Started by upstream project "hpo.annotations" build number 1254 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 5051 [workspace] $ /bin/sh -xe /tmp/jenkins7803342440589677677.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 --2018-06-13 22:19:28-- 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] --2018-06-13 22:19:29-- 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: 10421735 (9.9M) [application/octet-stream] Saving to: ‘jar/createGene2Phenotype.jar’ 0K .......... .......... .......... .......... .......... 0% 1.51M 7s 50K .......... .......... .......... .......... .......... 0% 3.65M 5s 100K .......... .......... .......... .......... .......... 1% 12.4M 3s 150K .......... .......... .......... .......... .......... 1% 5.64M 3s 200K .......... .......... .......... .......... .......... 2% 7.56M 3s 250K .......... .......... .......... .......... .......... 2% 6.99M 2s 300K .......... .......... .......... .......... .......... 3% 8.39M 2s 350K .......... .......... .......... .......... .......... 3% 5.06M 2s 400K .......... .......... .......... .......... .......... 4% 9.41M 2s 450K .......... .......... .......... .......... .......... 4% 6.94M 2s 500K .......... .......... .......... .......... .......... 5% 9.20M 2s 550K .......... .......... .......... .......... .......... 5% 9.64M 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10050K .......... .......... .......... .......... .......... 99% 75.7M 0s 10100K .......... .......... .......... .......... .......... 99% 22.8M 0s 10150K .......... .......... ....... 100% 149M=0.6s Last-modified header missing -- time-stamps turned off. 2018-06-13 22:19:30 (16.8 MB/s) - ‘jar/createGene2Phenotype.jar’ saved [10421735/10421735] wget -N -P jar https://github.com/Phenomics/hpo-build-jars/raw/master/createMysqlHPODbVersion.jar --2018-06-13 22:19:30-- https://github.com/Phenomics/hpo-build-jars/raw/master/createMysqlHPODbVersion.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/createMysqlHPODbVersion.jar [following] --2018-06-13 22:19:30-- https://raw.githubusercontent.com/Phenomics/hpo-build-jars/master/createMysqlHPODbVersion.jar Connecting to proxy.charite.de (proxy.charite.de)|141.42.1.215|:8080... connected. Proxy request sent, awaiting response... 200 OK Length: 11363315 (11M) [application/octet-stream] Saving to: ‘jar/createMysqlHPODbVersion.jar’ 0K .......... .......... .......... .......... .......... 0% 1.44M 8s 50K .......... .......... .......... .......... .......... 0% 4.09M 5s 100K .......... .......... .......... .......... .......... 1% 10.5M 4s 150K .......... .......... .......... .......... .......... 1% 4.70M 3s 200K .......... .......... .......... .......... .......... 2% 7.52M 3s 250K .......... .......... .......... .......... .......... 2% 6.38M 3s 300K .......... .......... .......... .......... .......... 3% 8.43M 2s 350K .......... .......... .......... .......... .......... 3% 5.80M 2s 400K .......... .......... .......... .......... .......... 4% 6.76M 2s 450K .......... .......... .......... .......... .......... 4% 7.00M 2s 500K .......... .......... .......... .......... .......... 4% 8.42M 2s 550K .......... .......... .......... .......... .......... 5% 7.24M 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.......... .......... 48% 28.3M 0s 5350K .......... .......... .......... .......... .......... 48% 20.9M 0s 5400K .......... .......... .......... .......... .......... 49% 31.9M 0s 5450K .......... .......... .......... .......... .......... 49% 18.1M 0s 5500K .......... .......... .......... .......... .......... 50% 27.2M 0s 5550K .......... .......... .......... .......... .......... 50% 25.7M 0s 5600K .......... .......... .......... .......... .......... 50% 15.2M 0s 5650K .......... .......... .......... .......... .......... 51% 42.3M 0s 5700K .......... .......... .......... .......... .......... 51% 25.3M 0s 5750K .......... .......... .......... .......... .......... 52% 21.5M 0s 5800K .......... .......... .......... .......... .......... 52% 24.7M 0s 5850K .......... .......... .......... .......... .......... 53% 27.1M 0s 5900K .......... .......... .......... .......... .......... 53% 43.3M 0s 5950K .......... .......... .......... .......... .......... 54% 16.4M 0s 6000K .......... .......... .......... .......... .......... 54% 23.9M 0s 6050K .......... .......... .......... .......... .......... 54% 27.8M 0s 6100K .......... .......... .......... .......... .......... 55% 27.2M 0s 6150K .......... .......... .......... .......... .......... 55% 18.0M 0s 6200K .......... .......... .......... .......... .......... 56% 18.9M 0s 6250K .......... .......... .......... .......... .......... 56% 102M 0s 6300K .......... .......... .......... .......... .......... 57% 23.7M 0s 6350K .......... .......... .......... .......... .......... 57% 27.1M 0s 6400K .......... .......... .......... .......... .......... 58% 21.5M 0s 6450K .......... .......... .......... .......... .......... 58% 25.9M 0s 6500K .......... .......... .......... .......... .......... 59% 37.4M 0s 6550K .......... .......... .......... .......... .......... 59% 22.4M 0s 6600K .......... .......... .......... .......... .......... 59% 22.5M 0s 6650K .......... .......... .......... 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.......... .......... .......... .......... 96% 46.7M 0s 10750K .......... .......... .......... .......... .......... 97% 32.4M 0s 10800K .......... .......... .......... .......... .......... 97% 47.5M 0s 10850K .......... .......... .......... .......... .......... 98% 68.3M 0s 10900K .......... .......... .......... .......... .......... 98% 46.5M 0s 10950K .......... .......... .......... .......... .......... 99% 52.3M 0s 11000K .......... .......... .......... .......... .......... 99% 54.7M 0s 11050K .......... .......... .......... .......... ...... 100% 29.0M=0.6s Last-modified header missing -- time-stamps turned off. 2018-06-13 22:19:31 (17.3 MB/s) - ‘jar/createMysqlHPODbVersion.jar’ saved [11363315/11363315] # 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 - --2018-06-13 22:19:31-- 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: 761906 (744K) [text/plain] Saving to: ‘mim2gene_medgen’ 0K .......... .......... .......... .......... .......... 