SuccessConsole Output

Started by upstream project "hpo.annotations" build number 1269
originally caused by:
 Started by user koehler
Running as SYSTEM
Building in workspace /var/lib/jenkins/jobs/hpo.annotations.monthly/workspace
Cleaning local Directory .
Checking out https://github.com/monarch-initiative/hpo-annotation-data/trunk/util@HEAD at revision HEAD
A         annotation
A         annotation/.gitignore
A         annotation/external_data.txt
A         annotation/makefile
A         tools
A         tools/hpo_mysqldb
A         tools/hpo_mysqldb/schemabackup_2010-06-18.sql
At revision 5653
no change for https://github.com/monarch-initiative/hpo-annotation-data/trunk/util since the previous build
[workspace] $ /bin/sh -xe /tmp/jenkins5858529323707829940.sh
+ make -C annotation
make: Entering directory '/var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation'
mkdir -p data
#some cleanup beforehand
rm -f data/hp.obo
rm -f data/phenotype_annotation.tab
rm -f data/mim2*
mkdir -p jar
wget -N -P jar https://github.com/Phenomics/hpo-build-jars/raw/master/createGene2Phenotype.jar
--2019-11-15 21:59:19--  https://github.com/Phenomics/hpo-build-jars/raw/master/createGene2Phenotype.jar
Resolving proxy.charite.de (proxy.charite.de)... 141.42.5.215
Connecting to proxy.charite.de (proxy.charite.de)|141.42.5.215|:8080... connected.
Proxy request sent, awaiting response... 302 Found
Location: https://raw.githubusercontent.com/Phenomics/hpo-build-jars/master/createGene2Phenotype.jar [following]
--2019-11-15 21:59:19--  https://raw.githubusercontent.com/Phenomics/hpo-build-jars/master/createGene2Phenotype.jar
Connecting to proxy.charite.de (proxy.charite.de)|141.42.5.215|:8080... connected.
Proxy request sent, awaiting response... 200 OK
Length: 16284033 (16M) [application/octet-stream]
Saving to: ‘jar/createGene2Phenotype.jar’

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 15900K ..                                                    100% 4532G=0.2s

Last-modified header missing -- time-stamps turned off.
2019-11-15 21:59:20 (73.0 MB/s) - ‘jar/createGene2Phenotype.jar’ saved [16284033/16284033]

# 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 -
--2019-11-15 21:59:20--  ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/mim2gene_medgen
Resolving proxy.charite.de (proxy.charite.de)... 141.42.5.215
Connecting to proxy.charite.de (proxy.charite.de)|141.42.5.215|:8080... connected.
Proxy request sent, awaiting response... 200 OK
Length: 779379 (761K) [text/plain]
Saving to: ‘mim2gene_medgen’

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   750K .......... .                                          100% 40.4M=0.02s

2019-11-15 21:59:23 (34.8 MB/s) - ‘mim2gene_medgen’ saved [779379/779379]

--2019-11-15 21:59:23--  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: 2836417 (2.7M) [text/plain]
Saving to: ‘Homo_sapiens.gene_info.gz’

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2019-11-15 21:59:25 (36.9 MB/s) - ‘Homo_sapiens.gene_info.gz’ saved [2836417/2836417]

--2019-11-15 21:59:25--  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: 16366718 (16M) [text/xml]
Saving to: ‘en_product6.xml’

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2019-11-15 21:59:26 (14.3 MB/s) - ‘en_product6.xml’ saved [16366718/16366718]

--2019-11-15 21:59:26--  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: 21742685 (21M) [application/octet-stream]
Saving to: ‘phenotype_annotation.tab’

