SuccessConsole Output

Started by upstream project "hpo.annotations" build number 1245
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 4739
no change for https://github.com/monarch-initiative/hpo-annotation-data/trunk/util since the previous build
[workspace] $ /bin/sh -xe /tmp/hudson8319278446594964142.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 10:37:34--  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% 17.3M 0s
    50K .......... .......... .......... .......... .......... 13% 35.1M 0s
   100K .......... .......... .......... .......... .......... 20% 22.1M 0s
   150K .......... .......... .......... .......... .......... 27% 31.3M 0s
   200K .......... .......... .......... .......... .......... 33% 18.0M 0s
   250K .......... .......... .......... .......... .......... 40% 42.4M 0s
   300K .......... .......... .......... .......... .......... 47% 38.9M 0s
   350K .......... .......... .......... .......... .......... 54% 16.6M 0s
   400K .......... .......... .......... .......... .......... 61% 22.2M 0s
   450K .......... .......... .......... .......... .......... 67% 42.8M 0s
   500K .......... .......... .......... .......... .......... 74% 41.3M 0s
   550K .......... .......... .......... .......... .......... 81% 42.3M 0s
   600K .......... .......... .......... .......... .......... 88% 66.3M 0s
   650K .......... .......... .......... .......... .......... 94% 29.7M 0s
   700K .......... .......... .......... ......               100% 95.3M=0.02s

2017-10-09 10:37:38 (29.4 MB/s) - ‘mim2gene_medgen’ saved [754593/754593]

--2017-10-09 10:37:38--  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: 2878788 (2.7M) [text/plain]
Saving to: ‘Homo_sapiens.gene_info.gz’

     0K .......... .......... .......... .......... ..........  1% 21.4M 0s
    50K .......... .......... .......... .......... ..........  3% 41.3M 0s
   100K .......... .......... .......... .......... ..........  5% 20.8K 43s
   150K .......... .......... .......... .......... ..........  7% 20.4M 31s
   200K .......... .......... .......... .......... ..........  8% 42.3M 25s
   250K .......... .......... .......... .......... .......... 10% 40.7M 20s
   300K .......... .......... .......... .......... .......... 12% 31.4M 17s
   350K .......... .......... .......... .......... .......... 14% 46.0M 15s
   400K .......... .......... .......... .......... .......... 16% 41.1M 13s
   450K .......... .......... .......... .......... .......... 17% 44.9M 11s
   500K .......... .......... .......... .......... .......... 19% 47.7M 10s
   550K .......... .......... .......... .......... .......... 21% 76.1M 9s
   600K .......... .......... .......... .......... .......... 23% 45.5M 8s
   650K .......... .......... .......... .......... .......... 24% 39.2M 7s
   700K .......... .......... .......... .......... .......... 26% 98.8M 7s
   750K .......... .......... .......... .......... .......... 28% 44.3M 6s
   800K .......... .......... .......... .......... .......... 30% 52.5M 6s
   850K .......... .......... .......... .......... .......... 32% 84.7M 5s
   900K .......... .......... .......... .......... .......... 33% 51.7M 5s
   950K .......... .......... .......... .......... .......... 35% 45.0M 4s
  1000K .......... .......... .......... .......... .......... 37%  116M 4s
  1050K .......... .......... .......... .......... .......... 39% 49.5M 4s
  1100K .......... .......... .......... .......... .......... 40% 42.0M 4s
  1150K .......... .......... .......... .......... .......... 42%  113M 3s
  1200K .......... .......... .......... .......... .......... 44% 53.5M 3s
  1250K .......... .......... .......... .......... .......... 46% 60.1M 3s
  1300K .......... .......... .......... .......... .......... 48% 72.5M 3s
  1350K .......... .......... .......... .......... .......... 49% 86.3M 2s
  1400K .......... .......... .......... .......... .......... 51% 43.2M 2s
  1450K .......... .......... .......... .......... .......... 53%  113M 2s
  1500K .......... .......... .......... .......... .......... 55% 63.9M 2s
  1550K .......... .......... .......... .......... .......... 56% 87.5M 2s
  1600K .......... .......... .......... .......... .......... 58% 59.6M 2s
  1650K .......... .......... .......... .......... .......... 60%  105M 2s
  1700K .......... .......... .......... .......... .......... 62% 64.1M 1s
  1750K .......... .......... .......... .......... .......... 64% 98.0M 1s
  1800K .......... .......... .......... .......... .......... 65% 79.1M 1s
  1850K .......... .......... .......... .......... .......... 67% 84.8M 1s
  1900K .......... .......... .......... .......... .......... 69% 98.9M 1s
  1950K .......... .......... .......... .......... .......... 71% 60.9M 1s
  2000K .......... .......... .......... .......... .......... 72%  113M 1s
  2050K .......... .......... .......... .......... .......... 74% 93.6M 1s
  2100K .......... .......... .......... .......... .......... 76% 66.9M 1s
  2150K .......... .......... .......... .......... .......... 78%  113M 1s
  2200K .......... .......... .......... .......... .......... 80% 93.1M 1s
  2250K .......... .......... .......... .......... .......... 81% 78.0M 1s
  2300K .......... .......... .......... .......... .......... 83% 98.0M 0s
  2350K .......... .......... .......... .......... .......... 85% 85.9M 0s
  2400K .......... .......... .......... .......... .......... 87% 45.6M 0s
  2450K .......... .......... .......... .......... .......... 88%  111M 0s
  2500K .......... .......... .......... .......... .......... 90%  111M 0s
  2550K .......... .......... .......... .......... .......... 92%  113M 0s
  2600K .......... .......... .......... .......... .......... 94% 81.8M 0s
  2650K .......... .......... .......... .......... .......... 96%  113M 0s
  2700K .......... .......... .......... .......... .......... 97%  113M 0s
  2750K .......... .......... .......... .......... .......... 99% 74.8M 0s
  2800K .......... .                                          100%  115M=2.4s

2017-10-09 10:37:44 (1.12 MB/s) - ‘Homo_sapiens.gene_info.gz’ saved [2878788/2878788]

--2017-10-09 10:37:44--  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%  372K 48s
    50K .......... .......... .......... .......... ..........  0% 1.09M 32s
   100K .......... .......... .......... .......... ..........  0% 1.08M 27s
   150K .......... .......... .......... .......... ..........  1% 1.10M 24s
   200K .......... .......... .......... .......... ..........  1% 1.13M 22s
   250K .......... .......... .......... .......... ..........  1% 1.10M 21s
   300K .......... .......... .......... .......... ..........  1% 1.12M 20s
   350K .......... .......... .......... .......... ..........  2% 1.14M 19s
   400K .......... .......... .......... .......... ..........  2% 91.1M 17s
   450K .......... .......... .......... .......... ..........  2% 1.15M 17s
   500K .......... .......... .......... .......... ..........  3%  101M 15s
   550K .......... .......... .......... .......... ..........  3% 1.12M 15s
   600K .......... .......... .......... .......... ..........  3% 1.12M 15s
   650K .......... .......... .......... .......... ..........  3% 46.0M 14s
   700K .......... .......... .......... .......... ..........  4% 70.9M 13s
   750K .......... .......... .......... .......... ..........  4% 1.11M 13s
   800K .......... .......... .......... .......... ..........  4% 63.2M 12s
   850K .......... .......... .......... .......... ..........  5% 96.0M 12s
   900K .......... .......... .......... .......... ..........  5% 1.19M 12s
   950K .......... .......... .......... .......... ..........  5% 98.1M 11s
  1000K .......... .......... .......... .......... ..........  5% 1.23M 11s
  1050K .......... .......... .......... .......... ..........  6% 38.5M 11s
  1100K .......... .......... .......... .......... ..........  6% 76.5M 10s
  1150K .......... .......... .......... .......... ..........  6% 1.23M 10s
  1200K .......... .......... .......... .......... ..........  6% 27.8M 10s
  1250K .......... .......... .......... .......... ..........  7% 1.23M 10s
  1300K .......... .......... .......... .......... ..........  7% 90.1M 10s
  1350K .......... .......... .......... .......... ..........  7% 87.3M 9s
  1400K .......... .......... .......... .......... ..........  8% 1.22M 9s
  1450K .......... .......... .......... .......... ..........  8% 32.6M 9s
  1500K .......... .......... .......... .......... ..........  8% 48.9M 9s
  1550K .......... .......... .......... .......... ..........  8% 88.4M 8s
  1600K .......... .......... .......... .......... ..........  9% 1.28M 9s
  1650K .......... .......... .......... .......... ..........  9% 72.2M 8s
  1700K .......... .......... .......... .......... ..........  9% 63.7M 8s
  1750K .......... .......... .......... .......... .......... 10% 54.4M 8s
