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/hpo_mysqldb
A         tools/hpo_mysqldb/schemabackup_2010-06-18.sql
At revision 5227
[workspace] $ /bin/sh -xe /tmp/jenkins1826126184505463591.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
--2018-07-27 17:11:44--  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]
--2018-07-27 17:11:44--  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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 13100K ....                                                  100% 88.6M=0.6s

Last-modified header missing -- time-stamps turned off.
2018-07-27 17:11:46 (22.4 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 -
--2018-07-27 17:11:46--  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: 766041 (748K) [text/plain]
Saving to: ‘mim2gene_medgen’

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2018-07-27 17:11:48 (59.0 MB/s) - ‘mim2gene_medgen’ saved [766041/766041]

--2018-07-27 17:11:48--  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: 2899054 (2.8M) [text/plain]
Saving to: ‘Homo_sapiens.gene_info.gz’

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2018-07-27 17:11:55 (881 KB/s) - ‘Homo_sapiens.gene_info.gz’ saved [2899054/2899054]

--2018-07-27 17:11:55--  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: 19088181 (18M) [text/xml]
Saving to: ‘en_product6.xml’

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 18600K .......... .......... .......... ..........           100% 19.7M=1.3s

2018-07-27 17:11:56 (14.1 MB/s) - ‘en_product6.xml’ saved [19088181/19088181]

--2018-07-27 17:11:56--  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: 18932849 (18M) [application/octet-stream]
Saving to: ‘phenotype_annotation.tab’

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2018-07-27 17:11:57 (96.1 MB/s) - ‘phenotype_annotation.tab’ saved [18932849/18932849]

--2018-07-27 17:11:57--  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]
--2018-07-27 17:11:57--  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: 6090942 (5.8M) [text/plain]
Saving to: ‘hp.obo’

