SuccessConsole Output

Started by user koehler
Building in workspace /var/lib/jenkins/jobs/hpo.annotations/workspace
Cleaning local Directory .
Checking out https://github.com/monarch-initiative/hpo-annotation-data/trunk/rare-diseases@HEAD at revision HEAD
A         README.txt
A         annotated
A         annotated/DECIPHER-1.tab
A         annotated/DECIPHER-14.tab
A         annotated/DECIPHER-15.tab
A         annotated/DECIPHER-16.tab
A         annotated/DECIPHER-17.tab
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A         annotated/DECIPHER-76.tab
A         annotated/DECIPHER-8.tab
A         annotated/DECIPHER-81.tab
A         annotated/DECIPHER-85.tab
A         annotated/DECIPHER-92.tab
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AU        annotated/OMIM-100650.tab
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AU        annotated/OMIM-616078.tab
AU        annotated/OMIM-616079.tab
AU        annotated/OMIM-616080.tab
AU        annotated/OMIM-616081.tab
AU        annotated/OMIM-616083.tab
AU        annotated/OMIM-616084.tab
A         annotated/OMIM-616089.tab
AU        annotated/OMIM-616094.tab
AU        annotated/OMIM-616095.tab
AU        annotated/OMIM-616098.tab
AU        annotated/OMIM-616099.tab
AU        annotated/OMIM-616100.tab
AU        annotated/OMIM-616106.tab
AU        annotated/OMIM-616108.tab
AU        annotated/OMIM-616111.tab
AU        annotated/OMIM-616113.tab
AU        annotated/OMIM-616115.tab
AU        annotated/OMIM-616116.tab
A         annotated/OMIM-616117.tab
AU        annotated/OMIM-616118.tab
AU        annotated/OMIM-616126.tab
AU        annotated/OMIM-616127.tab
AU        annotated/OMIM-616138.tab
AU        annotated/OMIM-616139.tab
AU        annotated/OMIM-616140.tab
AU        annotated/OMIM-616145.tab
A         annotated/OMIM-616151.tab
A         annotated/OMIM-616152.tab
AU        annotated/OMIM-616154.tab
AU        annotated/OMIM-616155.tab
AU        annotated/OMIM-616158.tab
AU        annotated/OMIM-616165.tab
AU        annotated/OMIM-616166.tab
AU        annotated/OMIM-616170.tab
AU        annotated/OMIM-616171.tab
AU        annotated/OMIM-616172.tab
AU        annotated/OMIM-616176.tab
AU        annotated/OMIM-616185.tab
AU        annotated/OMIM-616187.tab
AU        annotated/OMIM-616188.tab
AU        annotated/OMIM-616192.tab
AU        annotated/OMIM-616193.tab
AU        annotated/OMIM-616198.tab
AU        annotated/OMIM-616199.tab
AU        annotated/OMIM-616200.tab
AU        annotated/OMIM-616201.tab
AU        annotated/OMIM-616202.tab
AU        annotated/OMIM-616204.tab
AU        annotated/OMIM-616208.tab
AU        annotated/OMIM-616209.tab
AU        annotated/OMIM-616211.tab
AU        annotated/OMIM-616212.tab
AU        annotated/OMIM-616214.tab
AU        annotated/OMIM-616216.tab
AU        annotated/OMIM-616217.tab
AU        annotated/OMIM-616219.tab
AU        annotated/OMIM-616220.tab
A         annotated/OMIM-616221.tab
AU        annotated/OMIM-616222.tab
A         annotated/OMIM-616227.tab
AU        annotated/OMIM-616228.tab
AU        annotated/OMIM-616229.tab
AU        annotated/OMIM-616230.tab
AU        annotated/OMIM-616231.tab
AU        annotated/OMIM-616233.tab
AU        annotated/OMIM-616239.tab
AU        annotated/OMIM-616247.tab
AU        annotated/OMIM-616248.tab
AU        annotated/OMIM-616249.tab
AU        annotated/OMIM-616255.tab
AU        annotated/OMIM-616258.tab
AU        annotated/OMIM-616260.tab
AU        annotated/OMIM-616263.tab
AU        annotated/OMIM-616265.tab
AU        annotated/OMIM-616266.tab
AU        annotated/OMIM-616267.tab
AU        annotated/OMIM-616268.tab
AU        annotated/OMIM-616269.tab
A         annotated/OMIM-616270.tab
AU        annotated/OMIM-616271.tab
AU        annotated/OMIM-616276.tab
AU        annotated/OMIM-616277.tab
AU        annotated/OMIM-616278.tab
A         annotated/OMIM-616279.tab
AU        annotated/OMIM-616280.tab
A         annotated/OMIM-616281.tab
AU        annotated/OMIM-616282.tab
AU        annotated/OMIM-616286.tab
AU        annotated/OMIM-616287.tab
AU        annotated/OMIM-616289.tab
AU        annotated/OMIM-616291.tab
AU        annotated/OMIM-616294.tab
AU        annotated/OMIM-616295.tab
AU        annotated/OMIM-616298.tab
AU        annotated/OMIM-616299.tab
AU        annotated/OMIM-616300.tab
AU        annotated/OMIM-616304.tab
AU        annotated/OMIM-616307.tab
A         annotated/OMIM-616311.tab
AU        annotated/OMIM-616313.tab
AU        annotated/OMIM-616314.tab
AU        annotated/OMIM-616321.tab
AU        annotated/OMIM-616322.tab
AU        annotated/OMIM-616323.tab
AU        annotated/OMIM-616324.tab
AU        annotated/OMIM-616325.tab
AU        annotated/OMIM-616326.tab
AU        annotated/OMIM-616329.tab
AU        annotated/OMIM-616330.tab
AU        annotated/OMIM-616331.tab
AU        annotated/OMIM-616335.tab
AU        annotated/OMIM-616339.tab
AU        annotated/OMIM-616340.tab
AU        annotated/OMIM-616341.tab
AU        annotated/OMIM-616342.tab
A         annotated/OMIM-616345.tab
AU        annotated/OMIM-616346.tab
A         annotated/OMIM-616351.tab
AU        annotated/OMIM-616353.tab
AU        annotated/OMIM-616354.tab
