SuccessConsole Output

Started by upstream project "hpo.annotations" build number 1244
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/annotationupdate
A         tools/annotationupdate/external_data.txt
A         tools/annotationupdate/jar
A         tools/annotationupdate/jar/SuggestAnnotations.jar
A         tools/annotationupdate/makefile
A         tools/gene2phenotype
A         tools/gene2phenotype/createGene2Phenotype.jar
A         tools/hpo_mysqldb
A         tools/hpo_mysqldb/createMysqlHPODbVersion.jar
A         tools/hpo_mysqldb/schemabackup_2010-06-18.sql
At revision 4738
no change for https://github.com/monarch-initiative/hpo-annotation-data/trunk/util since the previous build
[workspace] $ /bin/sh -xe /tmp/hudson2921513409247758549.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*
# 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 -
--2017-10-09 10:33:16--  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: 754593 (737K) [text/plain]
Saving to: ‘mim2gene_medgen’

     0K .......... .......... .......... .......... ..........  6% 7.10M 0s
    50K .......... .......... .......... .......... .......... 13% 11.6M 0s
   100K .......... .......... .......... .......... .......... 20% 65.2M 0s
   150K .......... .......... .......... .......... .......... 27% 14.8M 0s
   200K .......... .......... .......... .......... .......... 33% 16.2M 0s
   250K .......... .......... .......... .......... .......... 40% 13.1M 0s
   300K .......... .......... .......... .......... .......... 47% 40.6M 0s
   350K .......... .......... .......... .......... .......... 54% 15.2M 0s
   400K .......... .......... .......... .......... .......... 61% 15.9M 0s
   450K .......... .......... .......... .......... .......... 67% 14.7M 0s
   500K .......... .......... .......... .......... .......... 74% 41.9M 0s
   550K .......... .......... .......... .......... .......... 81% 14.1M 0s
   600K .......... .......... .......... .......... .......... 88% 27.8M 0s
   650K .......... .......... .......... .......... .......... 94% 20.5M 0s
   700K .......... .......... .......... ......               100% 56.6M=0.04s

2017-10-09 10:33:19 (17.1 MB/s) - ‘mim2gene_medgen’ saved [754593/754593]

--2017-10-09 10:33:19--  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: 2878332 (2.7M) [text/plain]
Saving to: ‘Homo_sapiens.gene_info.gz’

     0K .......... .......... .......... .......... ..........  1% 9.27M 0s
    50K .......... .......... .......... .......... ..........  3% 17.5M 0s
   100K .......... .......... .......... .......... ..........  5% 21.6K 41s
   150K .......... .......... .......... .......... ..........  7% 7.92M 30s
   200K .......... .......... .......... .......... ..........  8% 16.8M 24s
   250K .......... .......... .......... .......... .......... 10% 20.2M 20s
   300K .......... .......... .......... .......... .......... 12% 17.1M 16s
   350K .......... .......... .......... .......... .......... 14% 52.5M 14s
   400K .......... .......... .......... .......... .......... 16% 18.7M 12s
   450K .......... .......... .......... .......... .......... 17% 19.1M 11s
   500K .......... .......... .......... .......... .......... 19% 46.5M 10s
   550K .......... .......... .......... .......... .......... 21% 14.9M 9s
   600K .......... .......... .......... .......... .......... 23% 96.3M 8s
   650K .......... .......... .......... .......... .......... 24% 16.1M 7s
   700K .......... .......... .......... .......... .......... 26% 18.4M 6s
   750K .......... .......... .......... .......... .......... 28% 83.5M 6s
   800K .......... .......... .......... .......... .......... 30% 18.8M 5s
   850K .......... .......... .......... .......... .......... 32% 94.0M 5s
   900K .......... .......... .......... .......... .......... 33% 16.5M 5s
   950K .......... .......... .......... .......... .......... 35% 84.7M 4s
  1000K .......... .......... .......... .......... .......... 37% 20.6M 4s
  1050K .......... .......... .......... .......... .......... 39% 69.7M 4s
  1100K .......... .......... .......... .......... .......... 40% 25.0M 3s
  1150K .......... .......... .......... .......... .......... 42% 64.9M 3s
  1200K .......... .......... .......... .......... .......... 44% 18.1M 3s
  1250K .......... .......... .......... .......... .......... 46% 36.6M 3s
  1300K .......... .......... .......... .......... .......... 48% 33.8M 3s
  1350K .......... .......... .......... .......... .......... 49% 60.8M 2s
  1400K .......... .......... .......... .......... .......... 51% 19.9M 2s
  1450K .......... .......... .......... .......... .......... 53% 36.5M 2s
  1500K .......... .......... .......... .......... .......... 55% 80.6M 2s
  1550K .......... .......... .......... .......... .......... 56% 51.0M 2s
  1600K .......... .......... .......... .......... .......... 58% 29.1M 2s
  1650K .......... .......... .......... .......... .......... 60% 48.6M 2s
  1700K .......... .......... .......... .......... .......... 62% 46.6M 1s
  1750K .......... .......... .......... .......... .......... 64% 46.2M 1s
  1800K .......... .......... .......... .......... .......... 65% 41.9M 1s
  1850K .......... .......... .......... .......... .......... 67% 28.2M 1s
  1900K .......... .......... .......... .......... .......... 69% 89.5M 1s
  1950K .......... .......... .......... .......... .......... 71% 22.1M 1s
  2000K .......... .......... .......... .......... .......... 72% 96.2M 1s
  2050K .......... .......... .......... .......... .......... 74% 44.3M 1s
  2100K .......... .......... .......... .......... .......... 76% 90.5M 1s
  2150K .......... .......... .......... .......... .......... 78% 20.9M 1s
  2200K .......... .......... .......... .......... .......... 80% 98.6M 1s
  2250K .......... .......... .......... .......... .......... 81% 56.6M 1s
  2300K .......... .......... .......... .......... .......... 83% 21.3M 0s
  2350K .......... .......... .......... .......... .......... 85% 74.5M 0s
  2400K .......... .......... .......... .......... .......... 87% 82.0M 0s
  2450K .......... .......... .......... .......... .......... 88% 33.7M 0s
  2500K .......... .......... .......... .......... .......... 90% 52.3M 0s
  2550K .......... .......... .......... .......... .......... 92% 96.9M 0s
  2600K .......... .......... .......... .......... .......... 94% 23.0M 0s
  2650K .......... .......... .......... .......... .......... 96%  112M 0s
  2700K .......... .......... .......... .......... .......... 97% 96.5M 0s
  2750K .......... .......... .......... .......... .......... 99% 97.4M 0s
  2800K ..........                                            100%  214M=2.4s

2017-10-09 10:33:24 (1.14 MB/s) - ‘Homo_sapiens.gene_info.gz’ saved [2878332/2878332]

--2017-10-09 10:33:24--  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: 18429919 (18M) [text/xml]
Saving to: ‘en_product6.xml’

