FailedConsole Output

Started by upstream project "hpo" build number 1698
originally caused by:
 Started by user koehler
Building in workspace /var/lib/jenkins/jobs/hpo.annotations/workspace
Cleaning up /var/lib/jenkins/jobs/hpo.annotations/workspace/.
Deleting /var/lib/jenkins/jobs/hpo.annotations/workspace/misc/phenotype_annotation_hpoteam.tab
Deleting /var/lib/jenkins/jobs/hpo.annotations/workspace/misc/hpo
Deleting /var/lib/jenkins/jobs/hpo.annotations/workspace/misc/curator-statistics.tab
Deleting /var/lib/jenkins/jobs/hpo.annotations/workspace/misc/negative_phenotype_annotation.tab
Deleting /var/lib/jenkins/jobs/hpo.annotations/workspace/misc/phenotype_annotation.tab
Deleting /var/lib/jenkins/jobs/hpo.annotations/workspace/misc/data_version.txt
Deleting /var/lib/jenkins/jobs/hpo.annotations/workspace/misc/orphanetmapping
Deleting /var/lib/jenkins/jobs/hpo.annotations/workspace/misc/external_orphanet
Updating https://github.com/monarch-initiative/hpo-annotation-data/trunk/rare-diseases@HEAD at revision HEAD
UU        annotated/OMIM-117650.tab
UU        annotated/OMIM-158901.tab
UU        annotated/OMIM-205100.tab
UU        annotated/OMIM-212140.tab
UU        annotated/OMIM-305390.tab
UC        misc/makefile
At revision 3129
[workspace] $ /bin/sh -xe /tmp/hudson4466655751457180841.sh
+ make -C misc
make: Entering directory '/var/lib/jenkins/jobs/hpo.annotations/workspace/misc'
# load orphanet data
mkdir -p external_orphanet
# Employ wget to retrieve all external ontologies as specified
# in external_ontologies. We also ignore lines starting with #
cd external_orphanet ; cat ../external_orphanet.txt | sed "/^#.*$/d" | wget --retry-connrefused -N -i -
--2016-01-13 12:01:27--  http://www.orphadata.org/data/xml/en_product1.xml
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: 20259500 (19M) [text/xml]
Saving to: ‘en_product1.xml’

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2016-01-13 12:01:28 (16.6 MB/s) - ‘en_product1.xml’ saved [20259500/20259500]

--2016-01-13 12:01:28--  http://www.orphadata.org/data/xml/en_product4.xml
Reusing existing connection to proxy.charite.de:8080.
Proxy request sent, awaiting response... 200 OK
Length: 15118367 (14M) [text/xml]
Saving to: ‘en_product4.xml’

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2016-01-13 12:01:29 (27.1 MB/s) - ‘en_product4.xml’ saved [15118367/15118367]

FINISHED --2016-01-13 12:01:29--
Total wall clock time: 2.1s
Downloaded: 2 files, 34M in 1.7s (19.9 MB/s)
# loads the mapping between orphanet's signs-and-symptoms and HPO
svn checkout https://github.com/obophenotype/human-phenotype-ontology/trunk/src/mappings/ orphanetmapping
A    orphanetmapping/LDDB2HPO-v2.csv
A    orphanetmapping/README_LICENSE.txt
A    orphanetmapping/hp-to-eom-mapping.tsv
A    orphanetmapping/medraMapping.tsv
A    orphanetmapping/onet_hpo.tsv
A    orphanetmapping/term2umls.out
Checked out revision 1027.
# loads the HPO
wget -N -P hpo http://compbio.charite.de/hudson/job/hpo/lastSuccessfulBuild/artifact/hp/hp.obo
--2016-01-13 12:01:37--  http://compbio.charite.de/hudson/job/hpo/lastSuccessfulBuild/artifact/hp/hp.obo
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... 301 Moved Permanently
Location: http://compbio.charite.de/jenkins/job/hpo/lastSuccessfulBuild/artifact/hp/hp.obo [following]
--2016-01-13 12:01:37--  http://compbio.charite.de/jenkins/job/hpo/lastSuccessfulBuild/artifact/hp/hp.obo
Reusing existing connection to proxy.charite.de:8080.
Proxy request sent, awaiting response... 200 OK
Length: 4388959 (4.2M) [application/octet-stream]
Saving to: ‘hpo/hp.obo’

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  3750K .......... .......... .......... .......... .......... 88% 95.3M 0s
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  4100K .......... .......... .......... .......... .......... 96% 81.8M 0s
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  4200K .......... .......... .......... .......... .......... 99%  111M 0s
  4250K .......... .......... .......... ......               100%  114M=0.7s

2016-01-13 12:01:38 (6.00 MB/s) - ‘hpo/hp.obo’ saved [4388959/4388959]

mkdir -p hpo
mv hpo/hp.obo hpo/human-phenotype-ontology.obo
java -Xmx1G -jar jarFiles/generateAnnotationFile.jar --orphadata "external_orphanet" --sign-mapping "orphanetmapping/onet_hpo.tsv" --out-folder "." --hpo_ontology "hpo" --berkeley-annotated "../annotated/"
Jan 13, 2016 12:01:38 PM ontologizer.go.OBOParser doParse
INFO: Got 11639 terms and 15300 relations in 96 ms
Details of parsed obo file:
  filename:		hpo/human-phenotype-ontology.obo
  date:			null
  format:		1.2
  term definitions:	11639
Jan 13, 2016 12:01:38 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
Jan 13, 2016 12:01:38 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118)
/var/lib/jenkins/jobs/hpo.annotations/workspace/misc/../annotated
.
................................................................................OOOOOHHHHHHHHHHOMIM:233430	GONADAL DYSGENESIS, XY TYPE, WITH ASSOCIATED ANOMALIES					HP:0002564	Malformation of the heart and great vessels			IEA	IEA							OMIM:233430	HPO	Feb 17, 2009	
not found: HP:0002564
makefile:45: recipe for target 'generate-annotation-file' failed
make: *** [generate-annotation-file] Error 1
make: Leaving directory '/var/lib/jenkins/jobs/hpo.annotations/workspace/misc'
Build step 'Execute shell' marked build as failure
Archiving artifacts
Sending e-mails to: sebastian.koehler@charite.de
Finished: FAILURE