A         annotated/OMIM-616355.tab
A         annotated/OMIM-616357.tab
AU        annotated/OMIM-616361.tab
A         annotated/OMIM-616362.tab
A         annotated/OMIM-616364.tab
AU        annotated/OMIM-616366.tab
AU        annotated/OMIM-616367.tab
AU        annotated/OMIM-616368.tab
AU        annotated/OMIM-616369.tab
AU        annotated/OMIM-616370.tab
AU        annotated/OMIM-616371.tab
AU        annotated/OMIM-616373.tab
A         annotated/OMIM-616389.tab
A         annotated/OMIM-616390.tab
AU        annotated/OMIM-616393.tab
AU        annotated/OMIM-616394.tab
A         annotated/OMIM-616395.tab
AU        annotated/OMIM-616398.tab
AU        annotated/OMIM-616399.tab
AU        annotated/OMIM-616400.tab
AU        annotated/OMIM-616402.tab
AU        annotated/OMIM-616409.tab
AU        annotated/OMIM-616410.tab
AU        annotated/OMIM-616411.tab
AU        annotated/OMIM-616413.tab
AU        annotated/OMIM-616414.tab
AU        annotated/OMIM-616415.tab
AU        annotated/OMIM-616418.tab
AU        annotated/OMIM-616420.tab
AU        annotated/OMIM-616421.tab
AU        annotated/OMIM-616425.tab
AU        annotated/OMIM-616428.tab
AU        annotated/OMIM-616430.tab
AU        annotated/OMIM-616433.tab
AU        annotated/OMIM-616435.tab
A         annotated/OMIM-616436.tab
AU        annotated/OMIM-616437.tab
AU        annotated/OMIM-616439.tab
AU        annotated/OMIM-616445.tab
AU        annotated/OMIM-616449.tab
AU        annotated/OMIM-616451.tab
AU        annotated/OMIM-616452.tab
AU        annotated/OMIM-616455.tab
AU        annotated/OMIM-616457.tab
AU        annotated/OMIM-616459.tab
AU        annotated/OMIM-616460.tab
AU        annotated/OMIM-616461.tab
AU        annotated/OMIM-616462.tab
AU        annotated/OMIM-616468.tab
AU        annotated/OMIM-616469.tab
A         annotated/OMIM-616470.tab
A         annotated/OMIM-616471.tab
AU        annotated/OMIM-616479.tab
AU        annotated/OMIM-616481.tab
AU        annotated/OMIM-616482.tab
AU        annotated/OMIM-616486.tab
AU        annotated/OMIM-616487.tab
AU        annotated/OMIM-616488.tab
AU        annotated/OMIM-616489.tab
AU        annotated/OMIM-616490.tab
AU        annotated/OMIM-616491.tab
AU        annotated/OMIM-616494.tab
AU        annotated/OMIM-616500.tab
AU        annotated/OMIM-616501.tab
AU        annotated/OMIM-616502.tab
AU        annotated/OMIM-616503.tab
AU        annotated/OMIM-616505.tab
AU        annotated/OMIM-616507.tab
AU        annotated/OMIM-616509.tab
AU        annotated/OMIM-616511.tab
A         annotated/OMIM-616515.tab
AU        annotated/OMIM-616516.tab
AU        annotated/OMIM-616517.tab
AU        annotated/OMIM-616521.tab
AU        annotated/OMIM-616531.tab
AU        annotated/OMIM-616532.tab
A         annotated/OMIM-616535.tab
AU        annotated/OMIM-616538.tab
AU        annotated/OMIM-616539.tab
AU        annotated/OMIM-616540.tab
AU        annotated/OMIM-616541.tab
AU        annotated/OMIM-616544.tab
AU        annotated/OMIM-616546.tab
AU        annotated/OMIM-616549.tab
AU        annotated/OMIM-616553.tab
AU        annotated/OMIM-616559.tab
AU        annotated/OMIM-616562.tab
AU        annotated/OMIM-616564.tab
AU        annotated/OMIM-616566.tab
AU        annotated/OMIM-616570.tab
AU        annotated/OMIM-616576.tab
AU        annotated/OMIM-616577.tab
AU        annotated/OMIM-616579.tab
AU        annotated/OMIM-616580.tab
AU        annotated/OMIM-616583.tab
AU        annotated/OMIM-616586.tab
AU        annotated/OMIM-616589.tab
AU        annotated/OMIM-616592.tab
AU        annotated/OMIM-616602.tab
AU        annotated/OMIM-616603.tab
AU        annotated/OMIM-616604.tab
AU        annotated/OMIM-616606.tab
AU        annotated/OMIM-616617.tab
AU        annotated/OMIM-616625.tab
AU        annotated/OMIM-616629.tab
AU        annotated/OMIM-616632.tab
AU        annotated/OMIM-616636.tab
AU        annotated/OMIM-616649.tab
AU        annotated/OMIM-616651.tab
AU        annotated/OMIM-616652.tab
AU        annotated/OMIM-616654.tab
AU        annotated/OMIM-616657.tab
AU        annotated/OMIM-616668.tab
AU        annotated/OMIM-616672.tab
AU        annotated/OMIM-616680.tab
AU        annotated/OMIM-616681.tab
AU        annotated/OMIM-616682.tab
AU        annotated/OMIM-616684.tab
AU        annotated/OMIM-616685.tab
AU        annotated/OMIM-616687.tab
AU        annotated/OMIM-616688.tab
AU        annotated/OMIM-616689.tab
AU        annotated/OMIM-616716.tab
AU        annotated/OMIM-616719.tab
AU        annotated/OMIM-616720.tab
AU        annotated/OMIM-616721.tab
AU        annotated/OMIM-616722.tab
AU        annotated/OMIM-616723.tab
AU        annotated/OMIM-616724.tab
AU        annotated/OMIM-616732.tab
AU        annotated/OMIM-616734.tab
AU        annotated/OMIM-616738.tab
A         annotated/OMIM-616777.tab
A         annotated/OMIM-616779.tab
A         ignore_for_annotation.txt
A         misc
A         misc/.gitignore
A         misc/cataract
A         misc/cataract/MIM-107250.tab
A         misc/cataract/MIM-115650.tab
A         misc/cataract/MIM-115665.tab
A         misc/cataract/MIM-116600.tab
A         misc/cataract/MIM-116800.tab
A         misc/cataract/MIM-123680.tab