     0K .......... .......... .......... .......... ..........  0%  645K 28s
    50K .......... .......... .......... .......... ..........  0%  624K 28s
   100K .......... .......... .......... .......... ..........  0% 1.15M 24s
   150K .......... .......... .......... .......... ..........  1% 1.13M 22s
   200K .......... .......... .......... .......... ..........  1% 1.11M 20s
   250K .......... .......... .......... .......... ..........  1% 1.11M 20s
   300K .......... .......... .......... .......... ..........  1% 1.18M 19s
   350K .......... .......... .......... .......... ..........  2% 1.13M 18s
   400K .......... .......... .......... .......... ..........  2% 45.5M 16s
   450K .......... .......... .......... .......... ..........  2% 1.17M 16s
   500K .......... .......... .......... .......... ..........  3% 66.1M 15s
   550K .......... .......... .......... .......... ..........  3% 1.16M 15s
   600K .......... .......... .......... .......... ..........  3% 49.8M 13s
   650K .......... .......... .......... .......... ..........  3%  102M 12s
   700K .......... .......... .......... .......... ..........  4% 1.10M 13s
   750K .......... .......... .......... .......... ..........  4% 88.8M 12s
   800K .......... .......... .......... .......... ..........  4%  903K 12s
   850K .......... .......... .......... .......... ..........  5%  121M 11s
   900K .......... .......... .......... .......... ..........  5%  114M 11s
   950K .......... .......... .......... .......... ..........  5% 1.37M 11s
  1000K .......... .......... .......... .......... ..........  5% 89.6M 10s
  1050K .......... .......... .......... .......... ..........  6% 1.12M 11s
  1100K .......... .......... .......... .......... ..........  6% 78.3M 10s
  1150K .......... .......... .......... .......... ..........  6% 77.4M 10s
  1200K .......... .......... .......... .......... ..........  6%  105M 9s
  1250K .......... .......... .......... .......... ..........  7% 1.11M 9s
  1300K .......... .......... .......... .......... ..........  7% 64.3M 9s
  1350K .......... .......... .......... .......... ..........  7% 86.9M 9s
  1400K .......... .......... .......... .......... ..........  8% 30.3M 8s
  1450K .......... .......... .......... .......... ..........  8% 1.11M 9s
  1500K .......... .......... .......... .......... ..........  8% 47.7M 8s
  1550K .......... .......... .......... .......... ..........  8% 5.84M 8s
  1600K .......... .......... .......... .......... ..........  9% 11.2M 8s
  1650K .......... .......... .......... .......... ..........  9% 63.4M 8s
  1700K .......... .......... .......... .......... ..........  9% 1.53M 8s
  1750K .......... .......... .......... .......... .......... 10% 30.0M 7s
  1800K .......... .......... .......... .......... .......... 10% 15.7M 7s
  1850K .......... .......... .......... .......... .......... 10% 43.2M 7s
  1900K .......... .......... .......... .......... .......... 10% 58.2M 7s
  1950K .......... .......... .......... .......... .......... 11% 35.2M 7s
  2000K .......... .......... .......... .......... .......... 11% 1.27M 7s
  2050K .......... .......... .......... .......... .......... 11% 63.9M 7s
  2100K .......... .......... .......... .......... .......... 11% 17.9M 6s
  2150K .......... .......... .......... .......... .......... 12% 47.0M 6s
  2200K .......... .......... .......... .......... .......... 12% 76.4M 6s
  2250K .......... .......... .......... .......... .......... 12% 44.6M 6s
  2300K .......... .......... .......... .......... .......... 13% 1.17M 6s
  2350K .......... .......... .......... .......... .......... 13% 86.0M 6s
  2400K .......... .......... .......... .......... .......... 13% 44.2M 6s
  2450K .......... .......... .......... .......... .......... 13% 17.7M 6s
  2500K .......... .......... .......... .......... .......... 14% 78.4M 6s
  2550K .......... .......... .......... .......... .......... 14% 63.0M 5s
  2600K .......... .......... .......... .......... .......... 14% 57.3M 5s
  2650K .......... .......... .......... .......... .......... 15% 1.15M 5s
  2700K .......... .......... .......... .......... .......... 15% 86.9M 5s
  2750K .......... .......... .......... .......... .......... 15% 61.5M 5s
  2800K .......... .......... .......... .......... .......... 15% 17.5M 5s
  2850K .......... .......... .......... .......... .......... 16% 65.4M 5s
  2900K .......... .......... .......... .......... .......... 16% 29.2M 5s
  2950K .......... .......... .......... .......... .......... 16% 57.3M 5s
  3000K .......... .......... .......... .......... .......... 16% 97.5M 5s
  3050K .......... .......... .......... .......... .......... 17% 1.29M 5s
  3100K .......... .......... .......... .......... .......... 17% 96.3M 5s
  3150K .......... .......... .......... .......... .......... 17% 82.9M 5s
  3200K .......... .......... .......... .......... .......... 18% 30.6M 5s
  3250K .......... .......... .......... .......... .......... 18% 62.1M 5s
  3300K .......... .......... .......... .......... .......... 18% 52.9M 4s
  3350K .......... .......... .......... .......... .......... 18% 20.8M 4s
  3400K .......... .......... .......... .......... .......... 19% 50.1M 4s
  3450K .......... .......... .......... .......... .......... 19% 79.4M 4s
  3500K .......... .......... .......... .......... .......... 19%  111M 4s
  3550K .......... .......... .......... .......... .......... 20% 1.53M 4s
  3600K .......... .......... .......... .......... .......... 20% 69.4M 4s
  3650K .......... .......... .......... .......... .......... 20% 98.0M 4s
  3700K .......... .......... .......... .......... .......... 20%  103M 4s
  3750K .......... .......... .......... .......... .......... 21% 21.8M 4s
  3800K .......... .......... .......... .......... .......... 21% 89.9M 4s
  3850K .......... .......... .......... .......... .......... 21% 71.4M 4s
  3900K .......... .......... .......... .......... .......... 21% 38.7M 4s
  3950K .......... .......... .......... .......... .......... 22% 67.0M 4s
  4000K .......... .......... .......... .......... .......... 22%  122M 4s
  4050K .......... .......... .......... .......... .......... 22%  113M 4s
  4100K .......... .......... .......... .......... .......... 23% 1.51M 4s
  4150K .......... .......... .......... .......... .......... 23% 72.0M 4s
  4200K .......... .......... .......... .......... .......... 23%  114M 4s
  4250K .......... .......... .......... .......... .......... 23%  106M 3s
  4300K .......... .......... .......... .......... .......... 24% 35.3M 3s
  4350K .......... .......... .......... .......... .......... 24% 84.0M 3s
  4400K .......... .......... .......... .......... .......... 24% 68.5M 3s
  4450K .......... .......... .......... .......... .......... 25% 93.2M 3s
  4500K .......... .......... .......... .......... .......... 25% 99.4M 3s
  4550K .......... .......... .......... .......... .......... 25% 39.3M 3s
  4600K .......... .......... .......... .......... .......... 25% 79.8M 3s
  4650K .......... .......... .......... .......... .......... 26%  109M 3s
  4700K .......... .......... .......... .......... .......... 26% 80.8M 3s
  4750K .......... .......... .......... .......... .......... 26% 72.0M 3s
  4800K .......... .......... .......... .......... .......... 26% 1.57M 3s
  4850K .......... .......... .......... .......... .......... 27% 86.1M 3s
  4900K .......... .......... .......... .......... .......... 27% 57.0M 3s
  4950K .......... .......... .......... .......... .......... 27% 52.5M 3s
  5000K .......... .......... .......... .......... .......... 28% 58.1M 3s
  5050K .......... .......... .......... .......... .......... 28% 89.8M 3s
  5100K .......... .......... .......... .......... .......... 28% 79.5M 3s
  5150K .......... .......... .......... .......... .......... 28% 73.4M 3s
  5200K .......... .......... .......... .......... .......... 29% 69.1M 3s
  5250K .......... .......... .......... .......... .......... 29% 63.5M 3s
  5300K .......... .......... .......... .......... .......... 29% 36.0M 3s
  5350K .......... .......... .......... .......... .......... 30% 51.3M 3s
  5400K .......... .......... .......... .......... .......... 30% 65.5M 3s
  5450K .......... .......... .......... .......... .......... 30% 93.1M 3s
  5500K .......... .......... .......... .......... .......... 30% 92.6M 3s
  5550K .......... .......... .......... .......... .......... 31% 1.73M 3s
  5600K .......... .......... .......... .......... .......... 31% 42.6M 3s
  5650K .......... .......... .......... .......... .......... 31% 83.2M 3s
  5700K .......... .......... .......... .......... .......... 31%  119M 3s
  5750K .......... .......... .......... .......... .......... 32% 93.6M 2s
  5800K .......... .......... .......... .......... .......... 32% 87.0M 2s
  5850K .......... .......... .......... .......... .......... 32% 59.8M 2s
  5900K .......... .......... .......... .......... .......... 33% 51.2M 2s
  5950K .......... .......... .......... .......... .......... 33% 81.7M 2s
