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’ 0K .......... .......... .......... .......... .......... 0% 821K 24s 50K .......... .......... .......... .......... .......... 0% 1.52M 18s 100K .......... .......... .......... .......... .......... 0% 1.31M 17s 150K .......... .......... .......... .......... .......... 1% 1.75M 15s 200K .......... .......... .......... .......... .......... 1% 1.47M 15s 250K .......... .......... .......... .......... .......... 1% 5.36M 13s 300K .......... .......... .......... .......... .......... 1% 2.28M 12s 350K .......... .......... .......... .......... .......... 2% 14.3M 11s 400K .......... .......... .......... .......... .......... 2% 1.87M 11s 450K .......... .......... .......... .......... .......... 2% 21.1M 10s 500K .......... .......... .......... .......... .......... 2% 1.55M 10s 550K .......... .......... .......... .......... .......... 3% 19.5M 9s 600K .......... 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.......... 71% 58.0M 0s 14100K .......... .......... .......... .......... .......... 71% 43.3M 0s 14150K .......... .......... .......... .......... .......... 71% 41.9M 0s 14200K .......... .......... .......... .......... .......... 72% 42.5M 0s 14250K .......... .......... .......... .......... .......... 72% 62.6M 0s 14300K .......... .......... .......... .......... .......... 72% 34.3M 0s 14350K .......... .......... .......... .......... .......... 72% 27.2M 0s 14400K .......... .......... .......... .......... .......... 73% 49.5M 0s 14450K .......... .......... .......... .......... .......... 73% 37.9M 0s 14500K .......... .......... .......... .......... .......... 73% 25.9M 0s 14550K .......... .......... .......... .......... .......... 73% 117M 0s 14600K .......... .......... .......... .......... .......... 74% 69.0M 0s 14650K .......... .......... .......... .......... .......... 74% 73.3M 0s 14700K .......... .......... .......... .......... .......... 74% 106M 0s 14750K .......... .......... .......... .......... .......... 74% 92.6M 0s 14800K .......... .......... .......... .......... .......... 75% 55.2M 0s 14850K .......... .......... .......... .......... .......... 75% 1.43M 0s 14900K .......... .......... .......... .......... .......... 75% 17.6M 0s 14950K .......... .......... .......... .......... .......... 75% 59.8M 0s 15000K .......... .......... .......... .......... .......... 76% 62.7M 0s 15050K .......... .......... .......... .......... .......... 76% 67.9M 0s 15100K .......... .......... .......... .......... .......... 76% 83.2M 0s 15150K .......... .......... .......... .......... .......... 76% 39.3M 0s 15200K .......... .......... .......... .......... .......... 77% 72.5M 0s 15250K .......... .......... .......... .......... .......... 77% 36.6M 0s 15300K .......... .......... .......... .......... .......... 77% 85.5M 0s 15350K .......... .......... .......... .......... .......... 77% 84.2M 0s 15400K .......... 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.......... .......... 81% 69.6M 0s 16100K .......... .......... .......... .......... .......... 81% 33.6M 0s 16150K .......... .......... .......... .......... .......... 81% 74.4M 0s 16200K .......... .......... .......... .......... .......... 82% 107M 0s 16250K .......... .......... .......... .......... .......... 82% 67.2M 0s 16300K .......... .......... .......... .......... .......... 82% 105M 0s 16350K .......... .......... .......... .......... .......... 82% 117M 0s 16400K .......... .......... .......... .......... .......... 83% 104M 0s 16450K .......... .......... .......... .......... .......... 83% 118M 0s 16500K .......... .......... .......... .......... .......... 83% 110M 0s 16550K .......... .......... .......... .......... .......... 83% 35.8M 0s 16600K .......... .......... .......... .......... .......... 84% 118M 0s 16650K .......... .......... .......... .......... .......... 84% 104M 0s 16700K .......... .......... .......... .......... .......... 84% 103M 0s 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.......... .......... .......... 88% 114M 0s 17450K .......... .......... .......... .......... .......... 88% 111M 0s 17500K .......... .......... .......... .......... .......... 88% 111M 0s 17550K .......... .......... .......... .......... .......... 88% 79.3M 0s 17600K .......... .......... .......... .......... .......... 89% 83.4M 0s 17650K .......... .......... .......... .......... .......... 