A         misc/cataract/MIM-123730.tab
A         misc/cataract/MIM-154050.tab
A         misc/cataract/MIM-600897.tab
A         misc/cataract/MIM-601885.tab
A         misc/cataract/MIM-604307.tab
A         misc/cataract/MIM-607304.tab
A         misc/cataract/MIM-608810-AR.tab
A         misc/cataract/MIM-608810.tab
A         misc/cataract/MIM-610634.tab
A         misc/cataract/MIM-611597.tab
A         misc/excelfiles
A         misc/excelfiles/Analysis_Table.xls
A         misc/excelfiles/Analysis_Table_NEW_13-09-11.xls
A         misc/excelfiles/Analysis_novel_18-09-11.xls
A         misc/excelfiles/Prioritized DECIPHER_for_Annotation.xls
A         misc/excelfiles/Prioritized-Disease-List.xls
A         misc/excelfiles/candidates_alpha-3.xls
A         misc/helpscripts
A         misc/helpscripts/fixDate.pl
A         misc/jarFiles
A         misc/jarFiles/generateAnnotationFile.jar
A         misc/makefile
A         misc/phenote
A         misc/phenote/hpo.cfg
A         omim-genes
A         omim-genes/OMIM-100640.tab
AU        omim-genes/OMIM-100650.tab
A         omim-genes/OMIM-100675.tab
At revision 4582
[workspace] $ /bin/sh -xe /tmp/hudson5570881140423739116.sh
+ make -C misc
make: Entering directory '/var/lib/jenkins/jobs/hpo.annotations/workspace/misc'
mkdir -p data
# load orphanet data
wget -N -P data http://www.orphadata.org/data/xml/en_product4_HPO.xml
--2017-01-23 20:45:09--  http://www.orphadata.org/data/xml/en_product4_HPO.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: 20594851 (20M) [text/xml]
Saving to: ‘data/en_product4_HPO.xml’

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  6650K .......... .......... .......... .......... .......... 33%  100M 2s
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  6750K .......... .......... .......... .......... .......... 33% 2.36M 2s
  6800K .......... .......... .......... .......... .......... 34% 55.0M 2s
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 20100K .......... ..                                         100%  125M=1.3s

2017-01-23 20:45:11 (15.2 MB/s) - ‘data/en_product4_HPO.xml’ saved [20594851/20594851]

# loads the HPO
wget -N -P data http://compbio.charite.de/jenkins/job/hpo/lastSuccessfulBuild/artifact/hp/hp.obo
--2017-01-23 20:45:11--  http://compbio.charite.de/jenkins/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... 200 OK
Length: 5152218 (4.9M) [application/octet-stream]
Saving to: ‘data/hp.obo’

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    50K .......... .......... .......... .......... ..........  1% 13.3M 0s
   100K .......... .......... .......... .......... ..........  2% 6.65M 0s
   150K .......... .......... .......... .......... ..........  3% 3.40M 1s
   200K .......... .......... .......... .......... ..........  4% 3.95M 1s
   250K .......... .......... .......... .......... ..........  5% 23.4K 34s
   300K .......... .......... .......... .......... ..........  6% 19.7M 29s
   350K .......... .......... .......... .......... ..........  7% 15.4M 25s
   400K .......... .......... .......... .......... ..........  8% 32.3M 22s
   450K .......... .......... .......... .......... ..........  9% 21.2M 20s
   500K .......... .......... .......... .......... .......... 10% 28.3M 18s
   550K .......... .......... .......... .......... .......... 11% 29.4M 16s
   600K .......... .......... .......... .......... .......... 12% 24.3M 15s
   650K .......... .......... .......... .......... .......... 13% 24.0M 14s
   700K .......... .......... .......... .......... .......... 14% 38.1M 13s
   750K .......... .......... .......... .......... .......... 15% 28.9M 12s
   800K .......... .......... .......... .......... .......... 16% 23.7M 11s
   850K .......... .......... .......... .......... .......... 17% 30.2M 10s
   900K .......... .......... .......... .......... .......... 18% 30.6M 9s
   950K .......... .......... .......... .......... .......... 19% 30.5M 9s
  1000K .......... .......... .......... .......... .......... 20% 43.1M 8s
  1050K .......... .......... .......... .......... .......... 21% 43.4M 8s
  1100K .......... .......... .......... .......... .......... 22% 36.1M 7s
  1150K .......... .......... .......... .......... .......... 23% 37.4M 7s
  1200K .......... .......... .......... .......... .......... 24% 89.4M 7s
  1250K .......... .......... .......... .......... .......... 25% 39.9M 6s
  1300K .......... .......... .......... .......... .......... 26% 38.7M 6s
  1350K .......... .......... .......... .......... .......... 27% 50.0M 6s
  1400K .......... .......... .......... .......... .......... 28% 54.8M 5s
  1450K .......... .......... .......... .......... .......... 29% 54.1M 5s
  1500K .......... .......... .......... .......... .......... 30% 33.3M 5s
  1550K .......... .......... .......... .......... .......... 31% 36.8M 5s
  1600K .......... .......... .......... .......... .......... 32% 96.7M 5s
  1650K .......... .......... .......... .......... .......... 33% 33.2M 4s
  1700K .......... .......... .......... .......... .......... 34% 61.6M 4s
  1750K .......... .......... .......... .......... .......... 35% 45.8M 4s