6% 19.9M 0s 50K .......... .......... .......... .......... .......... 13% 21.4M 0s 100K .......... .......... .......... .......... .......... 20% 24.5M 0s 150K .......... .......... .......... .......... .......... 26% 20.9M 0s 200K .......... .......... .......... .......... .......... 33% 36.2M 0s 250K .......... .......... .......... .......... .......... 40% 37.9M 0s 300K .......... .......... .......... .......... .......... 47% 21.8M 0s 350K .......... .......... .......... .......... .......... 53% 41.0M 0s 400K .......... .......... .......... .......... .......... 60% 40.5M 0s 450K .......... .......... .......... .......... .......... 67% 39.3M 0s 500K .......... .......... .......... .......... .......... 73% 36.9M 0s 550K .......... .......... .......... .......... .......... 80% 40.3M 0s 600K .......... .......... .......... .......... .......... 87% 39.7M 0s 650K .......... .......... .......... .......... .......... 94% 31.3M 0s 700K .......... .......... .......... .......... .... 100% 40.3M=0.02s 2018-06-13 22:19:33 (30.3 MB/s) - ‘mim2gene_medgen’ saved [761906/761906] --2018-06-13 22:19:33-- 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: 2886669 (2.8M) [text/plain] Saving to: ‘Homo_sapiens.gene_info.gz’ 0K .......... .......... .......... .......... .......... 1% 22.5M 0s 50K .......... .......... .......... .......... .......... 3% 20.3M 0s 100K .......... .......... .......... .......... .......... 5% 2.28M 0s 150K .......... .......... .......... .......... .......... 7% 25.0M 0s 200K .......... .......... .......... .......... .......... 8% 41.2M 0s 250K .......... .......... .......... .......... .......... 10% 42.9M 0s 300K .......... .......... .......... .......... .......... 12% 94.7M 0s 350K .......... .......... .......... .......... .......... 14% 31.1M 0s 400K .......... .......... .......... .......... .......... 15% 70.5M 0s 450K .......... .......... .......... .......... .......... 17% 44.2M 0s 500K .......... .......... .......... .......... .......... 19% 42.7M 0s 550K .......... .......... .......... .......... .......... 21% 45.7M 0s 600K .......... .......... .......... .......... .......... 23% 59.0M 0s 650K .......... .......... .......... .......... .......... 24% 47.1M 0s 700K .......... .......... .......... .......... .......... 26% 65.3M 0s 750K .......... .......... .......... .......... .......... 28% 43.8M 0s 800K .......... .......... .......... .......... .......... 30% 48.3M 0s 850K .......... .......... .......... .......... .......... 31% 96.0M 0s 900K .......... .......... .......... .......... .......... 33% 45.5M 0s 950K .......... .......... .......... .......... .......... 35% 112M 0s 1000K .......... .......... .......... .......... .......... 37% 49.4M 0s 1050K .......... .......... .......... .......... .......... 39% 48.1M 0s 1100K .......... .......... .......... .......... .......... 40% 113M 0s 1150K .......... .......... .......... .......... .......... 42% 52.6M 0s 1200K .......... .......... .......... .......... .......... 44% 100M 0s 1250K .......... .......... .......... .......... .......... 46% 57.6M 0s 1300K .......... .......... .......... .......... .......... 47% 97.7M 0s 1350K .......... .......... .......... .......... .......... 49% 56.5M 0s 1400K .......... .......... .......... .......... .......... 51% 113M 0s 1450K .......... .......... .......... .......... .......... 53% 61.1M 0s 1500K .......... .......... .......... .......... .......... 54% 89.3M 0s 1550K .......... .......... .......... .......... .......... 56% 35.0M 0s 1600K .......... .......... .......... .......... .......... 58% 99.2M 0s 1650K .......... .......... .......... .......... .......... 60% 112M 0s 1700K .......... .......... .......... .......... .......... 62% 63.1M 0s 1750K .......... .......... .......... .......... .......... 63% 100M 0s 1800K .......... .......... .......... .......... .......... 65% 90.2M 0s 1850K .......... .......... .......... .......... .......... 67% 71.1M 0s 1900K .......... .......... .......... .......... .......... 69% 112M 0s 1950K .......... .......... .......... .......... .......... 70% 65.0M 0s 2000K .......... .......... .......... .......... .......... 72% 112M 0s 2050K .......... .......... .......... .......... .......... 74% 76.6M 0s 2100K .......... .......... .......... .......... .......... 76% 101M 0s 2150K .......... .......... .......... .......... .......... 78% 93.1M 0s 2200K .......... .......... .......... .......... .......... 79% 102M 0s 2250K .......... .......... .......... .......... .......... 81% 78.3M 0s 2300K .......... .......... .......... .......... .......... 83% 113M 0s 2350K .......... .......... .......... .......... .......... 85% 114M 0s 2400K .......... .......... .......... .......... .......... 86% 81.2M 0s 2450K .......... .......... .......... .......... .......... 88% 92.7M 0s 2500K .......... .......... .......... .......... .......... 90% 86.0M 0s 2550K .......... .......... .......... .......... .......... 92% 112M 0s 2600K .......... .......... .......... .......... .......... 94% 67.2M 0s 2650K .......... .......... .......... .......... .......... 95% 46.8M 0s 2700K .......... .......... .......... .......... .......... 97% 113M 0s 2750K .......... .......... .......... .......... .......... 99% 113M 0s 2800K .......... ......... 100% 99.7M=0.07s 2018-06-13 22:19:35 (41.8 MB/s) - ‘Homo_sapiens.gene_info.gz’ saved [2886669/2886669] --2018-06-13 22:19:35-- 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: 19067780 (18M) [text/xml] Saving to: ‘en_product6.xml’ 0K .......... .......... .......... .......... .......... 0% 1.52M 12s 50K .......... .......... .......... .......... .......... 0% 767K 18s 100K .......... .......... .......... .......... .......... 0% 1.49M 16s 150K .......... .......... .......... .......... .......... 1% 1.49M 15s 200K .......... .......... .......... .......... .......... 1% 37.2M 12s 250K .......... .......... .......... .......... .......... 