  1800K .......... .......... .......... .......... .......... 10% 1.24M 8s
  1850K .......... .......... .......... .......... .......... 10% 82.3M 8s
  1900K .......... .......... .......... .......... .......... 10% 40.3M 7s
  1950K .......... .......... .......... .......... .......... 11% 56.1M 7s
  2000K .......... .......... .......... .......... .......... 11% 94.2M 7s
  2050K .......... .......... .......... .......... .......... 11% 1.09M 7s
  2100K .......... .......... .......... .......... .......... 11% 96.6M 7s
  2150K .......... .......... .......... .......... .......... 12%  104M 7s
  2200K .......... .......... .......... .......... .......... 12%  112M 7s
  2250K .......... .......... .......... .......... .......... 12% 90.7M 7s
  2300K .......... .......... .......... .......... .......... 13% 1.14M 7s
  2350K .......... .......... .......... .......... .......... 13% 97.4M 7s
  2400K .......... .......... .......... .......... .......... 13% 87.1M 6s
  2450K .......... .......... .......... .......... .......... 13% 27.7M 6s
  2500K .......... .......... .......... .......... .......... 14% 78.3M 6s
  2550K .......... .......... .......... .......... .......... 14% 73.7M 6s
  2600K .......... .......... .......... .......... .......... 14% 1.21M 6s
  2650K .......... .......... .......... .......... .......... 15% 69.3M 6s
  2700K .......... .......... .......... .......... .......... 15% 76.7M 6s
  2750K .......... .......... .......... .......... .......... 15% 88.1M 6s
  2800K .......... .......... .......... .......... .......... 15% 60.3M 6s
  2850K .......... .......... .......... .......... .......... 16% 37.4M 5s
  2900K .......... .......... .......... .......... .......... 16% 61.0M 5s
  2950K .......... .......... .......... .......... .......... 16% 1.19M 5s
  3000K .......... .......... .......... .......... .......... 16% 68.6M 5s
  3050K .......... .......... .......... .......... .......... 17% 85.2M 5s
  3100K .......... .......... .......... .......... .......... 17%  108M 5s
  3150K .......... .......... .......... .......... .......... 17% 98.6M 5s
  3200K .......... .......... .......... .......... .......... 18%  106M 5s
  3250K .......... .......... .......... .......... .......... 18% 58.6M 5s
  3300K .......... .......... .......... .......... .......... 18% 1.22M 5s
  3350K .......... .......... .......... .......... .......... 18% 41.5M 5s
  3400K .......... .......... .......... .......... .......... 19% 48.2M 5s
  3450K .......... .......... .......... .......... .......... 19% 57.4M 5s
  3500K .......... .......... .......... .......... .......... 19%  117M 5s
  3550K .......... .......... .......... .......... .......... 20%  116M 5s
  3600K .......... .......... .......... .......... .......... 20% 98.9M 4s
  3650K .......... .......... .......... .......... .......... 20%  113M 4s
  3700K .......... .......... .......... .......... .......... 20% 1.19M 4s
  3750K .......... .......... .......... .......... .......... 21% 36.7M 4s
  3800K .......... .......... .......... .......... .......... 21% 93.1M 4s
  3850K .......... .......... .......... .......... .......... 21%  120M 4s
  3900K .......... .......... .......... .......... .......... 21%  100M 4s
  3950K .......... .......... .......... .......... .......... 22% 68.5M 4s
  4000K .......... .......... .......... .......... .......... 22%  105M 4s
  4050K .......... .......... .......... .......... .......... 22% 51.7M 4s
  4100K .......... .......... .......... .......... .......... 23%  104M 4s
  4150K .......... .......... .......... .......... .......... 23% 1.23M 4s
  4200K .......... .......... .......... .......... .......... 23% 49.3M 4s
  4250K .......... .......... .......... .......... .......... 23% 99.8M 4s
  4300K .......... .......... .......... .......... .......... 24%  114M 4s
  4350K .......... .......... .......... .......... .......... 24%  103M 4s
  4400K .......... .......... .......... .......... .......... 24% 87.5M 4s
  4450K .......... .......... .......... .......... .......... 25% 84.4M 4s
  4500K .......... .......... .......... .......... .......... 25%  118M 4s
  4550K .......... .......... .......... .......... .......... 25%  117M 4s
  4600K .......... .......... .......... .......... .......... 25% 47.5M 4s
  4650K .......... .......... .......... .......... .......... 26% 1.20M 4s
  4700K .......... .......... .......... .......... .......... 26% 76.8M 4s
  4750K .......... .......... .......... .......... .......... 26% 98.6M 3s
  4800K .......... .......... .......... .......... .......... 26%  112M 3s
  4850K .......... .......... .......... .......... .......... 27%  115M 3s
  4900K .......... .......... .......... .......... .......... 27% 77.4M 3s
  4950K .......... .......... .......... .......... .......... 27% 81.3M 3s
  5000K .......... .......... .......... .......... .......... 28% 88.9M 3s
  5050K .......... .......... .......... .......... .......... 28%  115M 3s
  5100K .......... .......... .......... .......... .......... 28%  101M 3s
  5150K .......... .......... .......... .......... .......... 28% 70.6M 3s
  5200K .......... .......... .......... .......... .......... 29%  114M 3s
  5250K .......... .......... .......... .......... .......... 29% 1.22M 3s
  5300K .......... .......... .......... .......... .......... 29%  104M 3s
  5350K .......... .......... .......... .......... .......... 30% 91.7M 3s
  5400K .......... .......... .......... .......... .......... 30%  110M 3s
  5450K .......... .......... .......... .......... .......... 30% 93.9M 3s
  5500K .......... .......... .......... .......... .......... 30%  112M 3s
  5550K .......... .......... .......... .......... .......... 31%  104M 3s
  5600K .......... .......... .......... .......... .......... 31% 82.5M 3s
  5650K .......... .......... .......... .......... .......... 31% 80.8M 3s
  5700K .......... .......... .......... .......... .......... 31% 73.5M 3s
  5750K .......... .......... .......... .......... .......... 32%  108M 3s
  5800K .......... .......... .......... .......... .......... 32% 98.8M 3s
  5850K .......... .......... .......... .......... .......... 32% 83.7M 3s
  5900K .......... .......... .......... .......... .......... 33%  118M 3s
  5950K .......... .......... .......... .......... .......... 33% 1.32M 3s
  6000K .......... .......... .......... .......... .......... 33% 85.4M 3s
  6050K .......... .......... .......... .......... .......... 33%  108M 3s
  6100K .......... .......... .......... .......... .......... 34%  115M 3s
  6150K .......... .......... .......... .......... .......... 34% 99.7M 3s
  6200K .......... .......... .......... .......... .......... 34% 53.5M 3s
  6250K .......... .......... .......... .......... .......... 35%  118M 3s
  6300K .......... .......... .......... .......... .......... 35% 99.4M 3s
  6350K .......... .......... .......... .......... .......... 35% 80.8M 2s
  6400K .......... .......... .......... .......... .......... 35%  114M 2s
  6450K .......... .......... .......... .......... .......... 36%  113M 2s
  6500K .......... .......... .......... .......... .......... 36%  115M 2s
  6550K .......... .......... .......... .......... .......... 36%  115M 2s
  6600K .......... .......... .......... .......... .......... 36%  104M 2s
  6650K .......... .......... .......... .......... .......... 37% 65.2M 2s
  6700K .......... .......... .......... .......... .......... 37% 92.2M 2s
  6750K .......... .......... .......... .......... .......... 37% 98.7M 2s
  6800K .......... .......... .......... .......... .......... 38% 1.34M 2s
  6850K .......... .......... .......... .......... .......... 38% 86.9M 2s
  6900K .......... .......... .......... .......... .......... 38%  114M 2s
  6950K .......... .......... .......... .......... .......... 38% 65.2M 2s
  7000K .......... .......... .......... .......... .......... 39% 86.1M 2s
  7050K .......... .......... .......... .......... .......... 39%  103M 2s
  7100K .......... .......... .......... .......... .......... 39%  116M 2s
  7150K .......... .......... .......... .......... .......... 40%  103M 2s
  7200K .......... .......... .......... .......... .......... 40%  116M 2s
  7250K .......... .......... .......... .......... .......... 40%  115M 2s
  7300K .......... .......... .......... .......... .......... 40%  100M 2s
  7350K .......... .......... .......... .......... .......... 41%  102M 2s
  7400K .......... .......... .......... .......... .......... 41%  113M 2s
  7450K .......... .......... .......... .......... .......... 41% 75.0M 2s
  7500K .......... .......... .......... .......... .......... 41%  113M 2s
  7550K .......... .......... .......... .......... .......... 42%  113M 2s
  7600K .......... .......... .......... .......... .......... 42%  112M 2s
  7650K .......... .......... .......... .......... .......... 42%  115M 2s