  1800K .......... .......... .......... .......... .......... 36% 33.2M 4s
  1850K .......... .......... .......... .......... .......... 37% 64.3M 4s
  1900K .......... .......... .......... .......... .......... 38% 67.9M 4s
  1950K .......... .......... .......... .......... .......... 39% 72.1M 3s
  2000K .......... .......... .......... .......... .......... 40% 71.3M 3s
  2050K .......... .......... .......... .......... .......... 41% 71.8M 3s
  2100K .......... .......... .......... .......... .......... 42% 65.4M 3s
  2150K .......... .......... .......... .......... .......... 43% 83.7M 3s
  2200K .......... .......... .......... .......... .......... 44% 48.5M 3s
  2250K .......... .......... .......... .......... .......... 45% 56.4M 3s
  2300K .......... .......... .......... .......... .......... 46% 63.4M 3s
  2350K .......... .......... .......... .......... .......... 47% 37.3M 2s
  2400K .......... .......... .......... .......... .......... 48% 99.2M 2s
  2450K .......... .......... .......... .......... .......... 49% 65.7M 2s
  2500K .......... .......... .......... .......... .......... 50% 84.6M 2s
  2550K .......... .......... .......... .......... .......... 51%  102M 2s
  2600K .......... .......... .......... .......... .......... 52% 60.8M 2s
  2650K .......... .......... .......... .......... .......... 53% 88.6M 2s
  2700K .......... .......... .......... .......... .......... 54% 94.8M 2s
  2750K .......... .......... .......... .......... .......... 55% 65.4M 2s
  2800K .......... .......... .......... .......... .......... 56% 94.4M 2s
  2850K .......... .......... .......... .......... .......... 57%  114M 2s
  2900K .......... .......... .......... .......... .......... 58% 75.2M 2s
  2950K .......... .......... .......... .......... .......... 59% 78.9M 2s
  3000K .......... .......... .......... .......... .......... 60% 58.3M 1s
  3050K .......... .......... .......... .......... .......... 61% 65.9M 1s
  3100K .......... .......... .......... .......... .......... 62% 97.7M 1s
  3150K .......... .......... .......... .......... .......... 63% 89.9M 1s
  3200K .......... .......... .......... .......... .......... 64% 68.9M 1s
  3250K .......... .......... .......... .......... .......... 65% 94.7M 1s
  3300K .......... .......... .......... .......... .......... 66% 52.7M 1s
  3350K .......... .......... .......... .......... .......... 67%  113M 1s
  3400K .......... .......... .......... .......... .......... 68% 97.2M 1s
  3450K .......... .......... .......... .......... .......... 69% 71.7M 1s
  3500K .......... .......... .......... .......... .......... 70%  113M 1s
  3550K .......... .......... .......... .......... .......... 71%  113M 1s
  3600K .......... .......... .......... .......... .......... 72%  113M 1s
  3650K .......... .......... .......... .......... .......... 73% 75.4M 1s
  3700K .......... .......... .......... .......... .......... 74%  113M 1s
  3750K .......... .......... .......... .......... .......... 75% 91.7M 1s
  3800K .......... .......... .......... .......... .......... 76% 82.0M 1s
  3850K .......... .......... .......... .......... .......... 77%  113M 1s
  3900K .......... .......... .......... .......... .......... 78% 69.9M 1s
  3950K .......... .......... .......... .......... .......... 79%  113M 1s
  4000K .......... .......... .......... .......... .......... 80%  113M 1s
  4050K .......... .......... .......... .......... .......... 81%  113M 1s
  4100K .......... .......... .......... .......... .......... 82%  112M 0s
  4150K .......... .......... .......... .......... .......... 83% 59.2M 0s
  4200K .......... .......... .......... .......... .......... 84% 95.1M 0s
  4250K .......... .......... .......... .......... .......... 85%  113M 0s
  4300K .......... .......... .......... .......... .......... 86%  113M 0s
  4350K .......... .......... .......... .......... .......... 87% 73.4M 0s
  4400K .......... .......... .......... .......... .......... 88%  114M 0s
  4450K .......... .......... .......... .......... .......... 89%  112M 0s
  4500K .......... .......... .......... .......... .......... 90% 81.2M 0s
  4550K .......... .......... .......... .......... .......... 91%  113M 0s
  4600K .......... .......... .......... .......... .......... 92%  113M 0s
  4650K .......... .......... .......... .......... .......... 93%  113M 0s
  4700K .......... .......... .......... .......... .......... 94%  113M 0s
  4750K .......... .......... .......... .......... .......... 95% 68.7M 0s
  4800K .......... .......... .......... .......... .......... 96%  113M 0s
  4850K .......... .......... .......... .......... .......... 97%  113M 0s
  4900K .......... .......... .......... .......... .......... 98% 75.0M 0s
  4950K .......... .......... .......... .......... .......... 99%  113M 0s
  5000K .......... .......... .......... .                    100%  116M=2.3s

2017-01-23 20:45:13 (2.17 MB/s) - ‘data/hp.obo’ saved [5152218/5152218]

java -Xmx1G -jar jarFiles/generateAnnotationFile.jar --orphadata "data/en_product4_HPO.xml" --out-folder "." --hpo_ontology "data/hp.obo" --berkeley-annotated "../annotated/" --only-before "01-01-2016"