1% 1.53M 12s 300K .......... .......... .......... .......... .......... 1% 1.51M 12s 350K .......... .......... .......... .......... .......... 2% 88.0M 10s 400K .......... .......... .......... .......... .......... 2% 1.50M 11s 450K .......... .......... .......... .......... .......... 2% 64.9M 10s 500K .......... .......... .......... .......... .......... 2% 82.1M 9s 550K .......... .......... .......... .......... .......... 3% 1.54M 9s 600K .......... .......... .......... .......... .......... 3% 87.4M 8s 650K .......... .......... .......... .......... .......... 3% 1.53M 8s 700K .......... .......... .......... .......... .......... 4% 65.8M 8s 750K .......... .......... .......... .......... .......... 4% 39.2M 7s 800K .......... .......... .......... .......... .......... 4% 1.59M 8s 850K .......... .......... .......... .......... .......... 4% 55.9M 7s 900K .......... .......... .......... .......... .......... 5% 55.1M 7s 950K .......... .......... .......... .......... .......... 5% 42.6M 6s 1000K .......... .......... .......... .......... .......... 5% 1.61M 7s 1050K .......... .......... .......... .......... .......... 5% 70.9M 6s 1100K .......... .......... .......... .......... .......... 6% 101M 6s 1150K .......... .......... .......... .......... .......... 6% 57.3M 6s 1200K .......... .......... .......... .......... .......... 6% 1.50M 6s 1250K .......... .......... .......... .......... .......... 6% 102M 6s 1300K .......... .......... .......... .......... .......... 7% 102M 5s 1350K .......... .......... .......... .......... .......... 7% 91.0M 5s 1400K .......... .......... .......... .......... .......... 7% 1.57M 5s 1450K .......... .......... .......... .......... .......... 8% 83.1M 5s 1500K .......... .......... .......... .......... .......... 8% 97.9M 5s 1550K .......... .......... .......... .......... .......... 8% 29.9M 5s 1600K .......... .......... .......... .......... .......... 8% 1.64M 5s 1650K .......... .......... .......... .......... .......... 9% 79.6M 5s 1700K .......... .......... .......... .......... .......... 9% 94.8M 5s 1750K .......... .......... .......... .......... .......... 9% 117M 5s 1800K .......... .......... .......... .......... .......... 9% 85.3M 4s 1850K .......... .......... .......... .......... .......... 10% 1.57M 5s 1900K .......... .......... .......... .......... .......... 10% 99.4M 4s 1950K .......... .......... .......... .......... .......... 10% 81.6M 4s 2000K .......... .......... .......... .......... .......... 11% 83.5M 4s 2050K .......... .......... .......... .......... .......... 11% 121M 4s 2100K .......... .......... .......... .......... .......... 11% 1.60M 4s 2150K .......... .......... .......... .......... .......... 11% 71.7M 4s 2200K .......... .......... .......... .......... .......... 12% 101M 4s 2250K .......... .......... .......... .......... .......... 12% 69.3M 4s 2300K .......... .......... .......... .......... .......... 12% 78.8M 4s 2350K .......... .......... .......... .......... .......... 12% 91.1M 4s 2400K .......... .......... .......... .......... .......... 13% 1.63M 4s 2450K .......... .......... .......... .......... .......... 13% 75.0M 4s 2500K .......... .......... .......... .......... .......... 13% 96.9M 4s 2550K .......... .......... .......... .......... .......... 13% 88.5M 4s 2600K .......... .......... .......... .......... .......... 14% 59.7M 4s 2650K .......... .......... .......... .......... .......... 14% 93.8M 4s 2700K .......... .......... .......... .......... .......... 14% 1.64M 4s 2750K .......... .......... .......... .......... .......... 15% 34.0M 4s 2800K .......... .......... .......... .......... .......... 15% 37.8M 3s 2850K .......... .......... .......... .......... .......... 15% 56.1M 3s 2900K .......... .......... .......... .......... .......... 15% 46.4M 3s 2950K .......... .......... .......... .......... .......... 16% 40.8M 3s 3000K .......... .......... .......... .......... .......... 16% 65.1M 3s 3050K .......... .......... .......... .......... .......... 16% 1.84M 3s 3100K .......... .......... .......... .......... .......... 16% 44.3M 3s 3150K .......... .......... .......... .......... .......... 17% 38.8M 3s 3200K .......... .......... .......... .......... .......... 17% 37.7M 3s 3250K .......... .......... .......... .......... .......... 17% 41.0M 3s 3300K .......... .......... .......... .......... .......... 17% 54.2M 3s 3350K .......... .......... .......... .......... .......... 18% 54.1M 3s 3400K .......... .......... .......... .......... .......... 18% 1.74M 3s 3450K .......... .......... .......... .......... .......... 18% 52.9M 3s 3500K .......... .......... .......... .......... .......... 19% 63.6M 3s 3550K .......... .......... .......... .......... .......... 19% 58.0M 3s 3600K .......... .......... .......... .......... .......... 19% 68.4M 3s 3650K .......... .......... .......... .......... .......... 19% 97.5M 3s 3700K .......... .......... .......... .......... .......... 20% 96.1M 3s 3750K .......... .......... .......... .......... .......... 20% 1.81M 3s 3800K .......... .......... .......... .......... .......... 20% 60.8M 3s 3850K .......... .......... .......... .......... .......... 20% 62.9M 3s 3900K .......... .......... .......... .......... .......... 21% 36.5M 3s 3950K .......... .......... .......... .......... .......... 21% 82.1M 3s 4000K .......... .......... .......... .......... .......... 21% 91.3M 3s 4050K .......... .......... .......... .......... .......... 22% 114M 3s 4100K .......... .......... .......... .......... .......... 22% 102M 3s 4150K .......... .......... .......... .......... .......... 22% 1.76M 3s 4200K .......... .......... .......... .......... .......... 22% 51.2M 3s 4250K .......... .......... .......... .......... .......... 23% 102M 3s 4300K .......... .......... .......... .......... .......... 23% 64.2M 2s 4350K .......... .......... .......... .......... .......... 23% 53.4M 2s 4400K .......... .......... .......... .......... .......... 23% 75.2M 2s 4450K .......... .......... .......... .......... .......... 