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  5150K .......... .......... .......... .......... .......... 24% 97.9M 0s
  5200K .......... .......... .......... .......... .......... 24%  113M 0s
  5250K .......... .......... .......... .......... .......... 24%  109M 0s
  5300K .......... .......... .......... .......... .......... 25% 98.6M 0s
  5350K .......... .......... .......... .......... .......... 25%  114M 0s
  5400K .......... .......... .......... .......... .......... 25%  114M 0s
  5450K .......... .......... .......... .......... .......... 25%  113M 0s
  5500K .......... .......... .......... .......... .......... 26%  102M 0s
  5550K .......... .......... .......... .......... .......... 26%  113M 0s
  5600K .......... .......... .......... .......... .......... 26%  102M 0s
  5650K .......... .......... .......... .......... .......... 26%  116M 0s
  5700K .......... .......... .......... .......... .......... 27%  114M 0s
  5750K .......... .......... .......... .......... .......... 27% 98.6M 0s
  5800K .......... .......... .......... .......... .......... 27%  111M 0s
  5850K .......... .......... .......... .......... .......... 27%  112M 0s
  5900K .......... .......... .......... .......... .......... 28%  103M 0s
  5950K .......... .......... .......... .......... .......... 28%  113M 0s
  6000K .......... .......... .......... .......... .......... 28%  119M 0s
  6050K .......... .......... .......... .......... .......... 28%  112M 0s
  6100K .......... .......... .......... .......... .......... 28%  112M 0s
  6150K .......... .......... .......... .......... .......... 29% 98.1M 0s
  6200K .......... .......... .......... .......... .......... 29%  116M 0s
  6250K .......... .......... .......... .......... .......... 29%  113M 0s
  6300K .......... .......... .......... .......... .......... 29%  105M 0s
  6350K .......... .......... .......... .......... .......... 30%  106M 0s
  6400K .......... .......... .......... .......... .......... 30%  113M 0s
  6450K .......... .......... .......... .......... .......... 30% 97.8M 0s
  6500K .......... .......... .......... .......... .......... 30%  115M 0s
  6550K .......... .......... .......... .......... .......... 31%  109M 0s
  6600K .......... .......... .......... .......... .......... 31%  116M 0s
  6650K .......... .......... .......... .......... .......... 31%  107M 0s
  6700K .......... .......... .......... .......... .......... 31%  103M 0s
  6750K .......... .......... .......... .......... .......... 32%  108M 0s
  6800K .......... .......... .......... .......... .......... 32%  111M 0s
  6850K .......... .......... .......... .......... .......... 32%  108M 0s
  6900K .......... .......... .......... .......... .......... 32%  111M 0s
  6950K .......... .......... .......... .......... .......... 32%  104M 0s
  7000K .......... .......... .......... .......... .......... 33%  111M 0s
  7050K .......... .......... .......... .......... .......... 33%  117M 0s
  7100K .......... .......... .......... .......... .......... 33%  101M 0s
  7150K .......... .......... .......... .......... .......... 33%  112M 0s
  7200K .......... .......... .......... .......... .......... 34%  109M 0s
  7250K .......... .......... .......... .......... .......... 34%  111M 0s
  7300K .......... .......... .......... .......... .......... 34% 99.9M 0s
  7350K .......... .......... .......... .......... .......... 34%  112M 0s
  7400K .......... .......... .......... .......... .......... 35%  116M 0s
  7450K .......... .......... .......... .......... .......... 35%  112M 0s
  7500K .......... .......... .......... .......... .......... 35% 76.1M 0s
  7550K .......... .......... .......... .......... .......... 35% 96.7M 0s
  7600K .......... .......... .......... .......... .......... 36%  107M 0s
  7650K .......... .......... .......... .......... .......... 36%  110M 0s
  7700K .......... .......... .......... .......... .......... 36%  112M 0s
  7750K .......... .......... .......... .......... .......... 36%  113M 0s
  7800K .......... .......... .......... .......... .......... 36%  106M 0s
  7850K .......... .......... .......... .......... .......... 37%  111M 0s
  7900K .......... .......... .......... .......... .......... 37% 42.7M 0s
  7950K .......... .......... .......... .......... .......... 37%  113M 0s
  8000K .......... .......... .......... .......... .......... 37%  113M 0s
  8050K .......... .......... .......... .......... .......... 38%  107M 0s