parse: data/hp.obo
Jan 23, 2017 8:45:14 PM ontologizer.go.OBOParser doParse
INFO: Got 12243 terms and 15909 relations in 183 ms
Details of parsed obo file:
  data-version:		releases/2017-01-23
  format:		1.2
  term definitions:	12243
Jan 23, 2017 8:45:14 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
Jan 23, 2017 8:45:14 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
.
......................................................................................filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000006	Autosomal dominant inheritance			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0004322	Short stature			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000256	Macrocephaly			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000248	Brachycephaly			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000337	Broad forehead			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000348	High forehead			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000324	Facial asymmetry			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000322	Short philtrum			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000396	Overfolded helix			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000389	Chronic otitis media			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0011228	Horizontal eyebrow			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000527	Long eyelashes			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000455	Broad nasal tip			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000347	Micrognathia			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000218	High palate			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000699	Diastema			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0001643	Patent ductus arteriosus			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0012450	Chronic constipation			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000028	Cryptorchidism			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000122	Unilateral renal agenesis			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000126	Hydronephrosis			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000965	Cutis marmorata			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0001252	Muscular hypotonia			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0001263	Global developmental delay			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0001250	Seizures			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000238	Hydrocephalus			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0001288	Gait disturbance			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0002119	Ventriculomegaly			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0002079	Hypoplasia of the corpus callosum			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0001320	Cerebellar vermis hypoplasia			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000739	Anxiety			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0007018	Attention deficit hyperactivity disorder			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000729	Autistic behavior			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
filter this Thu Feb 25 00:00:00 CET 2016
OMIM:609757	#609757 WILLIAMS-BEUREN REGION DUPLICATION SYNDROME					HP:0000824	Growth hormone deficiency			TAS	TAS							OMIM	HPO:skoehler	Feb 25, 2016	
..............
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....................................................................................................
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....................................................................................................
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....................................................................................................
...........................................filter this Fri Jul 08 00:00:00 CEST 2016
OMIM:215150	#215150 OTOSPONDYLOMEGAEPIPHYSEAL DYSPLASIA; OSMED;;CHONDRODYSTROPHY WITH SENSORINEURAL DEAFNESS;;NANCE-INSLEY SYNDROME;;NANCE-SWEENEY CHONDRODYSPLASIA					HP:0004568	Beaking of vertebral bodies			TAS	TAS							OMIM:215150	HPO:probinson	08-Jul-2016	
.........................................................
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....................................................................................................
....................................................................................................
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....................................................................................................
............................................filter this Mon Feb 01 00:00:00 CET 2016
OMIM:600204	#600204 EPIPHYSEAL DYSPLASIA, MULTIPLE, 2; EDM2					HP:0010585	Small epiphyses			TAS	TAS							OMIM:600204	HPO:probinson	Feb 1, 2016
filter this Mon Feb 01 00:00:00 CET 2016
OMIM:600204	#600204 EPIPHYSEAL DYSPLASIA, MULTIPLE, 2; EDM2					HP:0011463	Childhood onset			TAS	TAS							OMIM:600204	HPO:probinson	Feb 1, 2016
........................................................