24% 98.8M 2s 4500K .......... .......... .......... .......... .......... 24% 98.3M 2s 4550K .......... .......... .......... .......... .......... 24% 1.77M 2s 4600K .......... .......... .......... .......... .......... 24% 59.5M 2s 4650K .......... .......... .......... .......... .......... 25% 56.6M 2s 4700K .......... .......... .......... .......... .......... 25% 73.0M 2s 4750K .......... .......... .......... .......... .......... 25% 76.4M 2s 4800K .......... .......... .......... .......... .......... 26% 105M 2s 4850K .......... .......... .......... .......... .......... 26% 42.3M 2s 4900K .......... .......... .......... .......... .......... 26% 82.5M 2s 4950K .......... .......... .......... .......... .......... 26% 88.8M 2s 5000K .......... .......... .......... .......... .......... 27% 99.0M 2s 5050K .......... .......... .......... .......... .......... 27% 1.78M 2s 5100K .......... .......... .......... .......... .......... 27% 86.3M 2s 5150K .......... .......... .......... .......... .......... 27% 91.5M 2s 5200K .......... .......... .......... .......... .......... 28% 105M 2s 5250K .......... .......... .......... .......... .......... 28% 86.3M 2s 5300K .......... .......... .......... .......... .......... 28% 89.8M 2s 5350K .......... .......... .......... .......... .......... 28% 41.1M 2s 5400K .......... .......... .......... .......... .......... 29% 87.4M 2s 5450K .......... .......... .......... .......... .......... 29% 98.2M 2s 5500K .......... .......... .......... .......... .......... 29% 103M 2s 5550K .......... .......... .......... .......... .......... 30% 1.89M 2s 5600K .......... .......... .......... .......... .......... 30% 31.7M 2s 5650K .......... .......... .......... .......... .......... 30% 70.2M 2s 5700K .......... .......... .......... .......... .......... 30% 40.5M 2s 5750K .......... .......... .......... .......... .......... 31% 34.2M 2s 5800K .......... .......... .......... .......... .......... 31% 83.0M 2s 5850K .......... .......... .......... .......... .......... 31% 91.0M 2s 5900K .......... .......... .......... .......... .......... 31% 101M 2s 5950K .......... .......... .......... .......... .......... 32% 106M 2s 6000K .......... .......... .......... .......... .......... 32% 115M 2s 6050K .......... .......... .......... .......... .......... 32% 101M 2s 6100K .......... .......... .......... .......... .......... 33% 111M 2s 6150K .......... .......... .......... .......... .......... 33% 1.93M 2s 6200K .......... .......... .......... .......... .......... 33% 67.3M 2s 6250K .......... .......... .......... .......... .......... 33% 68.5M 2s 6300K .......... .......... .......... .......... .......... 34% 93.8M 2s 6350K .......... .......... .......... .......... .......... 34% 25.5M 2s 6400K .......... .......... .......... .......... .......... 34% 93.3M 2s 6450K .......... .......... .......... .......... .......... 34% 98.5M 2s 6500K .......... .......... .......... .......... .......... 35% 120M 2s 6550K .......... .......... .......... .......... .......... 35% 103M 2s 6600K .......... .......... .......... .......... .......... 35% 88.2M 2s 6650K .......... .......... .......... .......... .......... 35% 41.9M 2s 6700K .......... .......... .......... .......... .......... 36% 115M 2s 6750K .......... .......... .......... .......... .......... 36% 2.00M 2s 6800K .......... .......... .......... .......... .......... 36% 60.9M 2s 6850K .......... .......... .......... .......... .......... 37% 81.9M 2s 6900K .......... .......... .......... .......... .......... 37% 76.5M 2s 6950K .......... .......... .......... .......... .......... 37% 88.3M 2s 7000K .......... .......... .......... .......... .......... 37% 37.7M 2s 7050K .......... .......... .......... .......... .......... 38% 75.0M 1s 7100K .......... .......... .......... .......... .......... 38% 105M 1s 7150K .......... .......... .......... .......... .......... 38% 99.9M 1s 7200K .......... .......... .......... .......... .......... 38% 97.9M 1s 7250K .......... .......... .......... .......... .......... 39% 96.2M 1s 7300K .......... .......... .......... .......... .......... 39% 99.5M 1s 7350K .......... .......... .......... .......... .......... 39% 86.4M 1s 7400K .......... .......... .......... .......... .......... 40% 1.97M 1s 7450K .......... .......... .......... .......... .......... 40% 70.3M 1s 7500K .......... .......... .......... .......... .......... 40% 98.4M 1s 7550K .......... .......... .......... .......... .......... 40% 57.0M 1s 7600K .......... .......... .......... .......... .......... 41% 102M 1s 7650K .......... .......... .......... .......... .......... 41% 101M 1s 7700K .......... .......... .......... .......... .......... 41% 47.7M 1s 7750K .......... .......... .......... .......... .......... 41% 92.2M 1s 7800K .......... .......... .......... .......... .......... 42% 118M 1s 7850K .......... .......... .......... .......... .......... 42% 99.1M 1s 7900K .......... .......... .......... .......... .......... 42% 114M 1s 7950K .......... .......... .......... .......... .......... 42% 98.4M 1s 8000K .......... .......... .......... .......... .......... 43% 108M 1s 8050K .......... .......... .......... .......... .......... 43% 108M 1s 8100K .......... .......... .......... .......... .......... 43% 114M 1s 8150K .......... .......... .......... .......... .......... 44% 1.95M 1s 8200K .......... .......... .......... .......... .......... 44% 64.2M 1s 8250K .......... .......... .......... .......... .......... 44% 80.6M 1s 8300K .......... .......... .......... .......... .......... 44% 89.4M 1s 8350K .......... .......... .......... .......... .......... 45% 88.9M 1s 8400K .......... .......... .......... .......... .......... 45% 87.4M 1s 8450K .......... .......... .......... .......... .......... 45% 108M 1s 8500K .......... .......... .......... .......... .......... 45% 81.7M 1s 8550K .......... .......... .......... .......... .......... 46% 66.9M 1s 8600K .......... .......... .......... .......... .......... 