SuccessConsole Output

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’

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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’

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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’

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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’

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 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’

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2018-10-09 10:03:09 (59.8 MB/s) - ‘phenotype_annotation.tab’ saved [19128987/19128987]

--2018-10-09 10:03:09--  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’

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   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 .......... .......... .......... .......... .......... 10% 7.61M 1s
   650K .......... .......... .......... .......... .......... 11% 7.39M 1s
   700K .......... .......... .......... .......... .......... 12% 5.70M 1s
   750K .......... .......... .......... .......... .......... 13% 12.8M 1s
   800K .......... .......... .......... .......... .......... 14% 5.90M 1s
   850K .......... .......... .......... .......... .......... 14% 8.59M 1s
   900K .......... .......... .......... .......... .......... 15% 7.40M 1s
   950K .......... .......... .......... .......... .......... 16% 8.70M 1s
  1000K .......... .......... .......... .......... .......... 17% 10.9M 1s
  1050K .......... .......... .......... .......... .......... 18% 9.36M 1s
  1100K .......... .......... .......... .......... .......... 19% 9.69M 1s
  1150K .......... .......... .......... .......... .......... 19% 8.86M 1s
  1200K .......... .......... .......... .......... .......... 20% 8.11M 1s
  1250K .......... .......... .......... .......... .......... 21% 8.94M 1s
  1300K .......... .......... .......... .......... .......... 22% 11.8M 1s
  1350K .......... .......... .......... .......... .......... 23% 7.06M 1s
  1400K .......... .......... .......... .......... .......... 23% 17.3M 1s
  1450K .......... .......... .......... .......... .......... 24% 9.06M 1s
  1500K .......... .......... .......... .......... .......... 25% 9.36M 1s
  1550K .......... .......... .......... .......... .......... 26% 7.62M 1s
  1600K .......... .......... .......... .......... .......... 27% 14.4M 1s
  1650K .......... .......... .......... .......... .......... 28% 5.90M 1s
  1700K .......... .......... .......... .......... .......... 28% 7.97M 1s
  1750K .......... .......... .......... .......... .......... 29% 15.9M 1s
  1800K .......... .......... .......... .......... .......... 30% 27.9M 1s
  1850K .......... .......... .......... .......... .......... 31% 8.80M 1s
  1900K .......... .......... .......... .......... .......... 32% 8.19M 1s
  1950K .......... .......... .......... .......... .......... 33% 9.05M 1s
  2000K .......... .......... .......... .......... .......... 33% 20.4M 1s
  2050K .......... .......... .......... .......... .......... 34% 12.1M 1s
  2100K .......... .......... .......... .......... .......... 35% 13.1M 1s
  2150K .......... .......... .......... .......... .......... 36% 12.0M 1s
  2200K .......... .......... .......... .......... .......... 37% 12.3M 0s
  2250K .......... .......... .......... .......... .......... 38% 9.81M 0s
  2300K .......... .......... .......... .......... .......... 38% 15.9M 0s
  2350K .......... .......... .......... .......... .......... 39% 13.5M 0s
  2400K .......... .......... .......... .......... .......... 40% 8.63M 0s
  2450K .......... .......... .......... .......... .......... 41% 15.2M 0s
  2500K .......... .......... .......... .......... .......... 42% 11.6M 0s
  2550K .......... .......... .......... .......... .......... 42% 29.0M 0s
  2600K .......... .......... .......... .......... .......... 43% 11.3M 0s
  2650K .......... .......... .......... .......... .......... 44% 15.3M 0s
  2700K .......... .......... .......... .......... .......... 45% 15.6M 0s
  2750K .......... .......... .......... .......... .......... 46% 16.7M 0s
  2800K .......... .......... .......... .......... .......... 47% 11.3M 0s
  2850K .......... .......... .......... .......... .......... 47% 12.2M 0s
  2900K .......... .......... .......... .......... .......... 48% 17.7M 0s
  2950K .......... .......... .......... .......... .......... 49% 14.3M 0s
  3000K .......... .......... .......... .......... .......... 50% 22.1M 0s