  7700K .......... .......... .......... .......... .......... 43%  101M 2s
  7750K .......... .......... .......... .......... .......... 43% 65.2M 2s
  7800K .......... .......... .......... .......... .......... 43% 1.35M 2s
  7850K .......... .......... .......... .......... .......... 43% 82.9M 2s
  7900K .......... .......... .......... .......... .......... 44%  116M 2s
  7950K .......... .......... .......... .......... .......... 44%  108M 2s
  8000K .......... .......... .......... .......... .......... 44% 42.9M 2s
  8050K .......... .......... .......... .......... .......... 45%  107M 2s
  8100K .......... .......... .......... .......... .......... 45%  109M 2s
  8150K .......... .......... .......... .......... .......... 45% 99.0M 2s
  8200K .......... .......... .......... .......... .......... 45%  107M 2s
  8250K .......... .......... .......... .......... .......... 46%  101M 2s
  8300K .......... .......... .......... .......... .......... 46%  115M 2s
  8350K .......... .......... .......... .......... .......... 46%  113M 2s
  8400K .......... .......... .......... .......... .......... 46%  102M 2s
  8450K .......... .......... .......... .......... .......... 47%  114M 2s
  8500K .......... .......... .......... .......... .......... 47%  113M 2s
  8550K .......... .......... .......... .......... .......... 47%  101M 2s
  8600K .......... .......... .......... .......... .......... 48%  113M 2s
  8650K .......... .......... .......... .......... .......... 48% 75.1M 2s
  8700K .......... .......... .......... .......... .......... 48%  112M 2s
  8750K .......... .......... .......... .......... .......... 48%  113M 2s
  8800K .......... .......... .......... .......... .......... 49%  113M 2s
  8850K .......... .......... .......... .......... .......... 49%  112M 1s
  8900K .......... .......... .......... .......... .......... 49%  108M 1s
  8950K .......... .......... .......... .......... .......... 50% 1.37M 1s
  9000K .......... .......... .......... .......... .......... 50% 48.0M 1s
  9050K .......... .......... .......... .......... .......... 50% 49.2M 1s
  9100K .......... .......... .......... .......... .......... 50% 84.1M 1s
  9150K .......... .......... .......... .......... .......... 51% 80.3M 1s
  9200K .......... .......... .......... .......... .......... 51%  104M 1s
  9250K .......... .......... .......... .......... .......... 51%  110M 1s
  9300K .......... .......... .......... .......... .......... 51% 90.6M 1s
  9350K .......... .......... .......... .......... .......... 52%  115M 1s
  9400K .......... .......... .......... .......... .......... 52%  106M 1s
  9450K .......... .......... .......... .......... .......... 52%  117M 1s
  9500K .......... .......... .......... .......... .......... 53%  120M 1s
  9550K .......... .......... .......... .......... .......... 53%  102M 1s
  9600K .......... .......... .......... .......... .......... 53%  113M 1s
  9650K .......... .......... .......... .......... .......... 53%  113M 1s
  9700K .......... .......... .......... .......... .......... 54%  115M 1s
  9750K .......... .......... .......... .......... .......... 54%  115M 1s
  9800K .......... .......... .......... .......... .......... 54%  106M 1s
  9850K .......... .......... .......... .......... .......... 55%  120M 1s
  9900K .......... .......... .......... .......... .......... 55%  102M 1s
  9950K .......... .......... .......... .......... .......... 55%  113M 1s
 10000K .......... .......... .......... .......... .......... 55%  115M 1s
 10050K .......... .......... .......... .......... .......... 56%  119M 1s
 10100K .......... .......... .......... .......... .......... 56%  105M 1s
 10150K .......... .......... .......... .......... .......... 56%  116M 1s
 10200K .......... .......... .......... .......... .......... 56%  101M 1s
 10250K .......... .......... .......... .......... .......... 57%  120M 1s
 10300K .......... .......... .......... .......... .......... 57% 1.54M 1s
 10350K .......... .......... .......... .......... .......... 57% 75.3M 1s
 10400K .......... .......... .......... .......... .......... 58%  120M 1s
 10450K .......... .......... .......... .......... .......... 58% 82.3M 1s
 10500K .......... .......... .......... .......... .......... 58%  113M 1s
 10550K .......... .......... .......... .......... .......... 58%  109M 1s
 10600K .......... .......... .......... .......... .......... 59%  101M 1s
 10650K .......... .......... .......... .......... .......... 59% 52.3M 1s
 10700K .......... .......... .......... .......... .......... 59%  107M 1s
 10750K .......... .......... .......... .......... .......... 60% 99.2M 1s
 10800K .......... .......... .......... .......... .......... 60% 66.3M 1s
 10850K .......... .......... .......... .......... .......... 60%  118M 1s
 10900K .......... .......... .......... .......... .......... 60%  120M 1s
 10950K .......... .......... .......... .......... .......... 61%  105M 1s
 11000K .......... .......... .......... .......... .......... 61%  101M 1s
 11050K .......... .......... .......... .......... .......... 61%  106M 1s
 11100K .......... .......... .......... .......... .......... 61% 83.6M 1s
 11150K .......... .......... .......... .......... .......... 62% 98.6M 1s
 11200K .......... .......... .......... .......... .......... 62%  115M 1s
 11250K .......... .......... .......... .......... .......... 62%  104M 1s
 11300K .......... .......... .......... .......... .......... 63%  117M 1s
 11350K .......... .......... .......... .......... .......... 63% 93.1M 1s
 11400K .......... .......... .......... .......... .......... 63%  104M 1s
 11450K .......... .......... .......... .......... .......... 63%  119M 1s
 11500K .......... .......... .......... .......... .......... 64%  105M 1s
 11550K .......... .......... .......... .......... .......... 64%  119M 1s
 11600K .......... .......... .......... .......... .......... 64%  101M 1s
 11650K .......... .......... .......... .......... .......... 65% 34.0M 1s
 11700K .......... .......... .......... .......... .......... 65% 23.5M 1s
 11750K .......... .......... .......... .......... .......... 65% 81.5M 1s
 11800K .......... .......... .......... .......... .......... 65% 1.76M 1s
 11850K .......... .......... .......... .......... .......... 66% 85.1M 1s
 11900K .......... .......... .......... .......... .......... 66%  116M 1s
 11950K .......... .......... .......... .......... .......... 66% 66.0M 1s
 12000K .......... .......... .......... .......... .......... 66% 74.6M 1s
 12050K .......... .......... .......... .......... .......... 67% 68.3M 1s
 12100K .......... .......... .......... .......... .......... 67%  112M 1s
 12150K .......... .......... .......... .......... .......... 67%  101M 1s
 12200K .......... .......... .......... .......... .......... 68%  118M 1s
 12250K .......... .......... .......... .......... .......... 68% 69.6M 1s
 12300K .......... .......... .......... .......... .......... 68%  113M 1s
 12350K .......... .......... .......... .......... .......... 68%  104M 1s
 12400K .......... .......... .......... .......... .......... 69% 93.8M 1s
 12450K .......... .......... .......... .......... .......... 69%  104M 1s
 12500K .......... .......... .......... .......... .......... 69%  115M 1s
 12550K .......... .......... .......... .......... .......... 70%  112M 1s
 12600K .......... .......... .......... .......... .......... 70%  114M 1s
 12650K .......... .......... .......... .......... .......... 70%  103M 1s
 12700K .......... .......... .......... .......... .......... 70%  119M 1s
 12750K .......... .......... .......... .......... .......... 71%  104M 1s
 12800K .......... .......... .......... .......... .......... 71% 70.5M 1s
 12850K .......... .......... .......... .......... .......... 71%  119M 1s
 12900K .......... .......... .......... .......... .......... 71%  104M 1s
 12950K .......... .......... .......... .......... .......... 72%  115M 1s
 13000K .......... .......... .......... .......... .......... 72%  116M 1s
 13050K .......... .......... .......... .......... .......... 72%  114M 1s
 13100K .......... .......... .......... .......... .......... 73%  110M 1s
 13150K .......... .......... .......... .......... .......... 73%  100M 1s
 13200K .......... .......... .......... .......... .......... 73% 80.2M 1s
 13250K .......... .......... .......... .......... .......... 73% 92.6M 1s
 13300K .......... .......... .......... .......... .......... 74%  118M 1s
 13350K .......... .......... .......... .......... .......... 74%  105M 1s
 13400K .......... .......... .......... .......... .......... 74% 99.9M 1s
 13450K .......... .......... .......... .......... .......... 75% 94.2M 1s
 13500K .......... .......... .......... .......... .......... 75% 1.72M 1s
 13550K .......... .......... .......... .......... .......... 75% 78.4M 1s
 13600K .......... .......... .......... .......... .......... 75% 59.3M 1s