  6000K .......... .......... .......... .......... .......... 33%  114M 2s
  6050K .......... .......... .......... .......... .......... 33%  113M 2s
  6100K .......... .......... .......... .......... .......... 34% 91.4M 2s
  6150K .......... .......... .......... .......... .......... 34% 83.4M 2s
  6200K .......... .......... .......... .......... .......... 34% 42.8M 2s
  6250K .......... .......... .......... .......... .......... 35%  117M 2s
  6300K .......... .......... .......... .......... .......... 35% 97.4M 2s
  6350K .......... .......... .......... .......... .......... 35%  116M 2s
  6400K .......... .......... .......... .......... .......... 35% 84.1M 2s
  6450K .......... .......... .......... .......... .......... 36% 1.78M 2s
  6500K .......... .......... .......... .......... .......... 36% 93.6M 2s
  6550K .......... .......... .......... .......... .......... 36%  116M 2s
  6600K .......... .......... .......... .......... .......... 36%  113M 2s
  6650K .......... .......... .......... .......... .......... 37% 56.9M 2s
  6700K .......... .......... .......... .......... .......... 37%  120M 2s
  6750K .......... .......... .......... .......... .......... 37% 85.2M 2s
  6800K .......... .......... .......... .......... .......... 38% 61.4M 2s
  6850K .......... .......... .......... .......... .......... 38%  111M 2s
  6900K .......... .......... .......... .......... .......... 38% 63.6M 2s
  6950K .......... .......... .......... .......... .......... 38%  116M 2s
  7000K .......... .......... .......... .......... .......... 39%  100M 2s
  7050K .......... .......... .......... .......... .......... 39% 82.0M 2s
  7100K .......... .......... .......... .......... .......... 39% 80.0M 2s
  7150K .......... .......... .......... .......... .......... 40% 58.5M 2s
  7200K .......... .......... .......... .......... .......... 40% 95.6M 2s
  7250K .......... .......... .......... .......... .......... 40% 13.6M 2s
  7300K .......... .......... .......... .......... .......... 40% 22.1M 2s
  7350K .......... .......... .......... .......... .......... 41% 98.9M 2s
  7400K .......... .......... .......... .......... .......... 41% 2.29M 2s
  7450K .......... .......... .......... .......... .......... 41% 77.1M 2s
  7500K .......... .......... .......... .......... .......... 41% 44.3M 2s
  7550K .......... .......... .......... .......... .......... 42% 65.5M 2s
  7600K .......... .......... .......... .......... .......... 42%  102M 2s
  7650K .......... .......... .......... .......... .......... 42% 27.4M 2s
  7700K .......... .......... .......... .......... .......... 43% 37.3M 2s
  7750K .......... .......... .......... .......... .......... 43% 65.6M 2s
  7800K .......... .......... .......... .......... .......... 43% 54.9M 2s
  7850K .......... .......... .......... .......... .......... 43%  118M 2s
  7900K .......... .......... .......... .......... .......... 44%  121M 2s
  7950K .......... .......... .......... .......... .......... 44%  100M 2s
  8000K .......... .......... .......... .......... .......... 44%  114M 2s
  8050K .......... .......... .......... .......... .......... 45% 56.4M 2s
  8100K .......... .......... .......... .......... .......... 45% 83.0M 2s
  8150K .......... .......... .......... .......... .......... 45%  112M 2s
  8200K .......... .......... .......... .......... .......... 45%  114M 1s
  8250K .......... .......... .......... .......... .......... 46% 84.5M 1s
  8300K .......... .......... .......... .......... .......... 46%  111M 1s
  8350K .......... .......... .......... .......... .......... 46% 80.9M 1s
  8400K .......... .......... .......... .......... .......... 46%  111M 1s
  8450K .......... .......... .......... .......... .......... 47%  111M 1s
  8500K .......... .......... .......... .......... .......... 47% 97.4M 1s
  8550K .......... .......... .......... .......... .......... 47% 2.25M 1s
  8600K .......... .......... .......... .......... .......... 48% 34.6M 1s
  8650K .......... .......... .......... .......... .......... 48% 68.0M 1s
  8700K .......... .......... .......... .......... .......... 48% 40.5M 1s
  8750K .......... .......... .......... .......... .......... 48% 45.1M 1s
  8800K .......... .......... .......... .......... .......... 49% 27.7M 1s
  8850K .......... .......... .......... .......... .......... 49% 30.7M 1s
  8900K .......... .......... .......... .......... .......... 49% 34.2M 1s
  8950K .......... .......... .......... .......... .......... 50% 23.5M 1s
  9000K .......... .......... .......... .......... .......... 50%  109M 1s
  9050K .......... .......... .......... .......... .......... 50% 25.2M 1s
  9100K .......... .......... .......... .......... .......... 50% 24.3M 1s
  9150K .......... .......... .......... .......... .......... 51% 39.7M 1s
  9200K .......... .......... .......... .......... .......... 51% 41.3M 1s
  9250K .......... .......... .......... .......... .......... 51% 93.5M 1s
  9300K .......... .......... .......... .......... .......... 51% 43.2M 1s
  9350K .......... .......... .......... .......... .......... 52% 96.9M 1s
  9400K .......... .......... .......... .......... .......... 52% 49.6M 1s
  9450K .......... .......... .......... .......... .......... 52% 42.8M 1s
  9500K .......... .......... .......... .......... .......... 53%  113M 1s
  9550K .......... .......... .......... .......... .......... 53% 44.8M 1s
  9600K .......... .......... .......... .......... .......... 53% 44.5M 1s
  9650K .......... .......... .......... .......... .......... 53% 27.6M 1s
  9700K .......... .......... .......... .......... .......... 54%  112M 1s
  9750K .......... .......... .......... .......... .......... 54% 40.7M 1s
  9800K .......... .......... .......... .......... .......... 54% 97.9M 1s
  9850K .......... .......... .......... .......... .......... 55% 6.26M 1s
  9900K .......... .......... .......... .......... .......... 55% 46.5M 1s
  9950K .......... .......... .......... .......... .......... 55% 43.2M 1s
 10000K .......... .......... .......... .......... .......... 55% 79.2M 1s
 10050K .......... .......... .......... .......... .......... 56% 51.9M 1s
 10100K .......... .......... .......... .......... .......... 56% 24.9M 1s
 10150K .......... .......... .......... .......... .......... 56% 92.7M 1s
 10200K .......... .......... .......... .......... .......... 56% 51.3M 1s
 10250K .......... .......... .......... .......... .......... 57%  109M 1s
 10300K .......... .......... .......... .......... .......... 57%  104M 1s
 10350K .......... .......... .......... .......... .......... 57% 85.6M 1s
 10400K .......... .......... .......... .......... .......... 58%  101M 1s
 10450K .......... .......... .......... .......... .......... 58% 70.8M 1s
 10500K .......... .......... .......... .......... .......... 58%  113M 1s
 10550K .......... .......... .......... .......... .......... 58% 44.3M 1s
 10600K .......... .......... .......... .......... .......... 59% 29.9M 1s
 10650K .......... .......... .......... .......... .......... 59% 49.5M 1s
 10700K .......... .......... .......... .......... .......... 59% 66.8M 1s
 10750K .......... .......... .......... .......... .......... 60%  112M 1s
 10800K .......... .......... .......... .......... .......... 60%  104M 1s
 10850K .......... .......... .......... .......... .......... 60% 68.4M 1s
 10900K .......... .......... .......... .......... .......... 60% 40.8M 1s
 10950K .......... .......... .......... .......... .......... 61% 44.2M 1s
 11000K .......... .......... .......... .......... .......... 61% 46.1M 1s
 11050K .......... .......... .......... .......... .......... 61% 81.3M 1s
 11100K .......... .......... .......... .......... .......... 61%  113M 1s
 11150K .......... .......... .......... .......... .......... 62% 87.6M 1s
 11200K .......... .......... .......... .......... .......... 62%  105M 1s
 11250K .......... .......... .......... .......... .......... 62% 98.6M 1s
 11300K .......... .......... .......... .......... .......... 63% 87.8M 1s
 11350K .......... .......... .......... .......... .......... 63% 4.29M 1s
 11400K .......... .......... .......... .......... .......... 63% 80.6M 1s
 11450K .......... .......... .......... .......... .......... 63% 42.8M 1s
 11500K .......... .......... .......... .......... .......... 64% 50.9M 1s
 11550K .......... .......... .......... .......... .......... 64% 86.6M 1s
 11600K .......... .......... .......... .......... .......... 64% 27.7M 1s
 11650K .......... .......... .......... .......... .......... 65% 66.3M 1s
 11700K .......... .......... .......... .......... .......... 65% 52.1M 1s
 11750K .......... .......... .......... .......... .......... 65%  121M 1s
 11800K .......... .......... .......... .......... .......... 65% 62.6M 1s
 11850K .......... .......... .......... .......... .......... 66% 80.2M 1s
 11900K .......... .......... .......... .......... .......... 66%  100M 1s
 11950K .......... .......... .......... .......... .......... 66% 89.7M 1s