  8100K .......... .......... .......... .......... .......... 38%  100M 0s
  8150K .......... .......... .......... .......... .......... 38%  113M 0s
  8200K .......... .......... .......... .......... .......... 38%  105M 0s
  8250K .......... .......... .......... .......... .......... 39%  111M 0s
  8300K .......... .......... .......... .......... .......... 39%  101M 0s
  8350K .......... .......... .......... .......... .......... 39%  107M 0s
  8400K .......... .......... .......... .......... .......... 39%  111M 0s
  8450K .......... .......... .......... .......... .......... 40%  102M 0s
  8500K .......... .......... .......... .......... .......... 40%  111M 0s
  8550K .......... .......... .......... .......... .......... 40% 98.3M 0s
  8600K .......... .......... .......... .......... .......... 40%  112M 0s
  8650K .......... .......... .......... .......... .......... 40%  101M 0s
  8700K .......... .......... .......... .......... .......... 41%  109M 0s
  8750K .......... .......... .......... .......... .......... 41%  109M 0s
  8800K .......... .......... .......... .......... .......... 41% 99.0M 0s
  8850K .......... .......... .......... .......... .......... 41%  113M 0s
  8900K .......... .......... .......... .......... .......... 42%  103M 0s
  8950K .......... .......... .......... .......... .......... 42% 99.1M 0s
  9000K .......... .......... .......... .......... .......... 42%  121M 0s
  9050K .......... .......... .......... .......... .......... 42%  100M 0s
  9100K .......... .......... .......... .......... .......... 43%  121M 0s
  9150K .......... .......... .......... .......... .......... 43% 98.1M 0s
  9200K .......... .......... .......... .......... .......... 43%  121M 0s
  9250K .......... .......... .......... .......... .......... 43% 58.0M 0s
  9300K .......... .......... .......... .......... .......... 44% 94.6M 0s
  9350K .......... .......... .......... .......... .......... 44%  113M 0s
  9400K .......... .......... .......... .......... .......... 44%  113M 0s
  9450K .......... .......... .......... .......... .......... 44%  106M 0s
  9500K .......... .......... .......... .......... .......... 44%  112M 0s
  9550K .......... .......... .......... .......... .......... 45%  111M 0s
  9600K .......... .......... .......... .......... .......... 45%  102M 0s
  9650K .......... .......... .......... .......... .......... 45%  114M 0s
  9700K .......... .......... .......... .......... .......... 45% 41.2M 0s
  9750K .......... .......... .......... .......... .......... 46% 71.2M 0s
  9800K .......... .......... .......... .......... .......... 46%  107M 0s
  9850K .......... .......... .......... .......... .......... 46%  113M 0s
  9900K .......... .......... .......... .......... .......... 46%  110M 0s
  9950K .......... .......... .......... .......... .......... 47% 57.1M 0s
 10000K .......... .......... .......... .......... .......... 47%  113M 0s
 10050K .......... .......... .......... .......... .......... 47% 94.6M 0s
 10100K .......... .......... .......... .......... .......... 47%  114M 0s
 10150K .......... .......... .......... .......... .......... 48% 51.9M 0s
 10200K .......... .......... .......... .......... .......... 48% 52.3M 0s
 10250K .......... .......... .......... .......... .......... 48% 94.3M 0s
 10300K .......... .......... .......... .......... .......... 48%  128M 0s
 10350K .......... .......... .......... .......... .......... 48% 99.7M 0s
 10400K .......... .......... .......... .......... .......... 49%  112M 0s
 10450K .......... .......... .......... .......... .......... 49%  109M 0s
 10500K .......... .......... .......... .......... .......... 49%  113M 0s
 10550K .......... .......... .......... .......... .......... 49%  113M 0s
 10600K .......... .......... .......... .......... .......... 50%  112M 0s
 10650K .......... .......... .......... .......... .......... 50% 94.5M 0s
 10700K .......... .......... .......... .......... .......... 50% 43.8M 0s
 10750K .......... .......... .......... .......... .......... 50% 98.0M 0s
 10800K .......... .......... .......... .......... .......... 51%  113M 0s
 10850K .......... .......... .......... .......... .......... 51%  111M 0s
 10900K .......... .......... .......... .......... .......... 51%  112M 0s
 10950K .......... .......... .......... .......... .......... 51%  110M 0s
 11000K .......... .......... .......... .......... .......... 52%  104M 0s