 13650K .......... .......... .......... .......... .......... 76%  114M 1s
 13700K .......... .......... .......... .......... .......... 76%  118M 1s
 13750K .......... .......... .......... .......... .......... 76% 91.6M 0s
 13800K .......... .......... .......... .......... .......... 76%  117M 0s
 13850K .......... .......... .......... .......... .......... 77% 69.2M 0s
 13900K .......... .......... .......... .......... .......... 77% 99.4M 0s
 13950K .......... .......... .......... .......... .......... 77%  115M 0s
 14000K .......... .......... .......... .......... .......... 78%  103M 0s
 14050K .......... .......... .......... .......... .......... 78%  117M 0s
 14100K .......... .......... .......... .......... .......... 78%  117M 0s
 14150K .......... .......... .......... .......... .......... 78%  105M 0s
 14200K .......... .......... .......... .......... .......... 79%  117M 0s
 14250K .......... .......... .......... .......... .......... 79%  106M 0s
 14300K .......... .......... .......... .......... .......... 79%  101M 0s
 14350K .......... .......... .......... .......... .......... 80%  115M 0s
 14400K .......... .......... .......... .......... .......... 80%  118M 0s
 14450K .......... .......... .......... .......... .......... 80%  105M 0s
 14500K .......... .......... .......... .......... .......... 80%  116M 0s
 14550K .......... .......... .......... .......... .......... 81%  101M 0s
 14600K .......... .......... .......... .......... .......... 81%  125M 0s
 14650K .......... .......... .......... .......... .......... 81%  104M 0s
 14700K .......... .......... .......... .......... .......... 81%  120M 0s
 14750K .......... .......... .......... .......... .......... 82%  105M 0s
 14800K .......... .......... .......... .......... .......... 82%  119M 0s
 14850K .......... .......... .......... .......... .......... 82%  108M 0s
 14900K .......... .......... .......... .......... .......... 83%  104M 0s
 14950K .......... .......... .......... .......... .......... 83%  121M 0s
 15000K .......... .......... .......... .......... .......... 83%  104M 0s
 15050K .......... .......... .......... .......... .......... 83%  121M 0s
 15100K .......... .......... .......... .......... .......... 84%  104M 0s
 15150K .......... .......... .......... .......... .......... 84% 80.7M 0s
 15200K .......... .......... .......... .......... .......... 84%  114M 0s
 15250K .......... .......... .......... .......... .......... 85% 48.8M 0s
 15300K .......... .......... .......... .......... .......... 85% 72.4M 0s
 15350K .......... .......... .......... .......... .......... 85% 19.1M 0s
 15400K .......... .......... .......... .......... .......... 85% 1.74M 0s
 15450K .......... .......... .......... .......... .......... 86% 89.3M 0s
 15500K .......... .......... .......... .......... .......... 86% 79.6M 0s
 15550K .......... .......... .......... .......... .......... 86% 68.2M 0s
 15600K .......... .......... .......... .......... .......... 86%  112M 0s
 15650K .......... .......... .......... .......... .......... 87% 87.6M 0s
 15700K .......... .......... .......... .......... .......... 87% 82.3M 0s
 15750K .......... .......... .......... .......... .......... 87% 98.0M 0s
 15800K .......... .......... .......... .......... .......... 88% 73.0M 0s
 15850K .......... .......... .......... .......... .......... 88% 51.8M 0s
 15900K .......... .......... .......... .......... .......... 88% 88.6M 0s
 15950K .......... .......... .......... .......... .......... 88% 87.7M 0s
 16000K .......... .......... .......... .......... .......... 89%  115M 0s
 16050K .......... .......... .......... .......... .......... 89%  116M 0s
 16100K .......... .......... .......... .......... .......... 89%  117M 0s
 16150K .......... .......... .......... .......... .......... 90%  105M 0s
 16200K .......... .......... .......... .......... .......... 90%  120M 0s
 16250K .......... .......... .......... .......... .......... 90%  106M 0s
 16300K .......... .......... .......... .......... .......... 90%  115M 0s
 16350K .......... .......... .......... .......... .......... 91%  106M 0s
 16400K .......... .......... .......... .......... .......... 91% 92.8M 0s
 16450K .......... .......... .......... .......... .......... 91%  113M 0s
 16500K .......... .......... .......... .......... .......... 91%  109M 0s
 16550K .......... .......... .......... .......... .......... 92%  104M 0s
 16600K .......... .......... .......... .......... .......... 92%  121M 0s
 16650K .......... .......... .......... .......... .......... 92% 94.0M 0s
 16700K .......... .......... .......... .......... .......... 93%  120M 0s
 16750K .......... .......... .......... .......... .......... 93%  114M 0s
 16800K .......... .......... .......... .......... .......... 93%  104M 0s
 16850K .......... .......... .......... .......... .......... 93%  120M 0s
 16900K .......... .......... .......... .......... .......... 94%  105M 0s
 16950K .......... .......... .......... .......... .......... 94%  120M 0s
 17000K .......... .......... .......... .......... .......... 94%  104M 0s
 17050K .......... .......... .......... .......... .......... 95%  118M 0s
 17100K .......... .......... .......... .......... .......... 95%  117M 0s
 17150K .......... .......... .......... .......... .......... 95%  104M 0s
 17200K .......... .......... .......... .......... .......... 95%  120M 0s
 17250K .......... .......... .......... .......... .......... 96%  104M 0s
 17300K .......... .......... .......... .......... .......... 96%  120M 0s
 17350K .......... .......... .......... .......... .......... 96%  100M 0s
 17400K .......... .......... .......... .......... .......... 96%  117M 0s
 17450K .......... .......... .......... .......... .......... 97%  117M 0s
 17500K .......... .......... .......... .......... .......... 97% 61.3M 0s
 17550K .......... .......... .......... .......... .......... 97% 2.01M 0s
 17600K .......... .......... .......... .......... .......... 98% 57.3M 0s
 17650K .......... .......... .......... .......... .......... 98%  101M 0s
 17700K .......... .......... .......... .......... .......... 98%  102M 0s
 17750K .......... .......... .......... .......... .......... 98%  117M 0s
 17800K .......... .......... .......... .......... .......... 99%  106M 0s
 17850K .......... .......... .......... .......... .......... 99%  120M 0s
 17900K .......... .......... .......... .......... .......... 99%  102M 0s
 17950K .......... .......... .......... .......... .......   100% 57.3M=1.7s

2017-10-09 10:37:45 (10.2 MB/s) - ‘en_product6.xml’ saved [18429919/18429919]

--2017-10-09 10:37:45--  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: 18502124 (18M) [application/octet-stream]
Saving to: ‘phenotype_annotation.tab’

     0K .......... .......... .......... .......... ..........  0% 34.3M 1s
    50K .......... .......... .......... .......... ..........  0% 21.6M 1s
   100K .......... .......... .......... .......... ..........  0% 23.9M 1s
   150K .......... .......... .......... .......... ..........  1% 28.1M 1s
   200K .......... .......... .......... .......... ..........  1% 27.0M 1s
   250K .......... .......... .......... .......... ..........  1% 29.1M 1s
   300K .......... .......... .......... .......... ..........  1% 30.0M 1s
   350K .......... .......... .......... .......... ..........  2% 43.9M 1s
   400K .......... .......... .......... .......... ..........  2% 17.0M 1s
   450K .......... .......... .......... .......... ..........  2% 42.2M 1s
   500K .......... .......... .......... .......... ..........  3%  101M 1s
   550K .......... .......... .......... .......... ..........  3% 13.8M 1s
   600K .......... .......... .......... .......... ..........  3% 39.5M 1s
   650K .......... .......... .......... .......... ..........  3% 54.9M 1s
   700K .......... .......... .......... .......... ..........  4% 30.8M 1s
   750K .......... .......... .......... .......... ..........  4% 93.0M 1s
   800K .......... .......... .......... .......... ..........  4% 31.3M 1s
   850K .......... .......... .......... .......... ..........  4% 48.1M 1s
   900K .......... .......... .......... .......... ..........  5% 60.2M 1s
   950K .......... .......... .......... .......... ..........  5% 28.9M 1s
  1000K .......... .......... .......... .......... ..........  5% 87.1M 1s
  1050K .......... .......... .......... .......... ..........  6% 71.6M 0s
  1100K .......... .......... .......... .......... ..........  6% 62.6M 0s
  1150K .......... .......... .......... .......... ..........  6% 42.5M 0s
  1200K .......... .......... .......... .......... ..........  6% 26.5M 0s
  1250K .......... .......... .......... .......... ..........  7% 71.4M 0s
  1300K .......... .......... .......... .......... ..........  7% 97.7M 0s