...............................................................filter this Tue Jul 19 00:00:00 CEST 2016
OMIM:115310	PARAGANGLIOMAS 4					HP:0006824	Cranial nerve paralysis			TAS	TAS							OMIM:115310	HPO:probinson	19-Jul-2016	
filter this Fri Jul 22 00:00:00 CEST 2016
OMIM:115310	PARAGANGLIOMAS 4					HP:0011976	Elevated urinary catecholamines			TAS	TAS						With pheochromocytoma	OMIM:115310	HPO:probinson	22-Jul-2016	
.......................Unknown header column: SEX
..............
....................................................................................................
...................................................................filter this Wed Jul 20 00:00:00 CEST 2016
OMIM:147891	SMALL PATELLA SYNDROME					HP:0004322	Short stature			TAS	TAS							OMIM:147891	HPO:probinson	20-Jul-2016	
filter this Wed Jul 20 00:00:00 CEST 2016
OMIM:147891	SMALL PATELLA SYNDROME					HP:0002812	Coxa vara			TAS	TAS							OMIM:147891	HPO:probinson	20-Jul-2016	
filter this Wed Jul 20 00:00:00 CEST 2016
OMIM:147891	SMALL PATELLA SYNDROME					HP:0008368	Tarsal synostosis			TAS	TAS							OMIM:147891	HPO:probinson	20-Jul-2016	
.................................
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...........................................................................filter this Tue Jul 19 00:00:00 CEST 2016
OMIM:605373	PARAGANGLIOMAS 3					HP:0006824	Cranial nerve paralysis			TAS	TAS							OMIM:605373	HPO:probinson	19-Jul-2016	
filter this Fri Jul 22 00:00:00 CEST 2016
OMIM:605373	PARAGANGLIOMAS 3					HP:0008629	Pulsatile tinnitus			TAS	TAS						With tympanic paraganglioma	OMIM:605373	HPO:probinson	22-Jul-2016	
filter this Mon Jul 25 00:00:00 CEST 2016
OMIM:605373	PARAGANGLIOMAS 3					HP:0001609	Hoarse voice			TAS	TAS						caused by tumor impingement	OMIM:605373	HPO:probinson	25-Jul-2016	
.........................
..........................................................filter this Mon Feb 01 00:00:00 CET 2016
OMIM:615237	CONGENITAL SHORT BOWEL SYNDROME; CSBS					HP:0000007	Autosomal recessive inheritance			TAS	TAS							OMIM:615237	HPO:skoehler	01-Feb-2016	
..........................................
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....................................................................................................
....................................................................................................
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....................................................................................................
.....................................................................filter this Tue Jul 19 00:00:00 CEST 2016
OMIM:601650	PARAGANGLIOMAS 2					HP:0006824	Cranial nerve paralysis			TAS	TAS							OMIM:601650	HPO:probinson	19-Jul-2016	
filter this Fri Jul 22 00:00:00 CEST 2016
OMIM:601650	PARAGANGLIOMAS 2					HP:0008629	Pulsatile tinnitus			TAS	TAS						With tympanic paraganglioma	OMIM:601650	HPO:probinson	22-Jul-2016	
filter this Mon Jul 25 00:00:00 CEST 2016
OMIM:601650	PARAGANGLIOMAS 2					HP:0001609	Hoarse voice			TAS	TAS						caused by tumor impingement	OMIM:601650	HPO:probinson	25-Jul-2016	
...............................
.......filter this Fri Jul 22 00:00:00 CEST 2016
OMIM:168000	PARAGANGLIOMAS 1					HP:0008629	Pulsatile tinnitus			TAS	TAS						With tympanic paraganglioma	OMIM:168000	HPO:probinson	22-Jul-2016	
filter this Mon Jul 25 00:00:00 CEST 2016
OMIM:168000	PARAGANGLIOMAS 1					HP:0001609	Hoarse voice			TAS	TAS						caused by tumor impingement	OMIM:168000	HPO:probinson	25-Jul-2016	
.............................................................................................
....................................................................................................
....................................................................................................
....................................................................................................
....................................................................................................
......................filter this Thu Mar 31 00:00:00 CEST 2016
OMIM:614380	#614380 COMPLEMENT COMPONENT 4A DEFICIENCY; C4AD;;C4A DEFICIENCY					HP:0000979	Purpura			TAS	TAS							OMIM:614380	HPO:skoehler	Mar 31, 2016	
........................filter this Wed Jul 20 00:00:00 CEST 2016
OMIM:218649	CRANIOSYNOSTOSIS-MENTAL RETARDATION SYNDROME OF LIN AND GETTIG					HP:0001188	Hand clenching			TAS	TAS							OMIM:218649	HPO	20-Jul-2016	
......................................................
....................................................................................................
..........filter this Sun Jul 03 00:00:00 CEST 2016
OMIM:243300	CHOLESTASIS, BENIGN RECURRENT INTRAHEPATIC 1					HP:0012202	Increased serum bile acid concentration			TAS	TAS							OMIM:243300	HPO:probinson	03-Jul-2016	
..........................................................................................