 12000K .......... .......... .......... .......... .......... 66% 80.6M 1s
 12050K .......... .......... .......... .......... .......... 67%  114M 1s
 12100K .......... .......... .......... .......... .......... 67% 90.4M 1s
 12150K .......... .......... .......... .......... .......... 67%  111M 1s
 12200K .......... .......... .......... .......... .......... 68% 61.6M 1s
 12250K .......... .......... .......... .......... .......... 68%  116M 1s
 12300K .......... .......... .......... .......... .......... 68% 97.1M 1s
 12350K .......... .......... .......... .......... .......... 68%  101M 1s
 12400K .......... .......... .......... .......... .......... 69% 90.6M 1s
 12450K .......... .......... .......... .......... .......... 69%  113M 1s
 12500K .......... .......... .......... .......... .......... 69%  115M 1s
 12550K .......... .......... .......... .......... .......... 70% 85.1M 1s
 12600K .......... .......... .......... .......... .......... 70% 52.4M 1s
 12650K .......... .......... .......... .......... .......... 70% 45.6M 1s
 12700K .......... .......... .......... .......... .......... 70%  113M 1s
 12750K .......... .......... .......... .......... .......... 71%  117M 1s
 12800K .......... .......... .......... .......... .......... 71%  102M 1s
 12850K .......... .......... .......... .......... .......... 71% 93.5M 1s
 12900K .......... .......... .......... .......... .......... 71% 87.6M 1s
 12950K .......... .......... .......... .......... .......... 72%  117M 1s
 13000K .......... .......... .......... .......... .......... 72%  104M 1s
 13050K .......... .......... .......... .......... .......... 72%  104M 1s
 13100K .......... .......... .......... .......... .......... 73%  117M 1s
 13150K .......... .......... .......... .......... .......... 73% 67.6M 1s
 13200K .......... .......... .......... .......... .......... 73% 3.50M 0s
 13250K .......... .......... .......... .......... .......... 73% 43.2M 0s
 13300K .......... .......... .......... .......... .......... 74%  109M 0s
 13350K .......... .......... .......... .......... .......... 74% 86.7M 0s
 13400K .......... .......... .......... .......... .......... 74%  114M 0s
 13450K .......... .......... .......... .......... .......... 75% 53.8M 0s
 13500K .......... .......... .......... .......... .......... 75%  100M 0s
 13550K .......... .......... .......... .......... .......... 75% 96.7M 0s
 13600K .......... .......... .......... .......... .......... 75%  109M 0s
 13650K .......... .......... .......... .......... .......... 76%  116M 0s
 13700K .......... .......... .......... .......... .......... 76% 25.9M 0s
 13750K .......... .......... .......... .......... .......... 76% 63.6M 0s
 13800K .......... .......... .......... .......... .......... 76% 99.8M 0s
 13850K .......... .......... .......... .......... .......... 77% 84.9M 0s
 13900K .......... .......... .......... .......... .......... 77%  115M 0s
 13950K .......... .......... .......... .......... .......... 77% 88.8M 0s
 14000K .......... .......... .......... .......... .......... 78% 15.4M 0s
 14050K .......... .......... .......... .......... .......... 78% 97.0M 0s
 14100K .......... .......... .......... .......... .......... 78%  102M 0s
 14150K .......... .......... .......... .......... .......... 78%  110M 0s
 14200K .......... .......... .......... .......... .......... 79% 85.8M 0s
 14250K .......... .......... .......... .......... .......... 79%  113M 0s
 14300K .......... .......... .......... .......... .......... 79% 87.1M 0s
 14350K .......... .......... .......... .......... .......... 80%  101M 0s
 14400K .......... .......... .......... .......... .......... 80%  113M 0s
 14450K .......... .......... .......... .......... .......... 80% 79.5M 0s
 14500K .......... .......... .......... .......... .......... 80%  115M 0s
 14550K .......... .......... .......... .......... .......... 81%  112M 0s
 14600K .......... .......... .......... .......... .......... 81% 84.9M 0s
 14650K .......... .......... .......... .......... .......... 81%  113M 0s
 14700K .......... .......... .......... .......... .......... 81%  114M 0s
 14750K .......... .......... .......... .......... .......... 82% 84.9M 0s
 14800K .......... .......... .......... .......... .......... 82% 87.2M 0s
 14850K .......... .......... .......... .......... .......... 82%  110M 0s
 14900K .......... .......... .......... .......... .......... 83%  113M 0s
 14950K .......... .......... .......... .......... .......... 83%  112M 0s
 15000K .......... .......... .......... .......... .......... 83% 90.6M 0s
 15050K .......... .......... .......... .......... .......... 83%  105M 0s
 15100K .......... .......... .......... .......... .......... 84%  112M 0s
 15150K .......... .......... .......... .......... .......... 84%  108M 0s
 15200K .......... .......... .......... .......... .......... 84% 86.0M 0s
 15250K .......... .......... .......... .......... .......... 85% 80.8M 0s
 15300K .......... .......... .......... .......... .......... 85%  113M 0s
 15350K .......... .......... .......... .......... .......... 85% 85.0M 0s
 15400K .......... .......... .......... .......... .......... 85% 7.17M 0s
 15450K .......... .......... .......... .......... .......... 86% 15.0M 0s
 15500K .......... .......... .......... .......... .......... 86% 75.5M 0s
 15550K .......... .......... .......... .......... .......... 86% 86.9M 0s
 15600K .......... .......... .......... .......... .......... 86% 46.4M 0s
 15650K .......... .......... .......... .......... .......... 87% 38.9M 0s
 15700K .......... .......... .......... .......... .......... 87%  103M 0s
 15750K .......... .......... .......... .......... .......... 87%  118M 0s
 15800K .......... .......... .......... .......... .......... 88% 83.6M 0s
 15850K .......... .......... .......... .......... .......... 88% 82.0M 0s
 15900K .......... .......... .......... .......... .......... 88%  114M 0s
 15950K .......... .......... .......... .......... .......... 88%  106M 0s
 16000K .......... .......... .......... .......... .......... 89% 90.0M 0s
 16050K .......... .......... .......... .......... .......... 89% 45.9M 0s
 16100K .......... .......... .......... .......... .......... 89% 41.5M 0s
 16150K .......... .......... .......... .......... .......... 90% 69.4M 0s
 16200K .......... .......... .......... .......... .......... 90% 43.8M 0s
 16250K .......... .......... .......... .......... .......... 90%  101M 0s
 16300K .......... .......... .......... .......... .......... 90% 79.9M 0s
 16350K .......... .......... .......... .......... .......... 91% 83.4M 0s
 16400K .......... .......... .......... .......... .......... 91% 51.9M 0s
 16450K .......... .......... .......... .......... .......... 91% 56.8M 0s
 16500K .......... .......... .......... .......... .......... 91% 98.5M 0s
 16550K .......... .......... .......... .......... .......... 92% 76.6M 0s
 16600K .......... .......... .......... .......... .......... 92% 91.4M 0s
 16650K .......... .......... .......... .......... .......... 92% 68.4M 0s
 16700K .......... .......... .......... .......... .......... 93% 39.2M 0s
 16750K .......... .......... .......... .......... .......... 93% 66.2M 0s
 16800K .......... .......... .......... .......... .......... 93% 31.8M 0s
 16850K .......... .......... .......... .......... .......... 93% 48.0M 0s
 16900K .......... .......... .......... .......... .......... 94% 70.9M 0s
 16950K .......... .......... .......... .......... .......... 94% 67.4M 0s
 17000K .......... .......... .......... .......... .......... 94% 90.1M 0s
 17050K .......... .......... .......... .......... .......... 95% 69.9M 0s
 17100K .......... .......... .......... .......... .......... 95% 85.6M 0s
 17150K .......... .......... .......... .......... .......... 95% 72.2M 0s
 17200K .......... .......... .......... .......... .......... 95% 35.9M 0s
 17250K .......... .......... .......... .......... .......... 96%  107M 0s
 17300K .......... .......... .......... .......... .......... 96% 83.1M 0s
 17350K .......... .......... .......... .......... .......... 96% 40.3M 0s
 17400K .......... .......... .......... .......... .......... 96% 52.3M 0s
 17450K .......... .......... .......... .......... .......... 97% 43.7M 0s
 17500K .......... .......... .......... .......... .......... 97% 73.2M 0s
 17550K .......... .......... .......... .......... .......... 97% 85.3M 0s
 17600K .......... .......... .......... .......... .......... 98% 48.9M 0s
 17650K .......... .......... .......... .......... .......... 98% 65.4M 0s
 17700K .......... .......... .......... .......... .......... 98% 80.2M 0s
 17750K .......... .......... .......... .......... .......... 98% 93.9M 0s
 17800K .......... .......... .......... .......... .......... 99% 85.7M 0s
 17850K .......... .......... .......... .......... .......... 99% 51.7M 0s
 17900K .......... .......... .......... .......... .......... 99% 60.6M 0s
 17950K .......... .......... .......... .......... .......   100% 26.8M=1.5s