  1350K .......... .......... .......... .......... ..........  7% 31.5M 0s
  1400K .......... .......... .......... .......... ..........  8% 56.2M 0s
  1450K .......... .......... .......... .......... ..........  8% 23.0M 0s
  1500K .......... .......... .......... .......... ..........  8% 87.6M 0s
  1550K .......... .......... .......... .......... ..........  8%  120M 0s
  1600K .......... .......... .......... .......... ..........  9% 97.5M 0s
  1650K .......... .......... .......... .......... ..........  9% 80.7M 0s
  1700K .......... .......... .......... .......... ..........  9% 44.1M 0s
  1750K .......... .......... .......... .......... ..........  9%  104M 0s
  1800K .......... .......... .......... .......... .......... 10% 62.0M 0s
  1850K .......... .......... .......... .......... .......... 10% 55.5M 0s
  1900K .......... .......... .......... .......... .......... 10% 96.2M 0s
  1950K .......... .......... .......... .......... .......... 11% 66.9M 0s
  2000K .......... .......... .......... .......... .......... 11% 57.4M 0s
  2050K .......... .......... .......... .......... .......... 11% 76.4M 0s
  2100K .......... .......... .......... .......... .......... 11% 79.2M 0s
  2150K .......... .......... .......... .......... .......... 12% 96.9M 0s
  2200K .......... .......... .......... .......... .......... 12% 62.9M 0s
  2250K .......... .......... .......... .......... .......... 12% 80.2M 0s
  2300K .......... .......... .......... .......... .......... 13% 55.8M 0s
  2350K .......... .......... .......... .......... .......... 13% 97.3M 0s
  2400K .......... .......... .......... .......... .......... 13% 74.3M 0s
  2450K .......... .......... .......... .......... .......... 13% 83.5M 0s
  2500K .......... .......... .......... .......... .......... 14% 75.0M 0s
  2550K .......... .......... .......... .......... .......... 14% 88.3M 0s
  2600K .......... .......... .......... .......... .......... 14%  106M 0s
  2650K .......... .......... .......... .......... .......... 14%  119M 0s
  2700K .......... .......... .......... .......... .......... 15% 67.5M 0s
  2750K .......... .......... .......... .......... .......... 15% 93.5M 0s
  2800K .......... .......... .......... .......... .......... 15% 79.4M 0s
  2850K .......... .......... .......... .......... .......... 16% 57.5M 0s
  2900K .......... .......... .......... .......... .......... 16% 97.1M 0s
  2950K .......... .......... .......... .......... .......... 16%  114M 0s
  3000K .......... .......... .......... .......... .......... 16%  102M 0s
  3050K .......... .......... .......... .......... .......... 17% 83.9M 0s
  3100K .......... .......... .......... .......... .......... 17% 73.9M 0s
  3150K .......... .......... .......... .......... .......... 17% 86.1M 0s
  3200K .......... .......... .......... .......... .......... 17% 96.5M 0s
  3250K .......... .......... .......... .......... .......... 18%  102M 0s
  3300K .......... .......... .......... .......... .......... 18% 76.0M 0s
  3350K .......... .......... .......... .......... .......... 18% 87.4M 0s
  3400K .......... .......... .......... .......... .......... 19% 87.4M 0s
  3450K .......... .......... .......... .......... .......... 19% 59.2M 0s
  3500K .......... .......... .......... .......... .......... 19% 34.4M 0s
  3550K .......... .......... .......... .......... .......... 19% 80.0M 0s
  3600K .......... .......... .......... .......... .......... 20% 77.6M 0s
  3650K .......... .......... .......... .......... .......... 20% 55.4M 0s
  3700K .......... .......... .......... .......... .......... 20% 36.0M 0s
  3750K .......... .......... .......... .......... .......... 21% 41.3M 0s
  3800K .......... .......... .......... .......... .......... 21% 32.6M 0s
  3850K .......... .......... .......... .......... .......... 21% 92.7M 0s
  3900K .......... .......... .......... .......... .......... 21% 69.8M 0s
  3950K .......... .......... .......... .......... .......... 22%  114M 0s
  4000K .......... .......... .......... .......... .......... 22% 72.0M 0s
  4050K .......... .......... .......... .......... .......... 22%  105M 0s
  4100K .......... .......... .......... .......... .......... 22%  116M 0s
  4150K .......... .......... .......... .......... .......... 23% 58.3M 0s
  4200K .......... .......... .......... .......... .......... 23%  113M 0s
  4250K .......... .......... .......... .......... .......... 23%  117M 0s
  4300K .......... .......... .......... .......... .......... 24%  113M 0s
  4350K .......... .......... .......... .......... .......... 24% 75.0M 0s
  4400K .......... .......... .......... .......... .......... 24%  111M 0s
  4450K .......... .......... .......... .......... .......... 24% 56.3M 0s
  4500K .......... .......... .......... .......... .......... 25% 51.8M 0s
  4550K .......... .......... .......... .......... .......... 25%  123M 0s
  4600K .......... .......... .......... .......... .......... 25% 77.2M 0s
  4650K .......... .......... .......... .......... .......... 26%  112M 0s
  4700K .......... .......... .......... .......... .......... 26%  110M 0s
  4750K .......... .......... .......... .......... .......... 26%  113M 0s
  4800K .......... .......... .......... .......... .......... 26% 76.4M 0s
  4850K .......... .......... .......... .......... .......... 27% 98.5M 0s
  4900K .......... .......... .......... .......... .......... 27% 85.2M 0s
  4950K .......... .......... .......... .......... .......... 27% 99.7M 0s
  5000K .......... .......... .......... .......... .......... 27%  113M 0s
  5050K .......... .......... .......... .......... .......... 28% 59.1M 0s
  5100K .......... .......... .......... .......... .......... 28%  113M 0s
  5150K .......... .......... .......... .......... .......... 28%  108M 0s
  5200K .......... .......... .......... .......... .......... 29%  113M 0s
  5250K .......... .......... .......... .......... .......... 29% 92.4M 0s
  5300K .......... .......... .......... .......... .......... 29%  113M 0s
  5350K .......... .......... .......... .......... .......... 29% 75.1M 0s
  5400K .......... .......... .......... .......... .......... 30%  114M 0s
  5450K .......... .......... .......... .......... .......... 30%  116M 0s
  5500K .......... .......... .......... .......... .......... 30% 69.4M 0s
  5550K .......... .......... .......... .......... .......... 30% 80.5M 0s
  5600K .......... .......... .......... .......... .......... 31% 97.7M 0s
  5650K .......... .......... .......... .......... .......... 31%  113M 0s
  5700K .......... .......... .......... .......... .......... 31% 77.8M 0s
  5750K .......... .......... .......... .......... .......... 32% 85.0M 0s
  5800K .......... .......... .......... .......... .......... 32% 66.6M 0s
  5850K .......... .......... .......... .......... .......... 32% 86.7M 0s
  5900K .......... .......... .......... .......... .......... 32% 98.0M 0s
  5950K .......... .......... .......... .......... .......... 33%  113M 0s
  6000K .......... .......... .......... .......... .......... 33%  112M 0s
  6050K .......... .......... .......... .......... .......... 33% 77.0M 0s
  6100K .......... .......... .......... .......... .......... 34%  106M 0s
  6150K .......... .......... .......... .......... .......... 34%  114M 0s
  6200K .......... .......... .......... .......... .......... 34% 70.2M 0s
  6250K .......... .......... .......... .......... .......... 34% 89.2M 0s
  6300K .......... .......... .......... .......... .......... 35% 72.1M 0s
  6350K .......... .......... .......... .......... .......... 35% 94.2M 0s
  6400K .......... .......... .......... .......... .......... 35%  102M 0s
  6450K .......... .......... .......... .......... .......... 35%  112M 0s
  6500K .......... .......... .......... .......... .......... 36% 86.3M 0s
  6550K .......... .......... .......... .......... .......... 36% 97.7M 0s
  6600K .......... .......... .......... .......... .......... 36%  112M 0s
  6650K .......... .......... .......... .......... .......... 37%  118M 0s
  6700K .......... .......... .......... .......... .......... 37% 92.8M 0s
  6750K .......... .......... .......... .......... .......... 37% 80.3M 0s
  6800K .......... .......... .......... .......... .......... 37% 94.3M 0s
  6850K .......... .......... .......... .......... .......... 38%  108M 0s
  6900K .......... .......... .......... .......... .......... 38% 96.4M 0s
  6950K .......... .......... .......... .......... .......... 38% 71.9M 0s
  7000K .......... .......... .......... .......... .......... 39% 69.0M 0s
  7050K .......... .......... .......... .......... .......... 39% 94.1M 0s
  7100K .......... .......... .......... .......... .......... 39%  113M 0s
  7150K .......... .......... .......... .......... .......... 39% 93.9M 0s
  7200K .......... .......... .......... .......... .......... 40% 87.4M 0s
