016
there were 31 unmappable HGNC-IDs: [3082, 14252, 37475, 21340, 3101, 33472, 30161, 22993, 34382, 22433, 23448, 35416, 31376, 39436, 32944, 17204, 3777, 12599, 26071, 20684, 14260, 33240, 43726, 25855, 8141, 43724, 32314, 33445, 16706, 33485, 13730]
diseaseId2entry.size(): 9557
 omim: 6918
 orphanet: 2592
 others: 47
Disease entries with at least one known disease gene: 5295
Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 9514
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
Apr 13, 2017 1:20:49 PM ontologizer.go.OBOParser doParse
INFO: Got 12358 terms and 16044 relations in 165 ms
Details of parsed obo file:
  data-version:		releases/2017-04-13
  format:		1.2
  term definitions:	12358
Apr 13, 2017 1:20:49 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
Apr 13, 2017 1:20:49 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118)
WARN: Frequency of 3577 terms was zero!!
Set IC of these to : 9.160519676992227
mims:9557 with inh: 6392
parse NCBI
summary of gene_info-file
  other: 860
  tRNA: 599
  rRNA: 57
  scRNA: 4
  protein-coding: 20591
  ncRNA: 17775
  pseudo: 16380
  snRNA: 64
  snoRNA: 541
  unknown: 2126
entrez2symbol size: 40491
there were 1 unidentified gene-IDs: [2439]
diseaseid-to-entrezid: 4424
ORPHANETPARSING: orphadisease2HGNCgenes:3567
ORPHANETPARSING: hgncid2entrez:27016
there were 31 unmappable HGNC-IDs: [3082, 14252, 37475, 21340, 3101, 33472, 30161, 22993, 34382, 22433, 23448, 35416, 31376, 39436, 32944, 17204, 3777, 12599, 26071, 20684, 14260, 33240, 43726, 25855, 8141, 43724, 32314, 33445, 16706, 33485, 13730]
diseaseId2entry.size(): 9557
 omim: 6918
 orphanet: 2592
 others: 47
Disease entries with at least one known disease gene: 5295
Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 9514
04_2017
make connection / created db
connecting to jdbc:mysql://localhost:3306/mysql
dropping database: MYHPO_04_2017 (if exists)
creating database: MYHPO_04_2017
create schema (tables, relations)
Execute: [mysql, --user=hudson_mysql, --password=hpo_hudson, --host=localhost, --port=3306, MYHPO_04_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: 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
insert graph-path
  allpathes.size() = 192062
insert term2term
Insert annotations:
dumping to file: ./MYHPO_04_2017.sql
  calling: [mysqldump, --user=hudson_mysql, --password=hpo_hudson, --host=localhost, --port=3306, MYHPO_04_2017]
Done dumping to file.
exiting...
make: Leaving directory '/var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation'
Archiving artifacts
Finished: SUCCESS