89% 113M 0s 17700K .......... .......... .......... .......... .......... 89% 113M 0s 17750K .......... .......... .......... .......... .......... 89% 99.6M 0s 17800K .......... .......... .......... .......... .......... 90% 99.0M 0s 17850K .......... .......... .......... .......... .......... 90% 112M 0s 17900K .......... .......... .......... .......... .......... 90% 111M 0s 17950K .......... .......... .......... .......... .......... 90% 112M 0s 18000K .......... .......... .......... .......... .......... 91% 97.6M 0s 18050K .......... .......... .......... .......... .......... 91% 103M 0s 18100K .......... .......... .......... .......... .......... 91% 8.42M 0s 18150K .......... .......... .......... .......... .......... 91% 36.7M 0s 18200K .......... .......... .......... .......... .......... 92% 89.1M 0s 18250K .......... .......... .......... .......... .......... 92% 24.1M 0s 18300K .......... .......... .......... .......... .......... 92% 70.9M 0s 18350K .......... .......... .......... .......... .......... 93% 118M 0s 18400K .......... .......... .......... .......... .......... 93% 105M 0s 18450K .......... .......... .......... .......... .......... 93% 14.1M 0s 18500K .......... .......... .......... .......... .......... 93% 9.45M 0s 18550K .......... .......... .......... .......... .......... 94% 25.3M 0s 18600K .......... .......... .......... .......... .......... 94% 30.9M 0s 18650K .......... .......... .......... .......... .......... 94% 15.5M 0s 18700K .......... .......... .......... .......... .......... 94% 99.2M 0s 18750K .......... .......... .......... .......... .......... 95% 43.7M 0s 18800K .......... .......... .......... .......... .......... 95% 40.3M 0s 18850K .......... .......... .......... .......... .......... 95% 55.7M 0s 18900K .......... .......... .......... .......... .......... 95% 104M 0s 18950K .......... .......... .......... .......... .......... 96% 66.8M 0s 19000K .......... .......... .......... .......... .......... 96% 6.93M 0s 19050K .......... .......... .......... .......... .......... 96% 12.3M 0s 19100K .......... .......... .......... .......... .......... 96% 72.9M 0s 19150K .......... .......... .......... .......... .......... 97% 102M 0s 19200K .......... .......... .......... .......... .......... 97% 45.8M 0s 19250K .......... .......... .......... .......... .......... 97% 28.3M 0s 19300K .......... .......... .......... .......... .......... 97% 33.3M 0s 19350K .......... .......... .......... .......... .......... 98% 44.5M 0s 19400K .......... .......... .......... .......... .......... 98% 13.9M 0s 19450K .......... .......... .......... .......... .......... 98% 32.9M 0s 19500K .......... .......... .......... .......... .......... 98% 45.2M 0s 19550K .......... .......... .......... .......... .......... 99% 78.9M 0s 19600K .......... .......... .......... .......... .......... 99% 9.98M 0s 19650K .......... .......... .......... .......... .......... 99% 38.9M 0s 19700K .......... .......... .......... .......... .......... 99% 53.9M 0s 19750K .......... .......... .......... .... 100% 60.1M=1.2s 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’ 0K .......... .......... .......... .......... .......... 0% 20.5M 1s 50K .......... .......... .......... .......... .......... 0% 14.2M 1s 100K .......... .......... .......... .......... .......... 1% 26.6M 1s 150K .......... .......... .......... .......... .......... 1% 15.0M 1s 200K .......... .......... .......... .......... .......... 1% 13.1M 1s 250K .......... .......... .......... .......... .......... 2% 37.8M 1s 300K .......... .......... .......... .......... .......... 2% 48.9M 1s 350K .......... .......... .......... .......... .......... 2% 72.8M 1s 400K .......... .......... .......... .......... .......... 3% 66.5M 1s 450K .......... .......... .......... .......... .......... 3% 81.7M 1s 500K .......... .......... .......... .......... .......... 3% 64.8M 1s 550K .......... .......... .......... .......... .......... 4% 119M 0s 600K .......... .......... .......... .......... .......... 4% 68.3M 0s 650K .......... .......... .......... .......... .......... 4% 75.4M 0s 700K .......... .......... .......... .......... .......... 5% 89.0M 0s 750K .......... .......... .......... .......... .......... 5% 98.5M 0s 800K .......... .......... .......... .......... .......... 5% 118M 0s 850K .......... .......... .......... .......... .......... 6% 4.75M 1s 900K .......... .......... .......... .......... .......... 