 11050K .......... .......... .......... .......... .......... 52%  113M 0s
 11100K .......... .......... .......... .......... .......... 52%  115M 0s
 11150K .......... .......... .......... .......... .......... 52%  108M 0s
 11200K .......... .......... .......... .......... .......... 52%  107M 0s
 11250K .......... .......... .......... .......... .......... 53%  113M 0s
 11300K .......... .......... .......... .......... .......... 53% 62.1M 0s
 11350K .......... .......... .......... .......... .......... 53% 37.4M 0s
 11400K .......... .......... .......... .......... .......... 53%  117M 0s
 11450K .......... .......... .......... .......... .......... 54% 99.5M 0s
 11500K .......... .......... .......... .......... .......... 54%  113M 0s
 11550K .......... .......... .......... .......... .......... 54%  116M 0s
 11600K .......... .......... .......... .......... .......... 54%  113M 0s
 11650K .......... .......... .......... .......... .......... 55%  101M 0s
 11700K .......... .......... .......... .......... .......... 55%  113M 0s
 11750K .......... .......... .......... .......... .......... 55%  108M 0s
 11800K .......... .......... .......... .......... .......... 55%  106M 0s
 11850K .......... .......... .......... .......... .......... 56%  101M 0s
 11900K .......... .......... .......... .......... .......... 56% 60.7M 0s
 11950K .......... .......... .......... .......... .......... 56% 35.7M 0s
 12000K .......... .......... .......... .......... .......... 56% 99.7M 0s
 12050K .......... .......... .......... .......... .......... 56%  112M 0s
 12100K .......... .......... .......... .......... .......... 57%  119M 0s
 12150K .......... .......... .......... .......... .......... 57% 73.5M 0s
 12200K .......... .......... .......... .......... .......... 57%  113M 0s
 12250K .......... .......... .......... .......... .......... 57%  109M 0s
 12300K .......... .......... .......... .......... .......... 58% 99.4M 0s
 12350K .......... .......... .......... .......... .......... 58% 98.1M 0s
 12400K .......... .......... .......... .......... .......... 58%  106M 0s
 12450K .......... .......... .......... .......... .......... 58%  104M 0s
 12500K .......... .......... .......... .......... .......... 59% 82.8M 0s
 12550K .......... .......... .......... .......... .......... 59%  112M 0s
 12600K .......... .......... .......... .......... .......... 59% 90.3M 0s
 12650K .......... .......... .......... .......... .......... 59%  117M 0s
 12700K .......... .......... .......... .......... .......... 60%  113M 0s
 12750K .......... .......... .......... .......... .......... 60% 54.1M 0s
 12800K .......... .......... .......... .......... .......... 60%  113M 0s
 12850K .......... .......... .......... .......... .......... 60%  106M 0s
 12900K .......... .......... .......... .......... .......... 60%  114M 0s
 12950K .......... .......... .......... .......... .......... 61%  112M 0s
 13000K .......... .......... .......... .......... .......... 61% 99.0M 0s
 13050K .......... .......... .......... .......... .......... 61%  123M 0s
 13100K .......... .......... .......... .......... .......... 61%  113M 0s
 13150K .......... .......... .......... .......... .......... 62%  105M 0s
 13200K .......... .......... .......... .......... .......... 62%  111M 0s
 13250K .......... .......... .......... .......... .......... 62% 95.1M 0s
 13300K .......... .......... .......... .......... .......... 62%  113M 0s
 13350K .......... .......... .......... .......... .......... 63% 96.3M 0s
 13400K .......... .......... .......... .......... .......... 63%  102M 0s
 13450K .......... .......... .......... .......... .......... 63%  104M 0s
 13500K .......... .......... .......... .......... .......... 63%  108M 0s
 13550K .......... .......... .......... .......... .......... 64% 99.9M 0s
 13600K .......... .......... .......... .......... .......... 64%  114M 0s
 13650K .......... .......... .......... .......... .......... 64%  113M 0s
 13700K .......... .......... .......... .......... .......... 64%  103M 0s
 13750K .......... .......... .......... .......... .......... 64%  112M 0s
 13800K .......... .......... .......... .......... .......... 65%  106M 0s
 13850K .......... .......... .......... .......... .......... 65%  117M 0s
 13900K .......... .......... .......... .......... .......... 65%  103M 0s
 13950K .......... .......... .......... .......... .......... 65%  112M 0s
 14000K .......... .......... .......... .......... .......... 66%  118M 0s