  7250K .......... .......... .......... .......... .......... 40%  101M 0s
  7300K .......... .......... .......... .......... .......... 40% 73.2M 0s
  7350K .......... .......... .......... .......... .......... 40% 99.6M 0s
  7400K .......... .......... .......... .......... .......... 41% 71.5M 0s
  7450K .......... .......... .......... .......... .......... 41%  108M 0s
  7500K .......... .......... .......... .......... .......... 41% 79.8M 0s
  7550K .......... .......... .......... .......... .......... 42%  113M 0s
  7600K .......... .......... .......... .......... .......... 42%  113M 0s
  7650K .......... .......... .......... .......... .......... 42% 86.5M 0s
  7700K .......... .......... .......... .......... .......... 42%  112M 0s
  7750K .......... .......... .......... .......... .......... 43%  113M 0s
  7800K .......... .......... .......... .......... .......... 43% 94.7M 0s
  7850K .......... .......... .......... .......... .......... 43% 85.9M 0s
  7900K .......... .......... .......... .......... .......... 43% 72.2M 0s
  7950K .......... .......... .......... .......... .......... 44%  110M 0s
  8000K .......... .......... .......... .......... .......... 44%  111M 0s
  8050K .......... .......... .......... .......... .......... 44% 71.6M 0s
  8100K .......... .......... .......... .......... .......... 45%  112M 0s
  8150K .......... .......... .......... .......... .......... 45% 87.4M 0s
  8200K .......... .......... .......... .......... .......... 45%  109M 0s
  8250K .......... .......... .......... .......... .......... 45%  113M 0s
  8300K .......... .......... .......... .......... .......... 46% 71.4M 0s
  8350K .......... .......... .......... .......... .......... 46% 94.7M 0s
  8400K .......... .......... .......... .......... .......... 46%  101M 0s
  8450K .......... .......... .......... .......... .......... 47%  109M 0s
  8500K .......... .......... .......... .......... .......... 47% 87.7M 0s
  8550K .......... .......... .......... .......... .......... 47% 65.7M 0s
  8600K .......... .......... .......... .......... .......... 47%  112M 0s
  8650K .......... .......... .......... .......... .......... 48% 84.2M 0s
  8700K .......... .......... .......... .......... .......... 48%  113M 0s
  8750K .......... .......... .......... .......... .......... 48%  113M 0s
  8800K .......... .......... .......... .......... .......... 48% 71.4M 0s
  8850K .......... .......... .......... .......... .......... 49% 86.4M 0s
  8900K .......... .......... .......... .......... .......... 49%  111M 0s
  8950K .......... .......... .......... .......... .......... 49%  113M 0s
  9000K .......... .......... .......... .......... .......... 50% 64.1M 0s
  9050K .......... .......... .......... .......... .......... 50%  112M 0s
  9100K .......... .......... .......... .......... .......... 50% 99.2M 0s
  9150K .......... .......... .......... .......... .......... 50%  112M 0s
  9200K .......... .......... .......... .......... .......... 51% 86.8M 0s
  9250K .......... .......... .......... .......... .......... 51% 98.4M 0s
  9300K .......... .......... .......... .......... .......... 51% 64.5M 0s
  9350K .......... .......... .......... .......... .......... 52% 65.4M 0s
  9400K .......... .......... .......... .......... .......... 52%  114M 0s
  9450K .......... .......... .......... .......... .......... 52% 85.9M 0s
  9500K .......... .......... .......... .......... .......... 52%  111M 0s
  9550K .......... .......... .......... .......... .......... 53% 87.0M 0s
  9600K .......... .......... .......... .......... .......... 53% 98.3M 0s
  9650K .......... .......... .......... .......... .......... 53%  113M 0s
  9700K .......... .......... .......... .......... .......... 53% 75.9M 0s
  9750K .......... .......... .......... .......... .......... 54% 80.2M 0s
  9800K .......... .......... .......... .......... .......... 54%  109M 0s
  9850K .......... .......... .......... .......... .......... 54%  113M 0s
  9900K .......... .......... .......... .......... .......... 55%  113M 0s
  9950K .......... .......... .......... .......... .......... 55% 84.9M 0s
 10000K .......... .......... .......... .......... .......... 55%  112M 0s
 10050K .......... .......... .......... .......... .......... 55% 77.8M 0s
 10100K .......... .......... .......... .......... .......... 56%  113M 0s
 10150K .......... .......... .......... .......... .......... 56%  113M 0s
 10200K .......... .......... .......... .......... .......... 56% 77.7M 0s
 10250K .......... .......... .......... .......... .......... 57%  113M 0s
 10300K .......... .......... .......... .......... .......... 57% 69.2M 0s
 10350K .......... .......... .......... .......... .......... 57%  101M 0s
 10400K .......... .......... .......... .......... .......... 57% 84.1M 0s
 10450K .......... .......... .......... .......... .......... 58% 89.0M 0s
 10500K .......... .......... .......... .......... .......... 58% 77.6M 0s
 10550K .......... .......... .......... .......... .......... 58%  113M 0s
 10600K .......... .......... .......... .......... .......... 58%  113M 0s
 10650K .......... .......... .......... .......... .......... 59% 95.9M 0s
 10700K .......... .......... .......... .......... .......... 59% 95.5M 0s
 10750K .......... .......... .......... .......... .......... 59%  100M 0s
 10800K .......... .......... .......... .......... .......... 60%  107M 0s
 10850K .......... .......... .......... .......... .......... 60% 88.8M 0s
 10900K .......... .......... .......... .......... .......... 60% 78.5M 0s
 10950K .......... .......... .......... .......... .......... 60% 88.2M 0s
 11000K .......... .......... .......... .......... .......... 61%  108M 0s
 11050K .......... .......... .......... .......... .......... 61% 85.7M 0s
 11100K .......... .......... .......... .......... .......... 61% 89.2M 0s
 11150K .......... .......... .......... .......... .......... 61%  101M 0s
 11200K .......... .......... .......... .......... .......... 62%  103M 0s
 11250K .......... .......... .......... .......... .......... 62%  113M 0s
 11300K .......... .......... .......... .......... .......... 62% 89.9M 0s
 11350K .......... .......... .......... .......... .......... 63% 86.0M 0s
 11400K .......... .......... .......... .......... .......... 63% 97.8M 0s
 11450K .......... .......... .......... .......... .......... 63%  105M 0s
 11500K .......... .......... .......... .......... .......... 63%  105M 0s
 11550K .......... .......... .......... .......... .......... 64% 78.5M 0s
 11600K .......... .......... .......... .......... .......... 64%  109M 0s
 11650K .......... .......... .......... .......... .......... 64% 87.1M 0s
 11700K .......... .......... .......... .......... .......... 65% 94.4M 0s
 11750K .......... .......... .......... .......... .......... 65%  117M 0s
 11800K .......... .......... .......... .......... .......... 65% 71.4M 0s
 11850K .......... .......... .......... .......... .......... 65% 96.7M 0s
 11900K .......... .......... .......... .......... .......... 66% 87.0M 0s
 11950K .......... .......... .......... .......... .......... 66%  113M 0s
 12000K .......... .......... .......... .......... .......... 66% 70.6M 0s
 12050K .......... .......... .......... .......... .......... 66%  112M 0s
 12100K .......... .......... .......... .......... .......... 67% 84.3M 0s
 12150K .......... .......... .......... .......... .......... 67%  109M 0s
 12200K .......... .......... .......... .......... .......... 67%  111M 0s
 12250K .......... .......... .......... .......... .......... 68% 57.2M 0s
 12300K .......... .......... .......... .......... .......... 68%  110M 0s
 12350K .......... .......... .......... .......... .......... 68% 85.6M 0s
 12400K .......... .......... .......... .......... .......... 68% 77.7M 0s
 12450K .......... .......... .......... .......... .......... 69%  113M 0s
 12500K .......... .......... .......... .......... .......... 69% 71.2M 0s
 12550K .......... .......... .......... .......... .......... 69% 77.9M 0s
 12600K .......... .......... .......... .......... .......... 70%  110M 0s
 12650K .......... .......... .......... .......... .......... 70%  113M 0s
 12700K .......... .......... .......... .......... .......... 70% 80.8M 0s
 12750K .......... .......... .......... .......... .......... 70%  112M 0s
 12800K .......... .......... .......... .......... .......... 71% 71.5M 0s
 12850K .......... .......... .......... .......... .......... 71% 86.9M 0s
 12900K .......... .......... .......... .......... .......... 71%  114M 0s
 12950K .......... .......... .......... .......... .......... 71% 96.9M 0s
 13000K .......... .......... .......... .......... .......... 72% 91.0M 0s
 13050K .......... .......... .......... .......... .......... 72% 58.0M 0s
 13100K .......... .......... .......... .......... .......... 72%  112M 0s