2017-10-09 10:33:25 (12.0 MB/s) - ‘en_product6.xml’ saved [18429919/18429919]

--2017-10-09 10:33:25--  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: 17705244 (17M) [application/octet-stream]
Saving to: ‘phenotype_annotation.tab’

     0K .......... .......... .......... .......... ..........  0% 27.1M 1s
    50K .......... .......... .......... .......... ..........  0% 55.8M 0s
   100K .......... .......... .......... .......... ..........  0% 35.8M 0s
   150K .......... .......... .......... .......... ..........  1% 27.0M 0s
   200K .......... .......... .......... .......... ..........  1% 38.8M 0s
   250K .......... .......... .......... .......... ..........  1% 12.4M 1s
   300K .......... .......... .......... .......... ..........  2% 65.1M 1s
   350K .......... .......... .......... .......... ..........  2% 79.7M 1s
   400K .......... .......... .......... .......... ..........  2% 33.3M 1s
   450K .......... .......... .......... .......... ..........  2% 36.3M 1s
   500K .......... .......... .......... .......... ..........  3% 41.8M 0s
   550K .......... .......... .......... .......... ..........  3% 27.2M 1s
   600K .......... .......... .......... .......... ..........  3% 14.0M 1s
   650K .......... .......... .......... .......... ..........  4% 91.5M 1s
   700K .......... .......... .......... .......... ..........  4% 95.2M 1s
   750K .......... .......... .......... .......... ..........  4% 42.9M 0s
   800K .......... .......... .......... .......... ..........  4% 33.4M 0s
   850K .......... .......... .......... .......... ..........  5% 45.0M 0s
   900K .......... .......... .......... .......... ..........  5% 28.8M 0s
   950K .......... .......... .......... .......... ..........  5% 62.6M 0s
  1000K .......... .......... .......... .......... ..........  6% 21.0M 0s
  1050K .......... .......... .......... .......... ..........  6%  110M 0s
  1100K .......... .......... .......... .......... ..........  6%  106M 0s
  1150K .......... .......... .......... .......... ..........  6% 73.0M 0s
  1200K .......... .......... .......... .......... ..........  7% 38.9M 0s
  1250K .......... .......... .......... .......... ..........  7% 16.5M 0s
  1300K .......... .......... .......... .......... ..........  7% 10.4M 0s
  1350K .......... .......... .......... .......... ..........  8% 22.0M 0s
  1400K .......... .......... .......... .......... ..........  8% 70.1M 0s
  1450K .......... .......... .......... .......... ..........  8% 74.1M 0s
  1500K .......... .......... .......... .......... ..........  8% 61.3M 0s
  1550K .......... .......... .......... .......... ..........  9%  109M 0s
  1600K .......... .......... .......... .......... ..........  9% 88.8M 0s
  1650K .......... .......... .......... .......... ..........  9% 66.3M 0s
  1700K .......... .......... .......... .......... .......... 10% 66.0M 0s
  1750K .......... .......... .......... .......... .......... 10% 82.9M 0s
  1800K .......... .......... .......... .......... .......... 10% 64.5M 0s
  1850K .......... .......... .......... .......... .......... 10% 53.9M 0s
  1900K .......... .......... .......... .......... .......... 11% 56.0M 0s
  1950K .......... .......... .......... .......... .......... 11% 54.3M 0s
  2000K .......... .......... .......... .......... .......... 11% 76.6M 0s
  2050K .......... .......... .......... .......... .......... 12% 61.8M 0s
  2100K .......... .......... .......... .......... .......... 12% 18.3M 0s
  2150K .......... .......... .......... .......... .......... 12% 59.9M 0s
  2200K .......... .......... .......... .......... .......... 13% 90.3M 0s
  2250K .......... .......... .......... .......... .......... 13% 99.6M 0s
  2300K .......... .......... .......... .......... .......... 13% 69.2M 0s
  2350K .......... .......... .......... .......... .......... 13% 67.0M 0s
  2400K .......... .......... .......... .......... .......... 14% 55.6M 0s
  2450K .......... .......... .......... .......... .......... 14% 35.6M 0s
  2500K .......... .......... .......... .......... .......... 14% 73.1M 0s
  2550K .......... .......... .......... .......... .......... 15% 82.3M 0s
  2600K .......... .......... .......... .......... .......... 15% 80.5M 0s
  2650K .......... .......... .......... .......... .......... 15% 57.2M 0s
  2700K .......... .......... .......... .......... .......... 15%  107M 0s
  2750K .......... .......... .......... .......... .......... 16% 15.0M 0s
  2800K .......... .......... .......... .......... .......... 16% 36.6M 0s
  2850K .......... .......... .......... .......... .......... 16% 31.4M 0s
  2900K .......... .......... .......... .......... .......... 17% 40.5M 0s
  2950K .......... .......... .......... .......... .......... 17% 20.8M 0s
  3000K .......... .......... .......... .......... .......... 17% 68.4M 0s
  3050K .......... .......... .......... .......... .......... 17% 12.8M 0s
  3100K .......... .......... .......... .......... .......... 18% 64.0M 0s
  3150K .......... .......... .......... .......... .......... 18% 46.4M 0s
  3200K .......... .......... .......... .......... .......... 18% 35.8M 0s
  3250K .......... .......... .......... .......... .......... 19% 10.8M 0s
  3300K .......... .......... .......... .......... .......... 19% 2.11M 0s
  3350K .......... .......... .......... .......... .......... 19% 18.4M 0s
  3400K .......... .......... .......... .......... .......... 19% 17.5M 0s
  3450K .......... .......... .......... .......... .......... 20% 11.6M 0s
  3500K .......... .......... .......... .......... .......... 20% 25.7M 0s
  3550K .......... .......... .......... .......... .......... 20% 74.8M 0s
  3600K .......... .......... .......... .......... .......... 21% 97.3M 0s
  3650K .......... .......... .......... .......... .......... 21% 84.2M 0s
  3700K .......... .......... .......... .......... .......... 21% 82.7M 0s
  3750K .......... .......... .......... .......... .......... 21% 45.2M 0s
  3800K .......... .......... .......... .......... .......... 22%  118M 0s
  3850K .......... .......... .......... .......... .......... 22%  102M 0s
  3900K .......... .......... .......... .......... .......... 22%  106M 0s
  3950K .......... .......... .......... .......... .......... 23% 47.9M 0s
  4000K .......... .......... .......... .......... .......... 23% 55.9M 0s
  4050K .......... .......... .......... .......... .......... 23% 38.0M 0s
  4100K .......... .......... .......... .......... .......... 24% 31.2M 0s
  4150K .......... .......... .......... .......... .......... 24% 38.5M 0s
  4200K .......... .......... .......... .......... .......... 24% 34.1M 0s
  4250K .......... .......... .......... .......... .......... 24% 78.5M 0s
  4300K .......... .......... .......... .......... .......... 25% 40.0M 0s
  4350K .......... .......... .......... .......... .......... 25% 23.7M 0s
  4400K .......... .......... .......... .......... .......... 25% 4.26M 0s
  4450K .......... .......... .......... .......... .......... 26% 9.79M 0s
  4500K .......... .......... .......... .......... .......... 26% 23.6M 0s
  4550K .......... .......... .......... .......... .......... 26% 23.7M 0s
  4600K .......... .......... .......... .......... .......... 26% 28.6M 0s
  4650K .......... .......... .......... .......... .......... 27% 46.4M 0s
  4700K .......... .......... .......... .......... .......... 27% 56.2M 0s
  4750K .......... .......... .......... .......... .......... 27% 43.0M 0s
  4800K .......... .......... .......... .......... .......... 28% 46.9M 0s
  4850K .......... .......... .......... .......... .......... 28% 53.0M 0s
  4900K .......... .......... .......... .......... .......... 28% 34.7M 0s
  4950K .......... .......... .......... .......... .......... 28% 70.5M 0s
  5000K .......... .......... .......... .......... .......... 29%  103M 0s
  5050K .......... .......... .......... .......... .......... 29% 87.9M 0s
  5100K .......... .......... .......... .......... .......... 29% 90.0M 0s
  5150K .......... .......... .......... .......... .......... 30%  114M 0s
  5200K .......... .......... .......... .......... .......... 30%  110M 0s
  5250K .......... .......... .......... .......... .......... 30% 85.8M 0s
  5300K .......... .......... .......... .......... .......... 30% 63.1M 0s
  5350K .......... .......... .......... .......... .......... 31% 98.2M 0s
  5400K .......... .......... .......... .......... .......... 31% 90.7M 0s
  5450K .......... .......... .......... .......... .......... 31%  112M 0s
  5500K .......... .......... .......... .......... .......... 32% 84.4M 0s
  5550K .......... .......... .......... .......... .......... 32%  103M 0s
  5600K .......... .......... .......... .......... .......... 32%  113M 0s