 14050K .......... .......... .......... .......... .......... 66% 99.4M 0s
 14100K .......... .......... .......... .......... .......... 66%  106M 0s
 14150K .......... .......... .......... .......... .......... 66%  106M 0s
 14200K .......... .......... .......... .......... .......... 67%  108M 0s
 14250K .......... .......... .......... .......... .......... 67%  106M 0s
 14300K .......... .......... .......... .......... .......... 67%  117M 0s
 14350K .......... .......... .......... .......... .......... 67%  115M 0s
 14400K .......... .......... .......... .......... .......... 68%  103M 0s
 14450K .......... .......... .......... .......... .......... 68%  108M 0s
 14500K .......... .......... .......... .......... .......... 68%  108M 0s
 14550K .......... .......... .......... .......... .......... 68%  114M 0s
 14600K .......... .......... .......... .......... .......... 68%  105M 0s
 14650K .......... .......... .......... .......... .......... 69% 94.3M 0s
 14700K .......... .......... .......... .......... .......... 69%  128M 0s
 14750K .......... .......... .......... .......... .......... 69%  107M 0s
 14800K .......... .......... .......... .......... .......... 69% 97.7M 0s
 14850K .......... .......... .......... .......... .......... 70%  105M 0s
 14900K .......... .......... .......... .......... .......... 70%  121M 0s
 14950K .......... .......... .......... .......... .......... 70% 85.9M 0s
 15000K .......... .......... .......... .......... .......... 70%  115M 0s
 15050K .......... .......... .......... .......... .......... 71%  112M 0s
 15100K .......... .......... .......... .......... .......... 71%  106M 0s
 15150K .......... .......... .......... .......... .......... 71%  111M 0s
 15200K .......... .......... .......... .......... .......... 71%  112M 0s
 15250K .......... .......... .......... .......... .......... 72% 99.7M 0s
 15300K .......... .......... .......... .......... .......... 72%  112M 0s
 15350K .......... .......... .......... .......... .......... 72%  112M 0s
 15400K .......... .......... .......... .......... .......... 72%  112M 0s
 15450K .......... .......... .......... .......... .......... 72%  113M 0s
 15500K .......... .......... .......... .......... .......... 73%  112M 0s
 15550K .......... .......... .......... .......... .......... 73%  112M 0s
 15600K .......... .......... .......... .......... .......... 73%  111M 0s
 15650K .......... .......... .......... .......... .......... 73%  100M 0s
 15700K .......... .......... .......... .......... .......... 74%  113M 0s
 15750K .......... .......... .......... .......... .......... 74%  112M 0s
 15800K .......... .......... .......... .......... .......... 74%  112M 0s
 15850K .......... .......... .......... .......... .......... 74%  111M 0s
 15900K .......... .......... .......... .......... .......... 75%  112M 0s
 15950K .......... .......... .......... .......... .......... 75%  106M 0s
 16000K .......... .......... .......... .......... .......... 75%  100M 0s
 16050K .......... .......... .......... .......... .......... 75% 94.5M 0s
 16100K .......... .......... .......... .......... .......... 76%  111M 0s
 16150K .......... .......... .......... .......... .......... 76%  112M 0s
 16200K .......... .......... .......... .......... .......... 76%  108M 0s
 16250K .......... .......... .......... .......... .......... 76%  107M 0s
 16300K .......... .......... .......... .......... .......... 77%  104M 0s
 16350K .......... .......... .......... .......... .......... 77%  110M 0s
 16400K .......... .......... .......... .......... .......... 77%  115M 0s
 16450K .......... .......... .......... .......... .......... 77%  105M 0s
 16500K .......... .......... .......... .......... .......... 77%  105M 0s
 16550K .......... .......... .......... .......... .......... 78%  115M 0s
 16600K .......... .......... .......... .......... .......... 78%  105M 0s
 16650K .......... .......... .......... .......... .......... 78%  112M 0s
 16700K .......... .......... .......... .......... .......... 78%  108M 0s
 16750K .......... .......... .......... .......... .......... 79%  109M 0s
 16800K .......... .......... .......... .......... .......... 79%  111M 0s
 16850K .......... .......... .......... .......... .......... 79%  105M 0s
 16900K .......... .......... .......... .......... .......... 79%  108M 0s
 16950K .......... .......... .......... .......... .......... 80% 97.8M 0s