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.................................................................
Reading Orphanet HPO annotation file...
number of Orphanet entries with annotation: 2501
number of Orphanet entries with name: 2501
...done
Start iterating the 2501 Orphanet entries.
processing orphanet number: 261102	number annotations: 14
processing orphanet number: 411777	number annotations: 8
processing orphanet number: 2793	number annotations: 13
processing orphanet number: 2792	number annotations: 23
processing orphanet number: 289916	number annotations: 22
processing orphanet number: 1461	number annotations: 13
processing orphanet number: 2790	number annotations: 13
processing orphanet number: 1458	number annotations: 33
processing orphanet number: 2305	number annotations: 12
processing orphanet number: 31112	number annotations: 6
processing orphanet number: 52055	number annotations: 24
processing orphanet number: 1457	number annotations: 18
processing orphanet number: 2787	number annotations: 10
processing orphanet number: 1455	number annotations: 5
processing orphanet number: 2785	number annotations: 23
processing orphanet number: 2301	number annotations: 7
processing orphanet number: 1454	number annotations: 48
processing orphanet number: 2300	number annotations: 3
processing orphanet number: 1453	number annotations: 7
processing orphanet number: 52056	number annotations: 12
processing orphanet number: 1452	number annotations: 55
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processing orphanet number: 261236	number annotations: 40
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processing orphanet number: 2019	number annotations: 10
processing orphanet number: 2017	number annotations: 4
processing orphanet number: 740	number annotations: 92
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processing orphanet number: 221016	number annotations: 28
processing orphanet number: 186	number annotations: 32
processing orphanet number: 189	number annotations: 29
processing orphanet number: 1842	number annotations: 39
processing orphanet number: 1849	number annotations: 1
processing orphanet number: 1848	number annotations: 18
processing orphanet number: 324723	number annotations: 2
processing orphanet number: 190	number annotations: 8
processing orphanet number: 191	number annotations: 62
processing orphanet number: 192	number annotations: 72
processing orphanet number: 193	number annotations: 64
processing orphanet number: 194	number annotations: 1
processing orphanet number: 79373	number annotations: 48
processing orphanet number: 93672	number annotations: 45
processing orphanet number: 195	number annotations: 20
processing orphanet number: 199	number annotations: 100
processing orphanet number: 2701	number annotations: 29
processing orphanet number: 314911	number annotations: 16
processing orphanet number: 1852	number annotations: 6
processing orphanet number: 314918	number annotations: 4
processing orphanet number: 1858	number annotations: 15
processing orphanet number: 2705	number annotations: 4
processing orphanet number: 2704	number annotations: 11
processing orphanet number: 1856	number annotations: 13
processing orphanet number: 70567	number annotations: 8
processing orphanet number: 90154	number annotations: 28
processing orphanet number: 90153	number annotations: 30
processing orphanet number: 324713	number annotations: 7
processing orphanet number: 90158	number annotations: 9
processing orphanet number: 90157	number annotations: 6
processing orphanet number: 444051	number annotations: 19
processing orphanet number: 79361	number annotations: 16
processing orphanet number: 1865	number annotations: 16
processing orphanet number: 2712	number annotations: 43
processing orphanet number: 2710	number annotations: 84
processing orphanet number: 1861	number annotations: 13
processing orphanet number: 1860	number annotations: 40
processing orphanet number: 2719	number annotations: 45
processing orphanet number: 309108	number annotations: 7
processing orphanet number: 2717	number annotations: 10
processing orphanet number: 2716	number annotations: 19
processing orphanet number: 2715	number annotations: 29
processing orphanet number: 1867	number annotations: 10
processing orphanet number: 324703	number annotations: 11
processing orphanet number: 1880	number annotations: 18
processing orphanet number: 324708	number annotations: 9
processing orphanet number: 86918	number annotations: 2
processing orphanet number: 79395	number annotations: 7
processing orphanet number: 86919	number annotations: 3
processing orphanet number: 79394	number annotations: 13
processing orphanet number: 79397	number annotations: 9
processing orphanet number: 79396	number annotations: 14
processing orphanet number: 1877	number annotations: 12
processing orphanet number: 2724	number annotations: 6
processing orphanet number: 79399	number annotations: 16
processing orphanet number: 1876	number annotations: 13
processing orphanet number: 59305	number annotations: 3
processing orphanet number: 1875	number annotations: 14
processing orphanet number: 2722	number annotations: 11
processing orphanet number: 86923	number annotations: 2
processing orphanet number: 1873	number annotations: 9
processing orphanet number: 2720	number annotations: 26
processing orphanet number: 1872	number annotations: 5
processing orphanet number: 1871	number annotations: 5
processing orphanet number: 59303	number annotations: 15
processing orphanet number: 1879	number annotations: 7
processing orphanet number: 1878	number annotations: 9
processing orphanet number: 2725	number annotations: 21
processing orphanet number: 1891	number annotations: 9