6% 17.9M 1s 950K .......... .......... .......... .......... .......... 6% 17.9M 1s 1000K .......... .......... .......... .......... .......... 7% 18.2M 1s 1050K .......... .......... .......... .......... .......... 7% 29.8M 1s 1100K .......... .......... .......... .......... .......... 7% 36.6M 1s 1150K .......... .......... .......... .......... .......... 8% 59.6M 1s 1200K .......... .......... .......... .......... .......... 8% 62.2M 0s 1250K .......... .......... .......... .......... .......... 8% 118M 0s 1300K .......... .......... .......... .......... .......... 9% 96.2M 0s 1350K .......... .......... .......... .......... .......... 9% 95.1M 0s 1400K .......... .......... .......... .......... .......... 9% 86.2M 0s 1450K .......... .......... .......... .......... .......... 10% 35.1M 0s 1500K .......... .......... .......... .......... .......... 10% 53.2M 0s 1550K .......... .......... .......... .......... .......... 10% 82.4M 0s 1600K .......... .......... .......... .......... .......... 11% 91.1M 0s 1650K .......... .......... .......... .......... .......... 11% 84.7M 0s 1700K .......... .......... .......... .......... .......... 11% 50.3M 0s 1750K .......... .......... .......... .......... .......... 12% 4.07M 0s 1800K .......... .......... .......... .......... .......... 12% 57.3M 0s 1850K .......... .......... .......... .......... .......... 12% 24.3M 0s 1900K .......... .......... .......... .......... .......... 13% 39.7M 0s 1950K .......... .......... .......... .......... .......... 13% 34.6M 0s 2000K .......... .......... .......... .......... .......... 13% 36.1M 0s 2050K .......... .......... .......... .......... .......... 14% 73.3M 0s 2100K .......... .......... .......... .......... .......... 14% 63.4M 0s 2150K .......... .......... .......... .......... .......... 14% 42.0M 0s 2200K .......... .......... .......... .......... .......... 15% 51.9M 0s 2250K .......... .......... .......... .......... .......... 15% 33.5M 0s 2300K .......... .......... .......... .......... .......... 15% 47.7M 0s 2350K .......... .......... .......... .......... .......... 16% 77.9M 0s 2400K .......... .......... .......... .......... .......... 16% 111M 0s 2450K .......... .......... .......... .......... .......... 16% 22.0M 0s 2500K .......... .......... .......... .......... .......... 17% 83.9M 0s 2550K .......... .......... .......... .......... .......... 17% 88.7M 0s 2600K .......... .......... .......... .......... .......... 17% 3.46M 0s 2650K .......... .......... .......... .......... .......... 18% 25.7M 0s 2700K .......... .......... .......... .......... .......... 18% 13.5M 0s 2750K .......... .......... .......... .......... .......... 18% 33.0M 0s 2800K .......... .......... .......... .......... .......... 19% 51.0M 0s 2850K .......... .......... .......... .......... .......... 19% 61.3M 0s 2900K .......... .......... .......... .......... .......... 19% 58.6M 0s 2950K .......... .......... .......... .......... .......... 20% 79.6M 0s 3000K .......... .......... .......... .......... .......... 20% 73.8M 0s 3050K .......... .......... .......... .......... .......... 20% 104M 0s 3100K .......... .......... .......... .......... .......... 21% 118M 0s 3150K .......... .......... .......... .......... .......... 21% 109M 0s 3200K .......... .......... .......... .......... .......... 22% 57.0M 0s 3250K .......... .......... .......... .......... .......... 22% 49.8M 0s 3300K .......... .......... .......... .......... .......... 22% 26.5M 0s 3350K .......... .......... .......... .......... .......... 23% 24.5M 0s 3400K .......... .......... .......... .......... .......... 23% 43.0M 0s 3450K .......... .......... .......... .......... .......... 23% 86.6M 0s 3500K .......... .......... .......... .......... .......... 24% 3.82M 0s 3550K .......... .......... .......... .......... .......... 24% 39.8M 0s 3600K .......... .......... .......... .......... .......... 24% 22.2M 0s 3650K .......... .......... .......... .......... .......... 25% 32.7M 0s 3700K .......... .......... .......... .......... .......... 25% 23.0M 0s 3750K .......... .......... .......... .......... .......... 25% 13.1M 0s 3800K .......... .......... .......... .......... .......... 26% 74.7M 0s 3850K .......... .......... .......... .......... .......... 26% 81.1M 0s 3900K .......... .......... .......... .......... .......... 26% 38.6M 0s 3950K .......... .......... .......... .......... .......... 