 17000K .......... .......... .......... .......... .......... 80%  117M 0s
 17050K .......... .......... .......... .......... .......... 80%  109M 0s
 17100K .......... .......... .......... .......... .......... 80%  113M 0s
 17150K .......... .......... .......... .......... .......... 81%  106M 0s
 17200K .......... .......... .......... .......... .......... 81%  112M 0s
 17250K .......... .......... .......... .......... .......... 81%  111M 0s
 17300K .......... .......... .......... .......... .......... 81%  113M 0s
 17350K .......... .......... .......... .......... .......... 81%  105M 0s
 17400K .......... .......... .......... .......... .......... 82%  113M 0s
 17450K .......... .......... .......... .......... .......... 82%  113M 0s
 17500K .......... .......... .......... .......... .......... 82%  109M 0s
 17550K .......... .......... .......... .......... .......... 82%  107M 0s
 17600K .......... .......... .......... .......... .......... 83%  101M 0s
 17650K .......... .......... .......... .......... .......... 83%  109M 0s
 17700K .......... .......... .......... .......... .......... 83%  114M 0s
 17750K .......... .......... .......... .......... .......... 83%  112M 0s
 17800K .......... .......... .......... .......... .......... 84%  110M 0s
 17850K .......... .......... .......... .......... .......... 84%  112M 0s
 17900K .......... .......... .......... .......... .......... 84%  112M 0s
 17950K .......... .......... .......... .......... .......... 84%  105M 0s
 18000K .......... .......... .......... .......... .......... 85%  109M 0s
 18050K .......... .......... .......... .......... .......... 85%  111M 0s
 18100K .......... .......... .......... .......... .......... 85%  112M 0s
 18150K .......... .......... .......... .......... .......... 85%  105M 0s
 18200K .......... .......... .......... .......... .......... 85%  111M 0s
 18250K .......... .......... .......... .......... .......... 86%  102M 0s
 18300K .......... .......... .......... .......... .......... 86%  105M 0s
 18350K .......... .......... .......... .......... .......... 86%  112M 0s
 18400K .......... .......... .......... .......... .......... 86%  108M 0s
 18450K .......... .......... .......... .......... .......... 87%  113M 0s
 18500K .......... .......... .......... .......... .......... 87%  113M 0s
 18550K .......... .......... .......... .......... .......... 87%  100M 0s
 18600K .......... .......... .......... .......... .......... 87%  114M 0s
 18650K .......... .......... .......... .......... .......... 88%  107M 0s
 18700K .......... .......... .......... .......... .......... 88%  119M 0s
 18750K .......... .......... .......... .......... .......... 88%  112M 0s
 18800K .......... .......... .......... .......... .......... 88%  109M 0s
 18850K .......... .......... .......... .......... .......... 89%  109M 0s
 18900K .......... .......... .......... .......... .......... 89%  110M 0s
 18950K .......... .......... .......... .......... .......... 89%  113M 0s
 19000K .......... .......... .......... .......... .......... 89% 97.4M 0s
 19050K .......... .......... .......... .......... .......... 89%  108M 0s
 19100K .......... .......... .......... .......... .......... 90%  108M 0s
 19150K .......... .......... .......... .......... .......... 90%  111M 0s
 19200K .......... .......... .......... .......... .......... 90%  113M 0s
 19250K .......... .......... .......... .......... .......... 90%  108M 0s
 19300K .......... .......... .......... .......... .......... 91%  108M 0s
 19350K .......... .......... .......... .......... .......... 91%  112M 0s
 19400K .......... .......... .......... .......... .......... 91%  110M 0s
 19450K .......... .......... .......... .......... .......... 91%  103M 0s
 19500K .......... .......... .......... .......... .......... 92%  112M 0s
 19550K .......... .......... .......... .......... .......... 92%  106M 0s
 19600K .......... .......... .......... .......... .......... 92%  125M 0s
 19650K .......... .......... .......... .......... .......... 92%  110M 0s
 19700K .......... .......... .......... .......... .......... 93%  103M 0s
 19750K .......... .......... .......... .......... .......... 93%  111M 0s
 19800K .......... .......... .......... .......... .......... 93%  112M 0s
 19850K .......... .......... .......... .......... .......... 93%  100M 0s
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 21200K .......... .......... .......... ...                  100%  137M=0.2s