46% 12.7M 1s 8650K .......... .......... .......... .......... .......... 46% 95.3M 1s 8700K .......... .......... .......... .......... .......... 46% 105M 1s 8750K .......... .......... .......... .......... .......... 47% 116M 1s 8800K .......... .......... .......... .......... .......... 47% 90.1M 1s 8850K .......... .......... .......... .......... .......... 47% 117M 1s 8900K .......... .......... .......... .......... .......... 48% 96.2M 1s 8950K .......... .......... .......... .......... .......... 48% 115M 1s 9000K .......... .......... .......... .......... .......... 48% 104M 1s 9050K .......... .......... .......... .......... .......... 48% 2.27M 1s 9100K .......... .......... .......... .......... .......... 49% 103M 1s 9150K .......... .......... .......... .......... .......... 49% 91.1M 1s 9200K .......... .......... .......... .......... .......... 49% 103M 1s 9250K .......... .......... .......... .......... .......... 49% 107M 1s 9300K .......... .......... .......... .......... .......... 50% 119M 1s 9350K .......... .......... .......... .......... .......... 50% 91.3M 1s 9400K .......... .......... .......... .......... .......... 50% 88.8M 1s 9450K .......... .......... .......... .......... .......... 51% 106M 1s 9500K .......... .......... .......... .......... .......... 51% 105M 1s 9550K .......... .......... .......... .......... .......... 51% 12.8M 1s 9600K .......... .......... .......... .......... .......... 51% 99.0M 1s 9650K .......... .......... .......... .......... .......... 52% 102M 1s 9700K .......... .......... .......... .......... .......... 52% 118M 1s 9750K .......... .......... .......... .......... .......... 52% 102M 1s 9800K .......... .......... .......... .......... .......... 52% 109M 1s 9850K .......... .......... .......... .......... .......... 53% 114M 1s 9900K .......... .......... .......... .......... .......... 53% 112M 1s 9950K .......... .......... .......... .......... .......... 53% 2.34M 1s 10000K .......... .......... .......... .......... .......... 53% 69.1M 1s 10050K .......... .......... .......... .......... .......... 54% 92.4M 1s 10100K .......... .......... .......... .......... .......... 54% 91.7M 1s 10150K .......... .......... .......... .......... .......... 54% 99.0M 1s 10200K .......... .......... .......... .......... .......... 55% 49.6M 1s 10250K .......... .......... .......... .......... .......... 55% 78.8M 1s 10300K .......... .......... .......... .......... .......... 55% 86.5M 1s 10350K .......... .......... .......... .......... .......... 55% 97.8M 1s 10400K .......... .......... .......... .......... .......... 56% 109M 1s 10450K .......... .......... .......... .......... .......... 56% 100M 1s 10500K .......... .......... .......... .......... .......... 56% 41.0M 1s 10550K .......... .......... .......... .......... .......... 56% 22.5M 1s 10600K .......... .......... .......... .......... .......... 57% 91.0M 1s 10650K .......... .......... .......... .......... .......... 57% 86.2M 1s 10700K .......... .......... .......... .......... .......... 57% 61.6M 1s 10750K .......... .......... .......... .......... .......... 57% 66.3M 1s 10800K .......... .......... .......... .......... .......... 58% 102M 1s 10850K .......... .......... .......... .......... .......... 58% 102M 1s 10900K .......... .......... .......... .......... .......... 58% 99.4M 1s 10950K .......... .......... .......... .......... .......... 59% 2.55M 1s 11000K .......... .......... .......... .......... .......... 59% 16.2M 1s 11050K .......... .......... .......... .......... .......... 59% 28.5M 1s 11100K .......... .......... .......... .......... .......... 59% 64.5M 1s 11150K .......... .......... .......... .......... .......... 60% 92.6M 1s 11200K .......... .......... .......... .......... .......... 60% 42.8M 1s 11250K .......... .......... .......... .......... .......... 60% 59.8M 1s 11300K .......... .......... .......... .......... .......... 60% 117M 1s 11350K .......... .......... .......... .......... .......... 61% 45.4M 1s 11400K .......... .......... 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64% 4.30M 1s 12100K .......... .......... .......... .......... .......... 65% 15.0M 1s 12150K .......... .......... .......... .......... .......... 65% 43.8M 1s 12200K .......... .......... .......... .......... .......... 65% 22.8M 1s 12250K .......... .......... .......... .......... .......... 66% 53.0M 1s 12300K .......... .......... .......... .......... .......... 66% 67.7M 1s 12350K .......... .......... .......... .......... .......... 66% 70.6M 1s 12400K .......... .......... .......... .......... .......... 66% 37.2M 1s 12450K .......... .......... .......... .......... .......... 67% 67.0M 1s 12500K .......... .......... .......... .......... .......... 67% 75.8M 1s 12550K .......... .......... .......... .......... .......... 67% 119M 1s 12600K .......... .......... .......... .......... .......... 67% 100M 1s 12650K .......... .......... .......... .......... .......... 68% 104M 1s 12700K .......... .......... .......... .......... .......... 68% 119M 1s 12750K 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.......... .......... 72% 31.5M 0s 13450K .......... .......... .......... .......... .......... 72% 34.4M 0s 13500K .......... .......... .......... .......... .......... 72% 64.4M 0s 13550K .......... .......... .......... .......... .......... 73% 17.6M 0s 13600K .......... .......... .......... .......... .......... 73% 71.0M 0s 13650K .......... .......... .......... .......... .......... 73% 45.3M 0s 13700K .......... .......... .......... .......... .......... 73% 49.3M 0s 13750K .......... .......... .......... .......... .......... 74% 91.9M 0s 13800K .......... .......... .......... .......... .......... 74% 68.1M 0s 13850K .......... .......... .......... .......... .......... 74% 104M 0s 13900K .......... .......... .......... .......... .......... 74% 63.9M 0s 13950K .......... .......... .......... .......... .......... 75% 121M 0s 14000K .......... .......... .......... .......... .......... 75% 67.1M 0s 14050K .......... .......... .......... .......... .......... 