27% 34.6M 0s 4000K .......... .......... .......... .......... .......... 27% 30.7M 0s 4050K .......... .......... .......... .......... .......... 27% 34.7M 0s 4100K .......... .......... .......... .......... .......... 28% 53.8M 0s 4150K .......... .......... .......... .......... .......... 28% 60.9M 0s 4200K .......... .......... .......... .......... .......... 28% 18.0M 0s 4250K .......... .......... .......... .......... .......... 29% 118M 0s 4300K .......... .......... .......... .......... .......... 29% 77.1M 0s 4350K .......... .......... .......... .......... .......... 29% 99.8M 0s 4400K .......... .......... .......... .......... .......... 30% 4.95M 0s 4450K .......... .......... .......... .......... .......... 30% 38.2M 0s 4500K .......... .......... .......... .......... .......... 30% 42.3M 0s 4550K .......... .......... .......... .......... .......... 31% 31.1M 0s 4600K .......... .......... .......... .......... .......... 31% 10.1M 0s 4650K .......... .......... .......... .......... .......... 31% 14.1M 0s 4700K .......... .......... .......... .......... .......... 32% 55.7M 0s 4750K .......... .......... .......... .......... .......... 32% 36.0M 0s 4800K .......... .......... .......... .......... .......... 32% 51.4M 0s 4850K .......... .......... .......... .......... .......... 33% 56.3M 0s 4900K .......... .......... .......... .......... .......... 33% 34.4M 0s 4950K .......... .......... .......... .......... .......... 33% 59.1M 0s 5000K .......... .......... .......... .......... .......... 34% 44.6M 0s 5050K .......... .......... .......... .......... .......... 34% 24.1M 0s 5100K .......... .......... .......... .......... .......... 34% 24.0M 0s 5150K .......... .......... .......... .......... .......... 35% 88.4M 0s 5200K .......... .......... .......... .......... .......... 35% 92.8M 0s 5250K .......... .......... .......... .......... .......... 35% 9.62M 0s 5300K .......... .......... .......... .......... .......... 36% 40.5M 0s 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.......... .......... 40% 61.2M 0s 6050K .......... .......... .......... .......... .......... 41% 27.2M 0s 6100K .......... .......... .......... .......... .......... 41% 70.1M 0s 6150K .......... .......... .......... .......... .......... 41% 5.60M 0s 6200K .......... .......... .......... .......... .......... 42% 36.5M 0s 6250K .......... .......... .......... .......... .......... 42% 23.8M 0s 6300K .......... .......... .......... .......... .......... 43% 21.1M 0s 6350K .......... .......... .......... .......... .......... 43% 41.1M 0s 6400K .......... .......... .......... .......... .......... 43% 42.2M 0s 6450K .......... .......... .......... .......... .......... 44% 28.4M 0s 6500K .......... .......... .......... .......... .......... 44% 37.2M 0s 6550K .......... .......... .......... .......... .......... 44% 35.8M 0s 6600K .......... .......... .......... .......... .......... 45% 22.7M 0s 6650K .......... .......... .......... .......... .......... 45% 65.1M 0s 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.......... 99% 91.9M 0s 14750K .......... .... 100% 109M=0.5s 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’ 0K .......... .......... .......... .......... .......... 1% 15.9M 0s 50K .......... .......... .......... .......... .......... 2% 12.7M 0s 100K .......... .......... .......... .......... .......... 3% 6.19M 0s 150K .......... .......... .......... .......... .......... 4% 2.71M 1s 200K .......... .......... .......... .......... .......... 5% 84.1K 10s 250K .......... .......... .......... .......... .......... 6% 19.3M 8s 300K .......... .......... .......... .......... .......... 8% 21.7M 7s 350K .......... .......... .......... .......... .......... 9% 23.3M 6s 400K .......... .......... .......... .......... .......... 10% 38.3M 5s 450K .......... .......... .......... .......... .......... 11% 23.4M 5s 500K .......... .......... .......... .......... .......... 12% 41.7M 4s 550K .......... .......... .......... .......... .......... 13% 38.2M 4s 600K 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.......... .......... 93% 111M 0s 4000K .......... .......... .......... .......... .......... 94% 95.0M 0s 4050K .......... .......... .......... .......... .......... 95% 112M 0s 4100K .......... .......... .......... .......... .......... 96% 81.8M 0s 4150K .......... .......... .......... .......... .......... 97% 111M 0s 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