  5650K .......... .......... .......... .......... .......... 32%  104M 0s
  5700K .......... .......... .......... .......... .......... 33% 71.8M 0s
  5750K .......... .......... .......... .......... .......... 33% 81.1M 0s
  5800K .......... .......... .......... .......... .......... 33% 77.6M 0s
  5850K .......... .......... .......... .......... .......... 34%  112M 0s
  5900K .......... .......... .......... .......... .......... 34% 95.7M 0s
  5950K .......... .......... .......... .......... .......... 34% 74.8M 0s
  6000K .......... .......... .......... .......... .......... 34% 67.1M 0s
  6050K .......... .......... .......... .......... .......... 35%  114M 0s
  6100K .......... .......... .......... .......... .......... 35%  111M 0s
  6150K .......... .......... .......... .......... .......... 35%  116M 0s
  6200K .......... .......... .......... .......... .......... 36% 86.1M 0s
  6250K .......... .......... .......... .......... .......... 36%  113M 0s
  6300K .......... .......... .......... .......... .......... 36% 60.1M 0s
  6350K .......... .......... .......... .......... .......... 37% 86.6M 0s
  6400K .......... .......... .......... .......... .......... 37% 98.8M 0s
  6450K .......... .......... .......... .......... .......... 37% 96.0M 0s
  6500K .......... .......... .......... .......... .......... 37% 79.9M 0s
  6550K .......... .......... .......... .......... .......... 38%  114M 0s
  6600K .......... .......... .......... .......... .......... 38% 70.8M 0s
  6650K .......... .......... .......... .......... .......... 38%  118M 0s
  6700K .......... .......... .......... .......... .......... 39% 66.8M 0s
  6750K .......... .......... .......... .......... .......... 39% 99.7M 0s
  6800K .......... .......... .......... .......... .......... 39% 61.2M 0s
  6850K .......... .......... .......... .......... .......... 39% 61.9M 0s
  6900K .......... .......... .......... .......... .......... 40% 81.1M 0s
  6950K .......... .......... .......... .......... .......... 40% 49.6M 0s
  7000K .......... .......... .......... .......... .......... 40% 89.5M 0s
  7050K .......... .......... .......... .......... .......... 41% 66.8M 0s
  7100K .......... .......... .......... .......... .......... 41% 8.62M 0s
  7150K .......... .......... .......... .......... .......... 41% 2.16M 0s
  7200K .......... .......... .......... .......... .......... 41% 5.66M 0s
  7250K .......... .......... .......... .......... .......... 42% 7.30M 0s
  7300K .......... .......... .......... .......... .......... 42% 41.4M 0s
  7350K .......... .......... .......... .......... .......... 42% 29.3M 0s
  7400K .......... .......... .......... .......... .......... 43% 43.6M 0s
  7450K .......... .......... .......... .......... .......... 43% 74.1M 0s
  7500K .......... .......... .......... .......... .......... 43% 62.8M 0s
  7550K .......... .......... .......... .......... .......... 43% 70.6M 0s
  7600K .......... .......... .......... .......... .......... 44% 70.8M 0s
  7650K .......... .......... .......... .......... .......... 44% 70.5M 0s
  7700K .......... .......... .......... .......... .......... 44%  100M 0s
  7750K .......... .......... .......... .......... .......... 45%  108M 0s
  7800K .......... .......... .......... .......... .......... 45% 82.7M 0s
  7850K .......... .......... .......... .......... .......... 45% 50.0M 0s
  7900K .......... .......... .......... .......... .......... 45% 59.2M 0s
  7950K .......... .......... .......... .......... .......... 46% 23.0M 0s
  8000K .......... .......... .......... .......... .......... 46% 57.1M 0s
  8050K .......... .......... .......... .......... .......... 46%  101M 0s
  8100K .......... .......... .......... .......... .......... 47%  114M 0s
  8150K .......... .......... .......... .......... .......... 47% 57.5M 0s
  8200K .......... .......... .......... .......... .......... 47% 98.2M 0s
  8250K .......... .......... .......... .......... .......... 48%  111M 0s
  8300K .......... .......... .......... .......... .......... 48% 87.5M 0s
  8350K .......... .......... .......... .......... .......... 48% 74.4M 0s
  8400K .......... .......... .......... .......... .......... 48% 79.0M 0s
  8450K .......... .......... .......... .......... .......... 49% 88.3M 0s
  8500K .......... .......... .......... .......... .......... 49%  102M 0s
  8550K .......... .......... .......... .......... .......... 49% 81.2M 0s
  8600K .......... .......... .......... .......... .......... 50% 88.7M 0s
  8650K .......... .......... .......... .......... .......... 50% 78.3M 0s
  8700K .......... .......... .......... .......... .......... 50% 97.9M 0s
  8750K .......... .......... .......... .......... .......... 50%  108M 0s
  8800K .......... .......... .......... .......... .......... 51% 66.4M 0s
  8850K .......... .......... .......... .......... .......... 51% 77.6M 0s
  8900K .......... .......... .......... .......... .......... 51% 70.0M 0s
  8950K .......... .......... .......... .......... .......... 52% 95.9M 0s
  9000K .......... .......... .......... .......... .......... 52%  103M 0s
  9050K .......... .......... .......... .......... .......... 52% 56.3M 0s
  9100K .......... .......... .......... .......... .......... 52% 72.2M 0s
  9150K .......... .......... .......... .......... .......... 53% 68.7M 0s
  9200K .......... .......... .......... .......... .......... 53% 99.3M 0s
  9250K .......... .......... .......... .......... .......... 53% 78.2M 0s
  9300K .......... .......... .......... .......... .......... 54% 71.3M 0s
  9350K .......... .......... .......... .......... .......... 54% 60.8M 0s
  9400K .......... .......... .......... .......... .......... 54%  111M 0s
  9450K .......... .......... .......... .......... .......... 54% 46.5M 0s
  9500K .......... .......... .......... .......... .......... 55%  112M 0s
  9550K .......... .......... .......... .......... .......... 55% 63.8M 0s
  9600K .......... .......... .......... .......... .......... 55%  101M 0s
  9650K .......... .......... .......... .......... .......... 56%  114M 0s
  9700K .......... .......... .......... .......... .......... 56% 94.3M 0s
  9750K .......... .......... .......... .......... .......... 56% 87.4M 0s
  9800K .......... .......... .......... .......... .......... 56% 86.6M 0s
  9850K .......... .......... .......... .......... .......... 57% 63.4M 0s
  9900K .......... .......... .......... .......... .......... 57%  114M 0s
  9950K .......... .......... .......... .......... .......... 57% 72.8M 0s
 10000K .......... .......... .......... .......... .......... 58% 77.5M 0s
 10050K .......... .......... .......... .......... .......... 58% 65.1M 0s
 10100K .......... .......... .......... .......... .......... 58% 62.5M 0s
 10150K .......... .......... .......... .......... .......... 58%  118M 0s
 10200K .......... .......... .......... .......... .......... 59% 60.2M 0s
 10250K .......... .......... .......... .......... .......... 59%  113M 0s
 10300K .......... .......... .......... .......... .......... 59%  112M 0s
 10350K .......... .......... .......... .......... .......... 60%  113M 0s
 10400K .......... .......... .......... .......... .......... 60% 63.5M 0s
 10450K .......... .......... .......... .......... .......... 60% 75.2M 0s
 10500K .......... .......... .......... .......... .......... 61% 55.7M 0s
 10550K .......... .......... .......... .......... .......... 61% 69.8M 0s
 10600K .......... .......... .......... .......... .......... 61%  113M 0s
 10650K .......... .......... .......... .......... .......... 61%  113M 0s
 10700K .......... .......... .......... .......... .......... 62% 62.9M 0s
 10750K .......... .......... .......... .......... .......... 62% 66.3M 0s
 10800K .......... .......... .......... .......... .......... 62%  109M 0s
 10850K .......... .......... .......... .......... .......... 63% 72.6M 0s
 10900K .......... .......... .......... .......... .......... 63% 54.9M 0s
 10950K .......... .......... .......... .......... .......... 63%  114M 0s
 11000K .......... .......... .......... .......... .......... 63% 48.0M 0s
 11050K .......... .......... .......... .......... .......... 64%  114M 0s
 11100K .......... .......... .......... .......... .......... 64% 23.1M 0s
 11150K .......... .......... .......... .......... .......... 64% 86.5M 0s
 11200K .......... .......... .......... .......... .......... 65% 24.9M 0s
 11250K .......... .......... .......... .......... .......... 65%  114M 0s
 11300K .......... .......... .......... .......... .......... 65%  100M 0s
 11350K .......... .......... .......... .......... .......... 65% 46.0M 0s
 11400K .......... .......... .......... .......... .......... 66% 27.9M 0s
 11450K .......... .......... .......... .......... .......... 66% 40.6M 0s