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   950K .......... .......... .......... .......... .......... 16% 11.3M 1s
  1000K .......... .......... .......... .......... .......... 17% 13.3M 1s
  1050K .......... .......... .......... .......... .......... 18% 10.0M 1s
  1100K .......... .......... .......... .......... .......... 19% 12.6M 1s
  1150K .......... .......... .......... .......... .......... 20% 10.3M 1s
  1200K .......... .......... .......... .......... .......... 21% 12.0M 1s
  1250K .......... .......... .......... .......... .......... 21% 9.15M 1s
  1300K .......... .......... .......... .......... .......... 22% 16.4M 1s
  1350K .......... .......... .......... .......... .......... 23% 16.6M 1s
  1400K .......... .......... .......... .......... .......... 24% 8.61M 1s
  1450K .......... .......... .......... .......... .......... 25% 16.8M 1s
  1500K .......... .......... .......... .......... .......... 26% 13.4M 1s
  1550K .......... .......... .......... .......... .......... 26% 8.37M 1s
  1600K .......... .......... .......... .......... .......... 27% 17.4M 1s
  1650K .......... .......... .......... .......... .......... 28% 16.8M 1s
  1700K .......... .......... .......... .......... .......... 29% 12.9M 1s
  1750K .......... .......... .......... .......... .......... 30% 11.3M 0s
  1800K .......... .......... .......... .......... .......... 31% 16.4M 0s
  1850K .......... .......... .......... .......... .......... 31% 17.8M 0s
  1900K .......... .......... .......... .......... .......... 32% 11.6M 0s
  1950K .......... .......... .......... .......... .......... 33% 10.1M 0s
  2000K .......... .......... .......... .......... .......... 34% 19.8M 0s
  2050K .......... .......... .......... .......... .......... 35% 16.6M 0s
  2100K .......... .......... .......... .......... .......... 36% 11.2M 0s
  2150K .......... .......... .......... .......... .......... 36% 19.7M 0s
  2200K .......... .......... .......... .......... .......... 37% 17.7M 0s
  2250K .......... .......... .......... .......... .......... 38% 15.1M 0s
  2300K .......... .......... .......... .......... .......... 39% 21.4M 0s
  2350K .......... .......... .......... .......... .......... 40% 11.1M 0s
  2400K .......... .......... .......... .......... .......... 41% 13.5M 0s
  2450K .......... .......... .......... .......... .......... 42% 20.1M 0s
  2500K .......... .......... .......... .......... .......... 42% 14.6M 0s
  2550K .......... .......... .......... .......... .......... 43% 24.0M 0s
  2600K .......... .......... .......... .......... .......... 44% 18.2M 0s
  2650K .......... .......... .......... .......... .......... 45% 13.9M 0s
  2700K .......... .......... .......... .......... .......... 46% 23.7M 0s
  2750K .......... .......... .......... .......... .......... 47% 12.9M 0s
  2800K .......... .......... .......... .......... .......... 47% 19.2M 0s
  2850K .......... .......... .......... .......... .......... 48% 12.7M 0s
  2900K .......... .......... .......... .......... .......... 49% 25.4M 0s
  2950K .......... .......... .......... .......... .......... 50% 15.1M 0s
  3000K .......... .......... .......... .......... .......... 51% 30.8M 0s
  3050K .......... .......... .......... .......... .......... 52% 15.4M 0s
  3100K .......... .......... .......... .......... .......... 52% 16.7M 0s
  3150K .......... .......... .......... .......... .......... 53% 19.6M 0s
  3200K .......... .......... .......... .......... .......... 54% 19.5M 0s
  3250K .......... .......... .......... .......... .......... 55% 24.4M 0s
  3300K .......... .......... .......... .......... .......... 56% 11.4M 0s
  3350K .......... .......... .......... .......... .......... 57% 26.1M 0s
  3400K .......... .......... .......... .......... .......... 58% 29.9M 0s
  3450K .......... .......... .......... .......... .......... 58% 20.3M 0s
  3500K .......... .......... .......... .......... .......... 59% 31.2M 0s
  3550K .......... .......... .......... .......... .......... 60% 9.16M 0s
  3600K .......... .......... .......... .......... .......... 61% 29.4M 0s
  3650K .......... .......... .......... .......... .......... 62% 34.0M 0s
  3700K .......... .......... .......... .......... .......... 63% 17.0M 0s
  3750K .......... .......... .......... .......... .......... 63% 21.1M 0s
  3800K .......... .......... .......... .......... .......... 64% 21.7M 0s
  3850K .......... .......... .......... .......... .......... 65% 17.1M 0s
  3900K .......... .......... .......... .......... .......... 66% 26.4M 0s
  3950K .......... .......... .......... .......... .......... 67% 19.8M 0s
  4000K .......... .......... .......... .......... .......... 68% 31.7M 0s
  4050K .......... .......... .......... .......... .......... 68% 15.7M 0s
  4100K .......... .......... .......... .......... .......... 69% 33.7M 0s
  4150K .......... .......... .......... .......... .......... 70% 17.3M 0s
  4200K .......... .......... .......... .......... .......... 71% 25.6M 0s
  4250K .......... .......... .......... .......... .......... 72% 29.1M 0s
  4300K .......... .......... .......... .......... .......... 73% 19.8M 0s
  4350K .......... .......... .......... .......... .......... 73% 19.1M 0s
  4400K .......... .......... .......... .......... .......... 74% 16.8M 0s
  4450K .......... .......... .......... .......... .......... 75% 34.3M 0s
  4500K .......... .......... .......... .......... .......... 76% 22.8M 0s
  4550K .......... .......... .......... .......... .......... 77% 47.9M 0s
  4600K .......... .......... .......... .......... .......... 78% 19.5M 0s
  4650K .......... .......... .......... .......... .......... 79% 57.4M 0s
  4700K .......... .......... .......... .......... .......... 79% 18.9M 0s
  4750K .......... .......... .......... .......... .......... 80% 14.7M 0s
  4800K .......... .......... .......... .......... .......... 81% 31.2M 0s
  4850K .......... .......... .......... .......... .......... 82% 31.1M 0s
  4900K .......... .......... .......... .......... .......... 83% 16.7M 0s
  4950K .......... .......... .......... .......... .......... 84% 49.5M 0s
  5000K .......... .......... .......... .......... .......... 84% 11.5M 0s
  5050K .......... .......... .......... .......... .......... 85% 86.0M 0s
  5100K .......... .......... .......... .......... .......... 86% 63.2M 0s
  5150K .......... .......... .......... .......... .......... 87% 19.8M 0s
  5200K .......... .......... .......... .......... .......... 88% 20.4M 0s
  5250K .......... .......... .......... .......... .......... 89% 45.8M 0s
  5300K .......... .......... .......... .......... .......... 89% 29.6M 0s
  5350K .......... .......... .......... .......... .......... 90% 13.1M 0s
  5400K .......... .......... .......... .......... .......... 91% 40.9M 0s
  5450K .......... .......... .......... .......... .......... 92% 40.2M 0s
  5500K .......... .......... .......... .......... .......... 93% 18.1M 0s
  5550K .......... .......... .......... .......... .......... 94% 41.1M 0s
  5600K .......... .......... .......... .......... .......... 94% 28.9M 0s
  5650K .......... .......... .......... .......... .......... 95% 41.1M 0s
  5700K .......... .......... .......... .......... .......... 96% 14.3M 0s
  5750K .......... .......... .......... .......... .......... 97% 42.4M 0s
  5800K .......... .......... .......... .......... .......... 98% 16.5M 0s
  5850K .......... .......... .......... .......... .......... 99% 56.6M 0s
  5900K .......... .......... .......... .......... ........  100% 75.7M=0.4s

Last-modified header missing -- time-stamps turned off.
2018-07-27 17:11:58 (13.9 MB/s) - ‘hp.obo’ saved [6090942/6090942]

FINISHED --2018-07-27 17:11:58--
Total wall clock time: 12s
Downloaded: 5 files, 46M in 5.1s (8.89 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
Jul 27, 2018 5:11:58 PM ontologizer.go.OBOParser doParse
INFO: Got 13815 terms and 17444 relations in 285 ms
Details of parsed obo file:
  data-version:		releases/2018-07-25
  format:		1.2
  term definitions:	13815
Jul 27, 2018 5:11:58 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
Jul 27, 2018 5:11:59 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118)
WARN: Frequency of 4324 terms was zero!!
Set IC of these to : 9.248117736310213 = -1 * (log(1 / 10385)
mims:10466 with inh: 6836
parse NCBI
summary of gene_info-file
  other: 859
  tRNA: 599
  rRNA: 59
  scRNA: 4
  biological-region: 3008
  protein-coding: 20361
  ncRNA: 17154
  pseudo: 16402
  snRNA: 64
  snoRNA: 541
  unknown: 1775
entrez2symbol size: 42649
there were 2 unidentified gene-IDs: [107305681, 2439]
diseaseid-to-entrezid: 4807
ORPHANETPARSING: orphadisease2HGNCgenes:3727
ORPHANETPARSING: hgncid2entrez:27394
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(): 10466
 omim: 7226
 orphanet: 3193
 others: 47
Disease entries with at least one known disease gene: 6129
Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 10385
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
Sending e-mails to: sebastian.koehler@charite.de
Finished: SUCCESS