  3050K .......... .......... .......... .......... .......... 51% 17.6M 0s
  3100K .......... .......... .......... .......... .......... 52% 12.4M 0s
  3150K .......... .......... .......... .......... .......... 52% 19.2M 0s
  3200K .......... .......... .......... .......... .......... 53% 11.1M 0s
  3250K .......... .......... .......... .......... .......... 54% 18.1M 0s
  3300K .......... .......... .......... .......... .......... 55% 11.4M 0s
  3350K .......... .......... .......... .......... .......... 56% 24.3M 0s
  3400K .......... .......... .......... .......... .......... 57% 14.8M 0s
  3450K .......... .......... .......... .......... .......... 57% 17.5M 0s
  3500K .......... .......... .......... .......... .......... 58% 23.1M 0s
  3550K .......... .......... .......... .......... .......... 59% 9.84M 0s
  3600K .......... .......... .......... .......... .......... 60% 20.4M 0s
  3650K .......... .......... .......... .......... .......... 61% 13.5M 0s
  3700K .......... .......... .......... .......... .......... 62% 40.9M 0s
  3750K .......... .......... .......... .......... .......... 62% 19.7M 0s
  3800K .......... .......... .......... .......... .......... 63% 11.3M 0s
  3850K .......... .......... .......... .......... .......... 64% 26.0M 0s
  3900K .......... .......... .......... .......... .......... 65% 18.1M 0s
  3950K .......... .......... .......... .......... .......... 66% 16.2M 0s
  4000K .......... .......... .......... .......... .......... 66% 17.2M 0s
  4050K .......... .......... .......... .......... .......... 67% 9.21M 0s
  4100K .......... .......... .......... .......... .......... 68% 26.5M 0s
  4150K .......... .......... .......... .......... .......... 69% 21.9M 0s
  4200K .......... .......... .......... .......... .......... 70% 28.3M 0s
  4250K .......... .......... .......... .......... .......... 71% 11.5M 0s
  4300K .......... .......... .......... .......... .......... 71% 41.1M 0s
  4350K .......... .......... .......... .......... .......... 72% 15.9M 0s
  4400K .......... .......... .......... .......... .......... 73% 17.3M 0s
  4450K .......... .......... .......... .......... .......... 74% 24.5M 0s
  4500K .......... .......... .......... .......... .......... 75% 29.3M 0s
  4550K .......... .......... .......... .......... .......... 76% 15.6M 0s
  4600K .......... .......... .......... .......... .......... 76% 17.6M 0s
  4650K .......... .......... .......... .......... .......... 77% 21.3M 0s
  4700K .......... .......... .......... .......... .......... 78% 20.4M 0s
  4750K .......... .......... .......... .......... .......... 79% 26.1M 0s
  4800K .......... .......... .......... .......... .......... 80% 22.6M 0s
  4850K .......... .......... .......... .......... .......... 81% 11.6M 0s
  4900K .......... .......... .......... .......... .......... 81% 47.4M 0s
  4950K .......... .......... .......... .......... .......... 82% 10.5M 0s
  5000K .......... .......... .......... .......... .......... 83% 17.5M 0s
  5050K .......... .......... .......... .......... .......... 84% 22.3M 0s
  5100K .......... .......... .......... .......... .......... 85%  116M 0s
  5150K .......... .......... .......... .......... .......... 85% 46.7M 0s
  5200K .......... .......... .......... .......... .......... 86% 10.3M 0s
  5250K .......... .......... .......... .......... .......... 87% 25.8M 0s
  5300K .......... .......... .......... .......... .......... 88% 20.4M 0s
  5350K .......... .......... .......... .......... .......... 89% 13.9M 0s
  5400K .......... .......... .......... .......... .......... 90% 35.4M 0s
  5450K .......... .......... .......... .......... .......... 90% 41.5M 0s
  5500K .......... .......... .......... .......... .......... 91% 47.0M 0s
  5550K .......... .......... .......... .......... .......... 92% 26.0M 0s
  5600K .......... .......... .......... .......... .......... 93% 14.9M 0s
  5650K .......... .......... .......... .......... .......... 94% 8.85M 0s
  5700K .......... .......... .......... .......... .......... 95% 16.3M 0s
  5750K .......... .......... .......... .......... .......... 95% 59.8M 0s
  5800K .......... .......... .......... .......... .......... 96% 48.8M 0s
  5850K .......... .......... .......... .......... .......... 97% 67.1M 0s
  5900K .......... .......... .......... .......... .......... 98% 51.4M 0s
  5950K .......... .......... .......... .......... .......... 99% 23.7M 0s
  6000K .......... .......... .......... .......... .......   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