 11500K .......... .......... .......... .......... .......... 66%  113M 0s
 11550K .......... .......... .......... .......... .......... 67% 19.1M 0s
 11600K .......... .......... .......... .......... .......... 67% 45.3M 0s
 11650K .......... .......... .......... .......... .......... 67% 46.6M 0s
 11700K .......... .......... .......... .......... .......... 67% 73.8M 0s
 11750K .......... .......... .......... .......... .......... 68% 90.7M 0s
 11800K .......... .......... .......... .......... .......... 68% 39.7M 0s
 11850K .......... .......... .......... .......... .......... 68% 33.8M 0s
 11900K .......... .......... .......... .......... .......... 69% 37.8M 0s
 11950K .......... .......... .......... .......... .......... 69% 35.4M 0s
 12000K .......... .......... .......... .......... .......... 69%  104M 0s
 12050K .......... .......... .......... .......... .......... 69% 30.0M 0s
 12100K .......... .......... .......... .......... .......... 70% 63.8M 0s
 12150K .......... .......... .......... .......... .......... 70% 35.5M 0s
 12200K .......... .......... .......... .......... .......... 70%  106M 0s
 12250K .......... .......... .......... .......... .......... 71% 75.8M 0s
 12300K .......... .......... .......... .......... .......... 71% 59.9M 0s
 12350K .......... .......... .......... .......... .......... 71% 46.0M 0s
 12400K .......... .......... .......... .......... .......... 72% 63.3M 0s
 12450K .......... .......... .......... .......... .......... 72%  110M 0s
 12500K .......... .......... .......... .......... .......... 72%  107M 0s
 12550K .......... .......... .......... .......... .......... 72% 46.3M 0s
 12600K .......... .......... .......... .......... .......... 73% 84.1M 0s
 12650K .......... .......... .......... .......... .......... 73% 46.3M 0s
 12700K .......... .......... .......... .......... .......... 73%  111M 0s
 12750K .......... .......... .......... .......... .......... 74% 77.6M 0s
 12800K .......... .......... .......... .......... .......... 74% 61.9M 0s
 12850K .......... .......... .......... .......... .......... 74%  105M 0s
 12900K .......... .......... .......... .......... .......... 74%  111M 0s
 12950K .......... .......... .......... .......... .......... 75% 52.9M 0s
 13000K .......... .......... .......... .......... .......... 75% 53.7M 0s
 13050K .......... .......... .......... .......... .......... 75% 78.2M 0s
 13100K .......... .......... .......... .......... .......... 76% 75.9M 0s
 13150K .......... .......... .......... .......... .......... 76%  106M 0s
 13200K .......... .......... .......... .......... .......... 76% 28.9M 0s
 13250K .......... .......... .......... .......... .......... 76% 43.1M 0s
 13300K .......... .......... .......... .......... .......... 77% 34.4M 0s
 13350K .......... .......... .......... .......... .......... 77% 71.6M 0s
 13400K .......... .......... .......... .......... .......... 77%  114M 0s
 13450K .......... .......... .......... .......... .......... 78% 35.8M 0s
 13500K .......... .......... .......... .......... .......... 78% 41.0M 0s
 13550K .......... .......... .......... .......... .......... 78% 50.1M 0s
 13600K .......... .......... .......... .......... .......... 78%  107M 0s
 13650K .......... .......... .......... .......... .......... 79% 32.7M 0s
 13700K .......... .......... .......... .......... .......... 79% 54.5M 0s
 13750K .......... .......... .......... .......... .......... 79% 73.4M 0s
 13800K .......... .......... .......... .......... .......... 80% 92.8M 0s
 13850K .......... .......... .......... .......... .......... 80% 85.2M 0s
 13900K .......... .......... .......... .......... .......... 80% 68.0M 0s
 13950K .......... .......... .......... .......... .......... 80%  100M 0s
 14000K .......... .......... .......... .......... .......... 81% 64.7M 0s
 14050K .......... .......... .......... .......... .......... 81%  113M 0s
 14100K .......... .......... .......... .......... .......... 81% 97.4M 0s
 14150K .......... .......... .......... .......... .......... 82% 80.9M 0s
 14200K .......... .......... .......... .......... .......... 82% 81.6M 0s
 14250K .......... .......... .......... .......... .......... 82% 92.2M 0s
 14300K .......... .......... .......... .......... .......... 82%  104M 0s
 14350K .......... .......... .......... .......... .......... 83% 81.8M 0s
 14400K .......... .......... .......... .......... .......... 83% 96.4M 0s
 14450K .......... .......... .......... .......... .......... 83% 61.5M 0s
 14500K .......... .......... .......... .......... .......... 84%  113M 0s
 14550K .......... .......... .......... .......... .......... 84%  110M 0s
 14600K .......... .......... .......... .......... .......... 84% 87.5M 0s
 14650K .......... .......... .......... .......... .......... 85%  113M 0s
 14700K .......... .......... .......... .......... .......... 85% 87.5M 0s
 14750K .......... .......... .......... .......... .......... 85%  111M 0s
 14800K .......... .......... .......... .......... .......... 85%  112M 0s
 14850K .......... .......... .......... .......... .......... 86% 79.4M 0s
 14900K .......... .......... .......... .......... .......... 86% 96.6M 0s
 14950K .......... .......... .......... .......... .......... 86% 86.5M 0s
 15000K .......... .......... .......... .......... .......... 87%  108M 0s
 15050K .......... .......... .......... .......... .......... 87%  101M 0s
 15100K .......... .......... .......... .......... .......... 87% 97.5M 0s
 15150K .......... .......... .......... .......... .......... 87% 97.4M 0s
 15200K .......... .......... .......... .......... .......... 88% 86.8M 0s
 15250K .......... .......... .......... .......... .......... 88%  113M 0s
 15300K .......... .......... .......... .......... .......... 88% 79.7M 0s
 15350K .......... .......... .......... .......... .......... 89% 98.1M 0s
 15400K .......... .......... .......... .......... .......... 89% 56.6M 0s
 15450K .......... .......... .......... .......... .......... 89% 84.6M 0s
 15500K .......... .......... .......... .......... .......... 89%  108M 0s
 15550K .......... .......... .......... .......... .......... 90% 47.0M 0s
 15600K .......... .......... .......... .......... .......... 90% 83.2M 0s
 15650K .......... .......... .......... .......... .......... 90% 63.9M 0s
 15700K .......... .......... .......... .......... .......... 91%  106M 0s
 15750K .......... .......... .......... .......... .......... 91% 58.9M 0s
 15800K .......... .......... .......... .......... .......... 91% 85.5M 0s
 15850K .......... .......... .......... .......... .......... 91% 77.4M 0s
 15900K .......... .......... .......... .......... .......... 92% 61.6M 0s
 15950K .......... .......... .......... .......... .......... 92%  113M 0s
 16000K .......... .......... .......... .......... .......... 92% 92.8M 0s
 16050K .......... .......... .......... .......... .......... 93% 55.6M 0s
 16100K .......... .......... .......... .......... .......... 93% 73.3M 0s
 16150K .......... .......... .......... .......... .......... 93% 53.7M 0s
 16200K .......... .......... .......... .......... .......... 93%  113M 0s
 16250K .......... .......... .......... .......... .......... 94% 84.6M 0s
 16300K .......... .......... .......... .......... .......... 94%  110M 0s
 16350K .......... .......... .......... .......... .......... 94% 73.5M 0s
 16400K .......... .......... .......... .......... .......... 95%  113M 0s
 16450K .......... .......... .......... .......... .......... 95%  113M 0s
 16500K .......... .......... .......... .......... .......... 95% 80.8M 0s
 16550K .......... .......... .......... .......... .......... 96% 99.0M 0s
 16600K .......... .......... .......... .......... .......... 96% 91.3M 0s
 16650K .......... .......... .......... .......... .......... 96%  113M 0s
 16700K .......... .......... .......... .......... .......... 96% 87.4M 0s
 16750K .......... .......... .......... .......... .......... 97%  112M 0s
 16800K .......... .......... .......... .......... .......... 97%  113M 0s
 16850K .......... .......... .......... .......... .......... 97% 64.1M 0s
 16900K .......... .......... .......... .......... .......... 98%  113M 0s
 16950K .......... .......... .......... .......... .......... 98% 57.0M 0s
 17000K .......... .......... .......... .......... .......... 98% 99.8M 0s
 17050K .......... .......... .......... .......... .......... 98% 99.4M 0s
 17100K .......... .......... .......... .......... .......... 99%  103M 0s
 17150K .......... .......... .......... .......... .......... 99% 80.0M 0s
 17200K .......... .......... .......... .......... .......... 99% 81.7M 0s
 17250K .......... .......... .......... ..........           100% 82.5M=0.4s