 13150K .......... .......... .......... .......... .......... 73%  112M 0s
 13200K .......... .......... .......... .......... .......... 73% 85.1M 0s
 13250K .......... .......... .......... .......... .......... 73%  112M 0s
 13300K .......... .......... .......... .......... .......... 73% 43.0M 0s
 13350K .......... .......... .......... .......... .......... 74%  110M 0s
 13400K .......... .......... .......... .......... .......... 74% 96.3M 0s
 13450K .......... .......... .......... .......... .......... 74%  113M 0s
 13500K .......... .......... .......... .......... .......... 74%  112M 0s
 13550K .......... .......... .......... .......... .......... 75% 53.8M 0s
 13600K .......... .......... .......... .......... .......... 75%  111M 0s
 13650K .......... .......... .......... .......... .......... 75% 43.1M 0s
 13700K .......... .......... .......... .......... .......... 76% 79.1M 0s
 13750K .......... .......... .......... .......... .......... 76% 51.5M 0s
 13800K .......... .......... .......... .......... .......... 76% 88.3M 0s
 13850K .......... .......... .......... .......... .......... 76% 99.7M 0s
 13900K .......... .......... .......... .......... .......... 77% 45.4M 0s
 13950K .......... .......... .......... .......... .......... 77% 39.1M 0s
 14000K .......... .......... .......... .......... .......... 77% 58.4M 0s
 14050K .......... .......... .......... .......... .......... 78%  115M 0s
 14100K .......... .......... .......... .......... .......... 78% 61.3M 0s
 14150K .......... .......... .......... .......... .......... 78% 39.3M 0s
 14200K .......... .......... .......... .......... .......... 78% 73.3M 0s
 14250K .......... .......... .......... .......... .......... 79%  114M 0s
 14300K .......... .......... .......... .......... .......... 79%  113M 0s
 14350K .......... .......... .......... .......... .......... 79% 45.3M 0s
 14400K .......... .......... .......... .......... .......... 79% 50.0M 0s
 14450K .......... .......... .......... .......... .......... 80% 43.7M 0s
 14500K .......... .......... .......... .......... .......... 80% 44.3M 0s
 14550K .......... .......... .......... .......... .......... 80%  115M 0s
 14600K .......... .......... .......... .......... .......... 81% 47.0M 0s
 14650K .......... .......... .......... .......... .......... 81% 49.1M 0s
 14700K .......... .......... .......... .......... .......... 81% 47.2M 0s
 14750K .......... .......... .......... .......... .......... 81%  106M 0s
 14800K .......... .......... .......... .......... .......... 82% 47.1M 0s
 14850K .......... .......... .......... .......... .......... 82% 49.2M 0s
 14900K .......... .......... .......... .......... .......... 82% 96.4M 0s
 14950K .......... .......... .......... .......... .......... 83% 27.9M 0s
 15000K .......... .......... .......... .......... .......... 83%  118M 0s
 15050K .......... .......... .......... .......... .......... 83% 59.6M 0s
 15100K .......... .......... .......... .......... .......... 83% 43.8M 0s
 15150K .......... .......... .......... .......... .......... 84% 48.3M 0s
 15200K .......... .......... .......... .......... .......... 84% 48.0M 0s
 15250K .......... .......... .......... .......... .......... 84%  114M 0s
 15300K .......... .......... .......... .......... .......... 84% 50.5M 0s
 15350K .......... .......... .......... .......... .......... 85% 49.7M 0s
 15400K .......... .......... .......... .......... .......... 85% 53.3M 0s
 15450K .......... .......... .......... .......... .......... 85%  104M 0s
 15500K .......... .......... .......... .......... .......... 86% 47.3M 0s
 15550K .......... .......... .......... .......... .......... 86% 49.3M 0s
 15600K .......... .......... .......... .......... .......... 86% 47.0M 0s
 15650K .......... .......... .......... .......... .......... 86% 53.4M 0s
 15700K .......... .......... .......... .......... .......... 87%  111M 0s
 15750K .......... .......... .......... .......... .......... 87% 52.1M 0s
 15800K .......... .......... .......... .......... .......... 87% 48.3M 0s
 15850K .......... .......... .......... .......... .......... 87% 43.5M 0s
 15900K .......... .......... .......... .......... .......... 88% 48.9M 0s
 15950K .......... .......... .......... .......... .......... 88%  101M 0s
 16000K .......... .......... .......... .......... .......... 88% 63.6M 0s
 16050K .......... .......... .......... .......... .......... 89% 41.8M 0s
 16100K .......... .......... .......... .......... .......... 89% 51.7M 0s
 16150K .......... .......... .......... .......... .......... 89%  106M 0s
 16200K .......... .......... .......... .......... .......... 89% 42.9M 0s
 16250K .......... .......... .......... .......... .......... 90% 52.3M 0s
 16300K .......... .......... .......... .......... .......... 90% 45.6M 0s
 16350K .......... .......... .......... .......... .......... 90% 55.0M 0s
 16400K .......... .......... .......... .......... .......... 91%  114M 0s
 16450K .......... .......... .......... .......... .......... 91% 46.8M 0s
 16500K .......... .......... .......... .......... .......... 91% 48.0M 0s
 16550K .......... .......... .......... .......... .......... 91% 51.8M 0s
 16600K .......... .......... .......... .......... .......... 92% 42.9M 0s
 16650K .......... .......... .......... .......... .......... 92%  113M 0s
 16700K .......... .......... .......... .......... .......... 92% 46.9M 0s
 16750K .......... .......... .......... .......... .......... 92% 68.6M 0s
 16800K .......... .......... .......... .......... .......... 93%  111M 0s
 16850K .......... .......... .......... .......... .......... 93%  110M 0s
 16900K .......... .......... .......... .......... .......... 93%  111M 0s
 16950K .......... .......... .......... .......... .......... 94%  103M 0s
 17000K .......... .......... .......... .......... .......... 94%  112M 0s
 17050K .......... .......... .......... .......... .......... 94% 84.7M 0s
 17100K .......... .......... .......... .......... .......... 94%  113M 0s
 17150K .......... .......... .......... .......... .......... 95%  114M 0s
 17200K .......... .......... .......... .......... .......... 95% 71.5M 0s
 17250K .......... .......... .......... .......... .......... 95%  113M 0s
 17300K .......... .......... .......... .......... .......... 96% 94.7M 0s
 17350K .......... .......... .......... .......... .......... 96% 99.4M 0s
 17400K .......... .......... .......... .......... .......... 96%  113M 0s
 17450K .......... .......... .......... .......... .......... 96%  113M 0s
 17500K .......... .......... .......... .......... .......... 97%  112M 0s
 17550K .......... .......... .......... .......... .......... 97% 98.6M 0s
 17600K .......... .......... .......... .......... .......... 97%  114M 0s
 17650K .......... .......... .......... .......... .......... 97%  113M 0s
 17700K .......... .......... .......... .......... .......... 98%  112M 0s
 17750K .......... .......... .......... .......... .......... 98%  113M 0s
 17800K .......... .......... .......... .......... .......... 98%  112M 0s
 17850K .......... .......... .......... .......... .......... 99%  103M 0s
 17900K .......... .......... .......... .......... .......... 99%  112M 0s
 17950K .......... .......... .......... .......... .......... 99%  105M 0s
 18000K .......... .......... .......... .......... .......... 99%  113M 0s
 18050K .......... ........                                   100%  120M=0.2s

2017-10-09 10:37:46 (71.9 MB/s) - ‘phenotype_annotation.tab’ saved [18502124/18502124]

--2017-10-09 10:37:46--  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 10:37:46--  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% 1.96M 3s
    50K .......... .......... .......... .......... ..........  1% 5.82M 2s
   100K .......... .......... .......... .......... ..........  2% 13.6M 1s
   150K .......... .......... .......... .......... ..........  3% 5.42M 1s
   200K .......... .......... .......... .......... ..........  4% 13.6M 1s
   250K .......... .......... .......... .......... ..........  5% 6.81M 1s
   300K .......... .......... .......... .......... ..........  6% 10.2M 1s
   350K .......... .......... .......... .......... ..........  7% 8.34M 1s
   400K .......... .......... .......... .......... ..........  8% 6.85M 1s
   450K .......... .......... .......... .......... ..........  9% 10.2M 1s
   500K .......... .......... .......... .......... ..........  9% 12.6M 1s
   550K .......... .......... .......... .......... .......... 10% 8.10M 1s
   600K .......... .......... .......... .......... .......... 11% 13.7M 1s
   650K .......... .......... .......... .......... .......... 12% 8.86M 1s
   700K .......... .......... .......... .......... .......... 13% 7.18M 1s
   750K .......... .......... .......... .......... .......... 14% 10.1M 1s
   800K .......... .......... .......... .......... .......... 15% 8.59M 1s