processing orphanet number: 86909	number annotations: 21
processing orphanet number: 86914	number annotations: 2
processing orphanet number: 1885	number annotations: 11
processing orphanet number: 2732	number annotations: 14
processing orphanet number: 1883	number annotations: 14
processing orphanet number: 1882	number annotations: 15
processing orphanet number: 59315	number annotations: 30
processing orphanet number: 1409	number annotations: 19
processing orphanet number: 1408	number annotations: 12
processing orphanet number: 1406	number annotations: 16
processing orphanet number: 69126	number annotations: 15
processing orphanet number: 70592	number annotations: 5
processing orphanet number: 2746	number annotations: 27
processing orphanet number: 1414	number annotations: 20
processing orphanet number: 2745	number annotations: 23
processing orphanet number: 2744	number annotations: 8
processing orphanet number: 1897	number annotations: 16
processing orphanet number: 1412	number annotations: 3
processing orphanet number: 1896	number annotations: 53
processing orphanet number: 1895	number annotations: 28
processing orphanet number: 2742	number annotations: 4
processing orphanet number: 1410	number annotations: 6
processing orphanet number: 2741	number annotations: 19
processing orphanet number: 1894	number annotations: 6
processing orphanet number: 1892	number annotations: 7
processing orphanet number: 2749	number annotations: 9
processing orphanet number: 95409	number annotations: 44
processing orphanet number: 1416	number annotations: 10
processing orphanet number: 238750	number annotations: 42
processing orphanet number: 2760	number annotations: 7
processing orphanet number: 261534	number annotations: 34
processing orphanet number: 1426	number annotations: 18
processing orphanet number: 1425	number annotations: 29
processing orphanet number: 1423	number annotations: 11
processing orphanet number: 1422	number annotations: 22
processing orphanet number: 1420	number annotations: 25
processing orphanet number: 2750	number annotations: 65
processing orphanet number: 1429	number annotations: 2
processing orphanet number: 411590	number annotations: 22
processing orphanet number: 1427	number annotations: 19
processing orphanet number: 93258	number annotations: 21
processing orphanet number: 93256	number annotations: 32
processing orphanet number: 397685	number annotations: 9
processing orphanet number: 93259	number annotations: 35
processing orphanet number: 2771	number annotations: 14
processing orphanet number: 261524	number annotations: 18
processing orphanet number: 2770	number annotations: 28
processing orphanet number: 98941	number annotations: 5
processing orphanet number: 261529	number annotations: 22
processing orphanet number: 226316	number annotations: 5
processing orphanet number: 1437	number annotations: 13
processing orphanet number: 2768	number annotations: 1
processing orphanet number: 1436	number annotations: 9
processing orphanet number: 1435	number annotations: 6
processing orphanet number: 1434	number annotations: 9
processing orphanet number: 1433	number annotations: 10
processing orphanet number: 281127	number annotations: 1
processing orphanet number: 2762	number annotations: 12
processing orphanet number: 281122	number annotations: 2
processing orphanet number: 83453	number annotations: 11
processing orphanet number: 1438	number annotations: 24
processing orphanet number: 95429	number annotations: 4
processing orphanet number: 46059	number annotations: 45
processing orphanet number: 1451	number annotations: 44
processing orphanet number: 226307	number annotations: 19
processing orphanet number: 1450	number annotations: 14
processing orphanet number: 2781	number annotations: 49
processing orphanet number: 1448	number annotations: 11
processing orphanet number: 2779	number annotations: 7
processing orphanet number: 226310	number annotations: 16
processing orphanet number: 1447	number annotations: 4
processing orphanet number: 2777	number annotations: 7
processing orphanet number: 261519	number annotations: 26
processing orphanet number: 2776	number annotations: 9
processing orphanet number: 226313	number annotations: 29
processing orphanet number: 2774	number annotations: 21
processing orphanet number: 36258	number annotations: 10
processing orphanet number: 2773	number annotations: 8
processing orphanet number: 2772	number annotations: 21
processing orphanet number: 238769	number annotations: 33
processing orphanet number: 230800	number annotations: 12
processing orphanet number: 306498	number annotations: 23
done parsing and merging: writing annotations to file /var/lib/jenkins/jobs/hpo.annotations/workspace/misc/./phenotype_annotation.tab
done.
printing warnings. please fix ASAP:
 ORPHANET:2489 annotated with obsolete term: obsolete Bilateral choroid coloboma (HP:0007956)
 ORPHANET:424 annotated with obsolete term: obsolete Tachycardia (with pheochromocytoma) (HP:0001673)
 ORPHANET:1359 annotated with obsolete term: obsolete Palpitations (with pheochromocytoma) (HP:0001676)
 ORPHANET:99819 annotated with obsolete term: obsolete Tachycardia (with pheochromocytoma) (HP:0001673)

cat phenotype_annotation.tab negative_phenotype_annotation.tab | awk -F'\t' '{print $14}'  | sort | uniq -c | sort -nr > curator-statistics.tab
echo "2017-01-23 20:45" > data_version.txt
make: Leaving directory '/var/lib/jenkins/jobs/hpo.annotations/workspace/misc'
Archiving artifacts
Sending e-mails to: sebastian.koehler@charite.de
Warning: you have no plugins providing access control for builds, so falling back to legacy behavior of permitting any downstream builds to be triggered
Triggering a new build of hpo.annotations.monthly
Finished: SUCCESS