75% 89.3M 0s 14100K .......... .......... .......... .......... .......... 75% 106M 0s 14150K .......... .......... .......... .......... .......... 76% 104M 0s 14200K .......... .......... .......... .......... .......... 76% 119M 0s 14250K .......... .......... .......... .......... .......... 76% 104M 0s 14300K .......... .......... .......... .......... .......... 77% 119M 0s 14350K .......... .......... .......... .......... .......... 77% 30.4M 0s 14400K .......... .......... .......... .......... .......... 77% 43.6M 0s 14450K .......... .......... .......... .......... .......... 77% 4.27M 0s 14500K .......... .......... .......... .......... .......... 78% 36.4M 0s 14550K .......... .......... .......... .......... .......... 78% 75.4M 0s 14600K .......... .......... .......... .......... .......... 78% 60.0M 0s 14650K .......... .......... .......... .......... .......... 78% 46.5M 0s 14700K .......... .......... .......... .......... .......... 79% 31.4M 0s 14750K .......... 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.......... .......... .......... .......... .......... 97% 108M 0s 18150K .......... .......... .......... .......... .......... 97% 117M 0s 18200K .......... .......... .......... .......... .......... 98% 119M 0s 18250K .......... .......... .......... .......... .......... 98% 101M 0s 18300K .......... .......... .......... .......... .......... 98% 116M 0s 18350K .......... .......... .......... .......... .......... 98% 117M 0s 18400K .......... .......... .......... .......... .......... 99% 98.9M 0s 18450K .......... .......... .......... .......... .......... 99% 94.7M 0s 18500K .......... .......... .......... .......... .......... 99% 84.1M 0s 18550K .......... .......... .......... .......... .......... 99% 113M 0s 18600K .......... .......... 100% 122M=1.3s 2018-06-13 22:19:37 (14.4 MB/s) - ‘en_product6.xml’ saved [19067780/19067780] --2018-06-13 22:19:37-- 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: 19332915 (18M) [application/octet-stream] Saving to: ‘phenotype_annotation.tab’ 0K .......... .......... .......... .......... .......... 0% 34.1M 1s 50K .......... .......... .......... .......... .......... 0% 16.8M 1s 100K .......... .......... .......... .......... .......... 0% 36.7M 1s 150K .......... .......... .......... .......... .......... 1% 24.5M 1s 200K .......... .......... .......... .......... .......... 1% 27.1M 1s 250K .......... .......... .......... .......... .......... 1% 29.1M 1s 300K .......... .......... .......... .......... .......... 1% 36.7M 1s 350K .......... .......... .......... .......... .......... 2% 27.3M 1s 400K .......... .......... .......... .......... .......... 2% 19.6M 1s 450K .......... .......... .......... .......... .......... 2% 61.7M 1s 500K .......... .......... .......... .......... .......... 2% 31.8M 1s 550K .......... .......... .......... .......... .......... 3% 37.3M 1s 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18850K .......... .......... ......... 100% 130M=0.2s 2018-06-13 22:19:37 (84.0 MB/s) - ‘phenotype_annotation.tab’ saved [19332915/19332915] --2018-06-13 22:19:37-- 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] --2018-06-13 22:19:37-- 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: 6004703 (5.7M) [text/plain] Saving to: ‘hp.obo’ 0K .......... .......... .......... .......... .......... 0% 1.46M 4s 50K .......... .......... .......... .......... .......... 1% 4.29M 3s 100K .......... .......... .......... .......... .......... 2% 8.23M 2s 150K .......... .......... .......... .......... .......... 3% 4.97M 2s 200K .......... .......... .......... .......... .......... 4% 6.20M 2s 250K .......... .......... .......... .......... .......... 5% 6.76M 1s 300K .......... .......... .......... .......... .......... 5% 4.43M 1s 350K .......... .......... .......... .......... .......... 6% 8.58M 1s 400K .......... .......... .......... .......... .......... 7% 5.77M 1s 450K .......... .......... .......... .......... .......... 8% 8.73M 1s 500K .......... .......... .......... .......... .......... 9% 7.75M 1s 550K .......... .......... .......... .......... .......... 10% 7.64M 1s 600K .......... .......... 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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 Jun 13, 2018 10:19:38 PM ontologizer.go.OBOParser doParse INFO: Got 13693 terms and 17338 relations in 191 ms Details of parsed obo file: data-version: releases/2018-06-13 format: 1.2 term definitions: 13693 Jun 13, 2018 10:19:38 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot INFO: Ontology contains a single level-one term (All (HP:0000001) Jun 13, 2018 10:19:39 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118) WARN: Frequency of 4250 terms was zero!! Set IC of these to : 9.244065241377804 = -1 * (log(1 / 10343) mims:10426 with inh: 6828 parse NCBI summary of gene_info-file other: 859 tRNA: 599 rRNA: 59 scRNA: 4 biological-region: 2667 protein-coding: 20386 ncRNA: 17142 pseudo: 16394 snRNA: 64 snoRNA: 541 unknown: 1775 entrez2symbol size: 42321 there were 2 unidentified gene-IDs: [107305681, 2439] diseaseid-to-entrezid: 4701 ORPHANETPARSING: orphadisease2HGNCgenes:3726 ORPHANETPARSING: hgncid2entrez:27365 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(): 10426 omim: 7220 orphanet: 3159 others: 47 Disease entries with at least one known disease gene: 6008 Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 10343 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 was null 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 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 = AnnotatedItem [itemId=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 = AnnotatedItem [itemId=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 = AnnotatedItem [itemId=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 = AnnotatedItem [itemId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0] annotations was null java -Xmx1G -jar jar/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 Jun 13, 2018 10:19:53 PM ontologizer.go.OBOParser doParse INFO: Got 13693 terms and 