2017-10-09 10:33:25 (44.7 MB/s) - ‘phenotype_annotation.tab’ saved [17705244/17705244]

--2017-10-09 10:33:25--  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]
--2017-10-09 10:33:26--  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: 5685945 (5.4M) [text/plain]
Saving to: ‘hp.obo’

     0K .......... .......... .......... .......... ..........  0% 1.92M 3s
    50K .......... .......... .......... .......... ..........  1% 4.19M 2s
   100K .......... .......... .......... .......... ..........  2% 4.19M 2s
   150K .......... .......... .......... .......... ..........  3% 5.26M 2s
   200K .......... .......... .......... .......... ..........  4% 5.03M 1s
   250K .......... .......... .......... .......... ..........  5% 4.79M 1s
   300K .......... .......... .......... .......... ..........  6% 6.87M 1s
   350K .......... .......... .......... .......... ..........  7% 5.71M 1s
   400K .......... .......... .......... .......... ..........  8% 4.68M 1s
   450K .......... .......... .......... .......... ..........  9% 5.43M 1s
   500K .......... .......... .......... .......... ..........  9% 5.97M 1s
   550K .......... .......... .......... .......... .......... 10% 6.51M 1s
   600K .......... .......... .......... .......... .......... 11% 5.90M 1s
   650K .......... .......... .......... .......... .......... 12% 9.84M 1s
   700K .......... .......... .......... .......... .......... 13% 6.96M 1s
   750K .......... .......... .......... .......... .......... 14% 7.07M 1s
   800K .......... .......... .......... .......... .......... 15% 5.73M 1s
   850K .......... .......... .......... .......... .......... 16% 7.85M 1s
   900K .......... .......... .......... .......... .......... 17% 7.87M 1s
   950K .......... .......... .......... .......... .......... 18% 7.42M 1s
  1000K .......... .......... .......... .......... .......... 18% 8.43M 1s
  1050K .......... .......... .......... .......... .......... 19% 9.23M 1s
  1100K .......... .......... .......... .......... .......... 20% 9.78M 1s
  1150K .......... .......... .......... .......... .......... 21% 8.44M 1s
  1200K .......... .......... .......... .......... .......... 22% 8.19M 1s
  1250K .......... .......... .......... .......... .......... 23% 8.75M 1s
  1300K .......... .......... .......... .......... .......... 24% 9.49M 1s
  1350K .......... .......... .......... .......... .......... 25% 10.2M 1s
  1400K .......... .......... .......... .......... .......... 26% 7.83M 1s
  1450K .......... .......... .......... .......... .......... 27% 15.4M 1s
  1500K .......... .......... .......... .......... .......... 27% 6.59M 1s
  1550K .......... .......... .......... .......... .......... 28% 14.3M 1s
  1600K .......... .......... .......... .......... .......... 29% 6.99M 1s
  1650K .......... .......... .......... .......... .......... 30% 10.2M 1s
  1700K .......... .......... .......... .......... .......... 31% 12.2M 1s
  1750K .......... .......... .......... .......... .......... 32% 15.9M 1s
  1800K .......... .......... .......... .......... .......... 33% 11.0M 1s
  1850K .......... .......... .......... .......... .......... 34% 13.7M 1s
  1900K .......... .......... .......... .......... .......... 35% 14.6M 1s
  1950K .......... .......... .......... .......... .......... 36% 10.4M 1s
  2000K .......... .......... .......... .......... .......... 36% 12.9M 0s
  2050K .......... .......... .......... .......... .......... 37% 9.72M 0s
  2100K .......... .......... .......... .......... .......... 38% 16.2M 0s
  2150K .......... .......... .......... .......... .......... 39% 12.3M 0s
  2200K .......... .......... .......... .......... .......... 40% 11.5M 0s
  2250K .......... .......... .......... .......... .......... 41% 11.5M 0s
  2300K .......... .......... .......... .......... .......... 42% 18.5M 0s
  2350K .......... .......... .......... .......... .......... 43% 12.1M 0s
  2400K .......... .......... .......... .......... .......... 44% 12.6M 0s
  2450K .......... .......... .......... .......... .......... 45% 21.7M 0s
  2500K .......... .......... .......... .......... .......... 45% 10.9M 0s
  2550K .......... .......... .......... .......... .......... 46% 12.7M 0s
  2600K .......... .......... .......... .......... .......... 47% 26.5M 0s
  2650K .......... .......... .......... .......... .......... 48% 13.5M 0s
  2700K .......... .......... .......... .......... .......... 49% 15.8M 0s
  2750K .......... .......... .......... .......... .......... 50% 16.2M 0s
  2800K .......... .......... .......... .......... .......... 51% 16.1M 0s
  2850K .......... .......... .......... .......... .......... 52% 16.3M 0s
  2900K .......... .......... .......... .......... .......... 53% 16.4M 0s
  2950K .......... .......... .......... .......... .......... 54% 18.1M 0s
  3000K .......... .......... .......... .......... .......... 54% 14.3M 0s
  3050K .......... .......... .......... .......... .......... 55% 15.4M 0s
  3100K .......... .......... .......... .......... .......... 56% 17.3M 0s
  3150K .......... .......... .......... .......... .......... 57% 29.6M 0s
  3200K .......... .......... .......... .......... .......... 58% 11.5M 0s
  3250K .......... .......... .......... .......... .......... 59% 16.1M 0s
  3300K .......... .......... .......... .......... .......... 60% 19.6M 0s
  3350K .......... .......... .......... .......... .......... 61% 23.8M 0s
  3400K .......... .......... .......... .......... .......... 62% 18.3M 0s
  3450K .......... .......... .......... .......... .......... 63% 12.9M 0s
  3500K .......... .......... .......... .......... .......... 63% 15.9M 0s
  3550K .......... .......... .......... .......... .......... 64% 56.3M 0s
  3600K .......... .......... .......... .......... .......... 65% 14.8M 0s
  3650K .......... .......... .......... .......... .......... 66% 14.4M 0s
  3700K .......... .......... .......... .......... .......... 67% 25.2M 0s
  3750K .......... .......... .......... .......... .......... 68% 26.6M 0s
  3800K .......... .......... .......... .......... .......... 69% 16.7M 0s
  3850K .......... .......... .......... .......... .......... 70% 18.5M 0s
  3900K .......... .......... .......... .......... .......... 71% 13.9M 0s
  3950K .......... .......... .......... .......... .......... 72% 47.7M 0s
  4000K .......... .......... .......... .......... .......... 72% 20.5M 0s
  4050K .......... .......... .......... .......... .......... 73% 18.1M 0s
  4100K .......... .......... .......... .......... .......... 74% 19.6M 0s
  4150K .......... .......... .......... .......... .......... 75% 19.1M 0s
  4200K .......... .......... .......... .......... .......... 76% 16.2M 0s
  4250K .......... .......... .......... .......... .......... 77% 65.6M 0s
  4300K .......... .......... .......... .......... .......... 78% 20.0M 0s
  4350K .......... .......... .......... .......... .......... 79% 19.0M 0s
  4400K .......... .......... .......... .......... .......... 80% 3.63M 0s
  4450K .......... .......... .......... .......... .......... 81% 25.7M 0s
  4500K .......... .......... .......... .......... .......... 81%  118M 0s
  4550K .......... .......... .......... .......... .......... 82% 20.8M 0s
  4600K .......... .......... .......... .......... .......... 83% 95.7M 0s
  4650K .......... .......... .......... .......... .......... 84% 22.1M 0s
  4700K .......... .......... .......... .......... .......... 85% 69.9M 0s
  4750K .......... .......... .......... .......... .......... 86% 20.4M 0s
  4800K .......... .......... .......... .......... .......... 87% 12.6M 0s
  4850K .......... .......... .......... .......... .......... 88% 14.3M 0s
  4900K .......... .......... .......... .......... .......... 89%  117M 0s
  4950K .......... .......... .......... .......... .......... 90% 29.0M 0s
  5000K .......... .......... .......... .......... .......... 90% 34.6M 0s
  5050K .......... .......... .......... .......... .......... 91% 32.8M 0s
  5100K .......... .......... .......... .......... .......... 92% 20.4M 0s
  5150K .......... .......... .......... .......... .......... 93% 61.0M 0s
  5200K .......... .......... .......... .......... .......... 94% 23.5M 0s
  5250K .......... .......... .......... .......... .......... 95% 26.9M 0s
  5300K .......... .......... .......... .......... .......... 96% 31.6M 0s
  5350K .......... .......... .......... .......... .......... 97% 22.0M 0s
  5400K .......... .......... .......... .......... .......... 98% 16.6M 0s
  5450K .......... .......... .......... .......... .......... 99% 15.4M 0s
  5500K .......... .......... .......... .......... .......... 99% 30.4M 0s
  5550K ..                                                    100% 78.0M=0.5s

Last-modified header missing -- time-stamps turned off.
2017-10-09 10:33:26 (11.3 MB/s) - ‘hp.obo’ saved [5685945/5685945]

FINISHED --2017-10-09 10:33:26--
Total wall clock time: 10s
Downloaded: 5 files, 43M in 4.8s (9.09 MB/s)
java -Xmx1G -jar ../tools/gene2phenotype/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
Oct 09, 2017 10:33:27 AM ontologizer.go.OBOParser doParse
INFO: Got 13156 terms and 16794 relations in 149 ms
Details of parsed obo file:
  data-version:		releases/2017-10-05
  format:		1.2
  term definitions:	13156
Oct 09, 2017 10:33:27 AM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
Oct 09, 2017 10:33:27 AM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118)
WARN: Frequency of 4100 terms was zero!!
Set IC of these to : 9.194007717355285
mims:9884 with inh: 6464
parse NCBI
summary of gene_info-file
  other: 864
  tRNA: 599
  rRNA: 59
  scRNA: 4
  biological-region: 1643
  protein-coding: 20451
  ncRNA: 17707
  pseudo: 16399
  snRNA: 64
  snoRNA: 541
  unknown: 1763
entrez2symbol size: 41932
there were 1 unidentified gene-IDs: [2439]
diseaseid-to-entrezid: 4546
ORPHANETPARSING: orphadisease2HGNCgenes:3625
ORPHANETPARSING: hgncid2entrez:27313
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(): 9884
 omim: 6997
 orphanet: 2840
 others: 47
Disease entries with at least one known disease gene: 5547
Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 9838
generating files for source-filter: OMIM and frequency-filter: FREQUENT_FEATURES
debug disease = DiseaseEntry [diseaseId=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 = DiseaseEntry [diseaseId=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 = DiseaseEntry [diseaseId=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 = DiseaseEntry [diseaseId=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 = DiseaseEntry [diseaseId=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 = DiseaseEntry [diseaseId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0]
annotations was null
java -Xmx1G -jar ../tools/hpo_mysqldb/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
Oct 09, 2017 10:33:41 AM ontologizer.go.OBOParser doParse
INFO: Got 13156 terms and 16794 relations in 139 ms
Details of parsed obo file:
  data-version:		releases/2017-10-05
  format:		1.2
  term definitions:	13156
Oct 09, 2017 10:33:41 AM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
Oct 09, 2017 10:33:41 AM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118)
WARN: Frequency of 4100 terms was zero!!
Set IC of these to : 9.194007717355285
mims:9884 with inh: 6464
parse NCBI
summary of gene_info-file
  other: 864
  tRNA: 599
  rRNA: 59
  scRNA: 4
  biological-region: 1643
  protein-coding: 20451
  ncRNA: 17707
  pseudo: 16399
  snRNA: 64
  snoRNA: 541
  unknown: 1763
entrez2symbol size: 41932
there were 1 unidentified gene-IDs: [2439]
diseaseid-to-entrezid: 4546
ORPHANETPARSING: orphadisease2HGNCgenes:3625
ORPHANETPARSING: hgncid2entrez:27313
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(): 9884
 omim: 6997
 orphanet: 2840
 others: 47
Disease entries with at least one known disease gene: 5547
Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 9838
10_2017
make connection / created db
connecting to jdbc:mysql://localhost:3306/mysql
dropping database: MYHPO_10_2017 (if exists)
creating database: MYHPO_10_2017
create schema (tables, relations)
Execute: [mysql, --user=hudson_mysql, --password=hpo_hudson, --host=localhost, --port=3306, MYHPO_10_2017, -e, source ../tools/hpo_mysqldb/schemabackup_2010-06-18.sql]
Done restore.
insert terms
WARN: invalid external object: 10.1007/978-0-387-79948-3_2046 / DOI
WARN: invalid external object: 0005291 / MP
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: 0004947 / MP
WARN: invalid external object: 0011478 / MP
WARN: invalid external object: 0008271 / MP
WARN: invalid external object: 3632007 / PMID
WARN: invalid external object: 0001764 / MP
WARN: invalid external object: 26079824 / PMID
WARN: invalid external object: 0005257 / MP
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: 20573927 / 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: 26379327 / PMID
WARN: invalid external object: 18616733 / PMID
WARN: invalid external object: 18809899 / PMID
WARN: invalid external object: sjwang / RGD
insert graph-path
  allpathes.size() = 201072
insert term2term
Insert annotations:
dumping to file: ./MYHPO_10_2017.sql
  calling: [mysqldump, --user=hudson_mysql, --password=hpo_hudson, --host=localhost, --port=3306, MYHPO_10_2017]
Done dumping to file.
exiting...
make: Leaving directory '/var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation'
Archiving artifacts
Finished: SUCCESS