   850K .......... .......... .......... .......... .......... 16% 11.3M 1s
   900K .......... .......... .......... .......... .......... 17% 13.9M 1s
   950K .......... .......... .......... .......... .......... 18% 10.5M 1s
  1000K .......... .......... .......... .......... .......... 18% 10.2M 1s
  1050K .......... .......... .......... .......... .......... 19% 10.8M 1s
  1100K .......... .......... .......... .......... .......... 20% 13.6M 1s
  1150K .......... .......... .......... .......... .......... 21% 12.9M 1s
  1200K .......... .......... .......... .......... .......... 22% 12.7M 1s
  1250K .......... .......... .......... .......... .......... 23% 10.5M 1s
  1300K .......... .......... .......... .......... .......... 24% 13.7M 0s
  1350K .......... .......... .......... .......... .......... 25% 18.5M 0s
  1400K .......... .......... .......... .......... .......... 26% 10.7M 0s
  1450K .......... .......... .......... .......... .......... 27% 13.8M 0s
  1500K .......... .......... .......... .......... .......... 27% 17.5M 0s
  1550K .......... .......... .......... .......... .......... 28% 11.8M 0s
  1600K .......... .......... .......... .......... .......... 29% 12.9M 0s
  1650K .......... .......... .......... .......... .......... 30% 15.3M 0s
  1700K .......... .......... .......... .......... .......... 31% 11.7M 0s
  1750K .......... .......... .......... .......... .......... 32% 18.6M 0s
  1800K .......... .......... .......... .......... .......... 33% 17.5M 0s
  1850K .......... .......... .......... .......... .......... 34% 13.6M 0s
  1900K .......... .......... .......... .......... .......... 35% 15.6M 0s
  1950K .......... .......... .......... .......... .......... 36% 22.4M 0s
  2000K .......... .......... .......... .......... .......... 36% 8.61M 0s
  2050K .......... .......... .......... .......... .......... 37% 23.4M 0s
  2100K .......... .......... .......... .......... .......... 38% 18.2M 0s
  2150K .......... .......... .......... .......... .......... 39% 23.9M 0s
  2200K .......... .......... .......... .......... .......... 40% 11.7M 0s
  2250K .......... .......... .......... .......... .......... 41% 26.5M 0s
  2300K .......... .......... .......... .......... .......... 42% 17.6M 0s
  2350K .......... .......... .......... .......... .......... 43% 21.1M 0s
  2400K .......... .......... .......... .......... .......... 44% 10.8M 0s
  2450K .......... .......... .......... .......... .......... 45% 24.9M 0s
  2500K .......... .......... .......... .......... .......... 45% 18.9M 0s
  2550K .......... .......... .......... .......... .......... 46% 25.5M 0s
  2600K .......... .......... .......... .......... .......... 47% 11.1M 0s
  2650K .......... .......... .......... .......... .......... 48% 27.9M 0s
  2700K .......... .......... .......... .......... .......... 49% 18.2M 0s
  2750K .......... .......... .......... .......... .......... 50% 19.6M 0s
  2800K .......... .......... .......... .......... .......... 51% 15.2M 0s
  2850K .......... .......... .......... .......... .......... 52% 21.7M 0s
  2900K .......... .......... .......... .......... .......... 53% 25.5M 0s
  2950K .......... .......... .......... .......... .......... 54% 25.3M 0s
  3000K .......... .......... .......... .......... .......... 54% 11.7M 0s
  3050K .......... .......... .......... .......... .......... 55% 27.3M 0s
  3100K .......... .......... .......... .......... .......... 56% 17.7M 0s
  3150K .......... .......... .......... .......... .......... 57% 28.1M 0s
  3200K .......... .......... .......... .......... .......... 58% 21.9M 0s
  3250K .......... .......... .......... .......... .......... 59% 14.5M 0s
  3300K .......... .......... .......... .......... .......... 60% 28.6M 0s
  3350K .......... .......... .......... .......... .......... 61% 28.0M 0s
  3400K .......... .......... .......... .......... .......... 62% 27.1M 0s
  3450K .......... .......... .......... .......... .......... 63% 13.7M 0s
  3500K .......... .......... .......... .......... .......... 63% 21.9M 0s
  3550K .......... .......... .......... .......... .......... 64% 26.4M 0s
  3600K .......... .......... .......... .......... .......... 65% 26.2M 0s
  3650K .......... .......... .......... .......... .......... 66% 29.9M 0s
  3700K .......... .......... .......... .......... .......... 67% 12.0M 0s
  3750K .......... .......... .......... .......... .......... 68% 23.3M 0s
  3800K .......... .......... .......... .......... .......... 69% 43.0M 0s
  3850K .......... .......... .......... .......... .......... 70% 30.2M 0s
  3900K .......... .......... .......... .......... .......... 71% 25.2M 0s
  3950K .......... .......... .......... .......... .......... 72% 15.8M 0s
  4000K .......... .......... .......... .......... .......... 72% 22.6M 0s
  4050K .......... .......... .......... .......... .......... 73% 36.7M 0s
  4100K .......... .......... .......... .......... .......... 74% 22.1M 0s
  4150K .......... .......... .......... .......... .......... 75% 43.9M 0s
  4200K .......... .......... .......... .......... .......... 76% 28.8M 0s
  4250K .......... .......... .......... .......... .......... 77% 18.2M 0s
  4300K .......... .......... .......... .......... .......... 78% 18.7M 0s
  4350K .......... .......... .......... .......... .......... 79% 38.6M 0s
  4400K .......... .......... .......... .......... .......... 80% 31.9M 0s
  4450K .......... .......... .......... .......... .......... 81% 28.3M 0s
  4500K .......... .......... .......... .......... .......... 81% 40.9M 0s
  4550K .......... .......... .......... .......... .......... 82% 13.9M 0s
  4600K .......... .......... .......... .......... .......... 83% 33.3M 0s
  4650K .......... .......... .......... .......... .......... 84% 34.7M 0s
  4700K .......... .......... .......... .......... .......... 85% 21.1M 0s
  4750K .......... .......... .......... .......... .......... 86% 44.0M 0s
  4800K .......... .......... .......... .......... .......... 87% 16.3M 0s
  4850K .......... .......... .......... .......... .......... 88% 32.9M 0s
  4900K .......... .......... .......... .......... .......... 89% 23.9M 0s
  4950K .......... .......... .......... .......... .......... 90% 51.0M 0s
  5000K .......... .......... .......... .......... .......... 90% 31.6M 0s
  5050K .......... .......... .......... .......... .......... 91% 32.5M 0s
  5100K .......... .......... .......... .......... .......... 92% 32.0M 0s
  5150K .......... .......... .......... .......... .......... 93% 16.0M 0s
  5200K .......... .......... .......... .......... .......... 94% 32.1M 0s
  5250K .......... .......... .......... .......... .......... 95% 37.5M 0s
  5300K .......... .......... .......... .......... .......... 96% 34.3M 0s
  5350K .......... .......... .......... .......... .......... 97% 36.5M 0s
  5400K .......... .......... .......... .......... .......... 98% 32.3M 0s
  5450K .......... .......... .......... .......... .......... 99% 18.9M 0s
  5500K .......... .......... .......... .......... .......... 99% 20.8M 0s
  5550K ..                                                    100% 5113G=0.4s

Last-modified header missing -- time-stamps turned off.
2017-10-09 10:37:46 (15.1 MB/s) - ‘hp.obo’ saved [5685945/5685945]

FINISHED --2017-10-09 10:37:46--
Total wall clock time: 12s
Downloaded: 5 files, 44M in 4.8s (9.18 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 10:37:47 AM ontologizer.go.OBOParser doParse
INFO: Got 13156 terms and 16794 relations in 160 ms
Details of parsed obo file:
  data-version:		releases/2017-10-05
  format:		1.2
  term definitions:	13156
Oct 09, 2017 10:37:47 AM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
Oct 09, 2017 10:37:47 AM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118)
WARN: Frequency of 3952 terms was zero!!
Set IC of these to : 9.221774749601845
mims:10209 with inh: 6910
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(): 10209
 omim: 7322
 orphanet: 2840
 others: 47
Disease entries with at least one known disease gene: 5785
Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 10115
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 10:38:01 AM ontologizer.go.OBOParser doParse
INFO: Got 13156 terms and 16794 relations in 157 ms
Details of parsed obo file:
  data-version:		releases/2017-10-05
  format:		1.2
  term definitions:	13156
Oct 09, 2017 10:38:01 AM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
Oct 09, 2017 10:38:02 AM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118)
WARN: Frequency of 3952 terms was zero!!
Set IC of these to : 9.221774749601845
mims:10209 with inh: 6910
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(): 10209
 omim: 7322
 orphanet: 2840
 others: 47
Disease entries with at least one known disease gene: 5785
Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 10115
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