17338 relations in 189 ms Details of parsed obo file: data-version: releases/2018-06-13 format: 1.2 term definitions: 13693 Jun 13, 2018 10:19:53 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot INFO: Ontology contains a single level-one term (All (HP:0000001) Jun 13, 2018 10:19:54 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118) WARN: Frequency of 4250 terms was zero!! Set IC of these to : 9.244065241377804 = -1 * (log(1 / 10343) mims:10426 with inh: 6828 parse NCBI summary of gene_info-file other: 859 tRNA: 599 rRNA: 59 scRNA: 4 biological-region: 2667 protein-coding: 20386 ncRNA: 17142 pseudo: 16394 snRNA: 64 snoRNA: 541 unknown: 1775 entrez2symbol size: 42321 there were 2 unidentified gene-IDs: [107305681, 2439] diseaseid-to-entrezid: 4701 ORPHANETPARSING: orphadisease2HGNCgenes:3726 ORPHANETPARSING: hgncid2entrez:27365 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(): 10426 omim: 7220 orphanet: 3159 others: 47 Disease entries with at least one known disease gene: 6008 Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 10343 06_2018 make connection / created db connecting to jdbc:mysql://localhost:3306/mysql dropping database: MYHPO_06_2018 (if exists) creating database: MYHPO_06_2018 create schema (tables, relations) Execute: [mysql, --user=hudson_mysql, --password=hpo_hudson, --host=localhost, --port=3306, MYHPO_06_2018, -e, source ../tools/hpo_mysqldb/schemabackup_2010-06-18.sql] Done restore. insert terms WARN: invalid external object: 4493 / Fyler WARN: invalid external object: 4504 / Fyler WARN: invalid external object: 4510 / Fyler WARN: invalid external object: 4507 / Fyler WARN: invalid external object: 4503 / Fyler WARN: invalid external object: 4508 / Fyler WARN: invalid external object: 4509 / Fyler WARN: invalid external object: 4502 / Fyler WARN: invalid external object: 4876 / Fyler WARN: invalid external object: 4875 / Fyler WARN: invalid external object: 4310 / Fyler WARN: invalid external object: 4335 / Fyler WARN: invalid external object: 4163 / Fyler WARN: invalid external object: 4868 / Fyler WARN: invalid external object: 4203 / Fyler WARN: invalid external object: 4865 / Fyler WARN: invalid external object: 4864 / Fyler WARN: invalid external object: 4877 / Fyler WARN: invalid external object: 4311 / Fyler WARN: invalid external object: 4866 / Fyler WARN: invalid external object: 4174 / Fyler WARN: invalid external object: 4321 / Fyler WARN: invalid external object: 4338 / Fyler WARN: invalid external object: 4336 / Fyler WARN: invalid external object: 4445 / Fyler WARN: invalid external object: 4404 / Fyler WARN: invalid external object: 1300 / Fyler WARN: invalid external object: 2050 / Fyler WARN: invalid external object: 1533 / Fyler WARN: invalid external object: 1840 / Fyler WARN: invalid external object: 1600 / Fyler WARN: invalid external object: 1602 / Fyler WARN: invalid external object: 1611 / Fyler WARN: invalid external object: 2100 / Fyler WARN: invalid external object: 1843 / Fyler WARN: invalid external object: 1400 / Fyler WARN: invalid external object: 1408 / Fyler WARN: invalid external object: 1411 / Fyler WARN: invalid external object: 0110 / Fyler WARN: invalid external object: 110 / Fyler WARN: invalid external object: 1151 / Fyler WARN: invalid external object: 2020 / Fyler WARN: invalid external object: 0500 / Fyler WARN: invalid external object: 500 / Fyler WARN: invalid external object: 3609 / Fyler WARN: invalid external object: 1120 / Fyler WARN: invalid external object: 1453 / Fyler WARN: invalid external object: 0170 / Fyler WARN: invalid external object: 170 / Fyler WARN: invalid external object: 2000 / Fyler WARN: invalid external object: 7013 / Fyler WARN: invalid external object: 0100 / Fyler WARN: invalid external object: 100 / Fyler WARN: invalid external object: 1900 / Fyler WARN: invalid external object: 1940 / Fyler WARN: invalid external object: 1733 / Fyler WARN: invalid external object: 1820 / Fyler WARN: invalid external object: 1810 / Fyler WARN: invalid external object: 3608 / Fyler WARN: invalid external object: 1511 / Fyler WARN: invalid external object: 600 / Fyler WARN: invalid external object: 606 / Fyler WARN: invalid external object: 4771 / Fyler WARN: invalid external object: 4772 / Fyler WARN: invalid external object: 0200 / Fyler WARN: invalid external object: 200 / Fyler WARN: invalid external object: 4171 / Fyler WARN: invalid external object: 2634 / Fyler WARN: invalid external object: 4444 / Fyler WARN: invalid external object: 4402 / Fyler WARN: invalid external object: 4443 / Fyler WARN: invalid external object: 4412 / Fyler WARN: invalid external object: 4406 / Fyler WARN: invalid external object: 4332 / Fyler WARN: invalid external object: 2201 / Fyler WARN: invalid external object: 4157 / Fyler WARN: invalid external object: 4309 / Fyler WARN: invalid external object: 4234 / Fyler WARN: invalid external object: 4202 / Fyler WARN: invalid external object: 2399 / Fyler WARN: invalid external object: 1432 / Fyler WARN: invalid external object: 4160 / Fyler WARN: invalid external object: 4200 / Fyler WARN: invalid external object: 3816 / Fyler WARN: invalid external object: 4108 / Fyler WARN: invalid external object: 4414 / Fyler WARN: invalid external object: 1430 / Fyler WARN: invalid external object: 0510 / Fyler WARN: invalid external object: 510 / Fyler WARN: invalid external object: 1622 / Fyler WARN: invalid external object: 7160 / Fyler WARN: invalid external object: 1821 / Fyler WARN: invalid external object: 2301 / Fyler WARN: invalid external object: 2708 / Fyler WARN: invalid external object: 2754 / Fyler WARN: invalid external object: 2310 / Fyler WARN: invalid external object: 2701 / Fyler WARN: invalid external object: 2966 / Fyler WARN: invalid external object: 4870 / Fyler WARN: invalid external object: 2706 / Fyler WARN: invalid external object: 1827 / Fyler WARN: invalid external object: 2333 / Fyler WARN: invalid external object: 3040 / Fyler WARN: invalid external object: 0900 / Fyler WARN: invalid external object: 900 / Fyler WARN: invalid external object: 1161 / Fyler WARN: invalid external object: 1601 / Fyler WARN: invalid external object: 4232 / Fyler WARN: invalid external object: 4206 / Fyler WARN: invalid external object: 4492 / Fyler WARN: invalid external object: 3002 / Fyler WARN: invalid external object: 2210 / Fyler WARN: invalid external object: 1889 / Fyler WARN: invalid external object: 0606 / Fyler WARN: invalid external object: 1100 / Fyler WARN: invalid external object: 3100 / Fyler WARN: invalid external object: 10.1007/978-0-387-79948-3_2046 / DOI WARN: invalid external object: 0005291 / MP WARN: invalid external object: 4173 / Fyler WARN: invalid external object: 1815 / Fyler WARN: invalid external object: 4103 / Fyler WARN: invalid external object: 1110 / Fyler WARN: invalid external object: 2030 / Fyler WARN: invalid external object: 3031 / Fyler WARN: invalid external object: 2760 / Fyler WARN: invalid external object: 1001 / Fyler WARN: invalid external object: 2600 / Fyler 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: 4133 / Fyler WARN: invalid external object: 0004947 / MP WARN: invalid external object: 0011478 / MP WARN: invalid external object: 4874 / Fyler WARN: invalid external object: 0150 / Fyler WARN: invalid external object: 150 / Fyler WARN: invalid external object: 0184 / Fyler WARN: invalid external object: 184 / Fyler WARN: invalid external object: 0310 / Fyler WARN: invalid external object: 310 / Fyler WARN: invalid external object: 1140 / Fyler WARN: invalid external object: 2854 / Fyler WARN: invalid external object: 2010 / Fyler WARN: invalid external object: 1720 / Fyler WARN: invalid external object: 1121 / Fyler WARN: invalid external object: 0650 / Fyler WARN: invalid external object: 650 / Fyler WARN: invalid external object: 2761 / Fyler WARN: invalid external object: 0140 / Fyler WARN: invalid external object: 140 / Fyler WARN: invalid external object: 0560 / Fyler WARN: invalid external object: 560 / Fyler WARN: invalid external object: 0520 / Fyler WARN: invalid external object: 520 / Fyler WARN: invalid external object: 0530 / Fyler WARN: invalid external object: 530 / Fyler WARN: invalid external object: 0540 / Fyler WARN: invalid external object: 540 / Fyler WARN: invalid external object: 1241 / Fyler WARN: invalid external object: 1250 / Fyler WARN: invalid external object: 1252 / Fyler WARN: invalid external object: 1340 / Fyler WARN: invalid external object: 1320 / Fyler WARN: invalid external object: 1910 / Fyler WARN: invalid external object: 3101 / Fyler WARN: invalid external object: 2230 / Fyler WARN: invalid external object: 2840 / Fyler WARN: invalid external object: 2316 / Fyler WARN: invalid external object: 0604 / Fyler WARN: invalid external object: 604 / Fyler WARN: invalid external object: 0603 / Fyler WARN: invalid external object: 603 / Fyler WARN: invalid external object: 0550 / Fyler WARN: invalid external object: 550 / Fyler WARN: invalid external object: 0400 / Fyler WARN: invalid external object: 400 / Fyler WARN: invalid external object: 1330 / Fyler WARN: invalid external object: 1310 / Fyler WARN: invalid external object: 7010 / Fyler WARN: invalid external object: 0910 / Fyler WARN: invalid external object: 910 / Fyler WARN: invalid external object: 0920 / Fyler WARN: invalid external object: 0930 / Fyler WARN: invalid external object: 920 / Fyler WARN: invalid external object: 930 / Fyler WARN: invalid external object: 0950 / Fyler WARN: invalid external object: 950 / Fyler WARN: invalid external object: 0008271 / MP WARN: invalid external object: 2002 / Fyler WARN: invalid external object: 2720 / Fyler WARN: invalid external object: 4512 / Fyler WARN: invalid external object: 4235 / Fyler WARN: invalid external object: 3632007 / PMID WARN: invalid external object: 2700 / Fyler WARN: invalid external object: 2704 / Fyler WARN: invalid external object: 0001764 / MP WARN: invalid external object: 4863 / Fyler WARN: invalid external object: 26079824 / PMID WARN: invalid external object: 0005257 / MP WARN: invalid external object: 4135 / Fyler WARN: invalid external object: 4300 / Fyler WARN: invalid external object: 7014 / Fyler WARN: invalid external object: 4447 / Fyler WARN: invalid external object: 4339 / Fyler WARN: invalid external object: 2820 / Fyler WARN: invalid external object: 2810 / Fyler WARN: invalid external object: 1452 / Fyler WARN: invalid external object: 3010 / Fyler WARN: invalid external object: 1770 / Fyler 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: 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 WARN: invalid external object: 1771 / Fyler WARN: invalid external object: 2859 / Fyler WARN: invalid external object: 0190 / Fyler WARN: invalid external object: 190 / Fyler WARN: invalid external object: 3129 / Fyler WARN: invalid external object: 2346 / Fyler WARN: invalid external object: 3000 / Fyler WARN: invalid external object: 26379327 / PMID WARN: invalid external object: 18616733 / PMID WARN: invalid external object: 18809899 / PMID WARN: invalid external object: 3011 / Fyler WARN: invalid external object: 3020 / Fyler WARN: invalid external object: 0700 / Fyler WARN: invalid external object: 700 / Fyler WARN: invalid external object: 4013 / Fyler WARN: invalid external object: sjwang / RGD WARN: invalid external object: 2233 / Fyler WARN: invalid external object: 2780 / Fyler WARN: invalid external object: 2240 / Fyler WARN: invalid external object: 3817 / Fyler WARN: invalid external object: 1652 / Fyler WARN: invalid external object: 1480 / Fyler WARN: invalid external object: 1486 / Fyler WARN: invalid external object: 1484 / Fyler WARN: invalid external object: 2732 / Fyler WARN: invalid external object: 4867 / Fyler WARN: invalid external object: 2841 / Fyler WARN: invalid external object: 1431 / Fyler WARN: invalid external object: D005264 / MeSH insert graph-path allpathes.size() = 206384 insert term2term Insert annotations: dumping to file: ./MYHPO_06_2018.sql calling: [mysqldump, --user=hudson_mysql, --password=hpo_hudson, --host=localhost, --port=3306, MYHPO_06_2018] Done dumping to file. exiting... make: Leaving directory '/var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation' Archiving artifacts Finished: SUCCESS