2019-11-15 21:59:27 (89.6 MB/s) - ‘phenotype_annotation.tab’ saved [21742685/21742685]

--2019-11-15 21:59:27--  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]
--2019-11-15 21:59:27--  https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo
Connecting to proxy.charite.de (proxy.charite.de)|141.42.5.215|:8080... connected.
Proxy request sent, awaiting response... 200 OK
Length: 6621678 (6.3M) [text/plain]
Saving to: ‘hp.obo’

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  6450K .......... ......                                     100% 52.7M=0.1s

Last-modified header missing -- time-stamps turned off.
2019-11-15 21:59:27 (53.4 MB/s) - ‘hp.obo’ saved [6621678/6621678]

FINISHED --2019-11-15 21:59:27--
Total wall clock time: 6.7s
Downloaded: 5 files, 46M in 1.5s (30.0 MB/s)
java -Xmx1G -jar jar/createGene2Phenotype.jar --data "data" --out-folder "."
User defined parameters set to:
hpo path: /var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation/data/hp.obo (exists: true)
out path: /var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation/. (exists: true)
 data path: /var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation/data (exists: true)
parse: /var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation/data/hp.obo
Nov 15, 2019 9:59:28 PM ontologizer.ontology.OBOParser doParse
INFO: Got 14586 terms and 18416 relations in 296 ms
Details of parsed obo file:
  data-version:		hp/releases/2019-11-08
  format:		1.2
  term definitions:	14586
Nov 15, 2019 9:59:28 PM ontologizer.ontology.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
Nov 15, 2019 9:59:28 PM ontologizer.ontology.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118)
  parsing annotation file...  ... done (took 1 s)
   WARN: Frequency of 4496 terms was zero. We set IC of these to : 9.353141170607854 = -1 * (log(1 / 11535)
mims:11576 with inh: 7592
parse NCBI
summary of gene_info-file
  other: 852
  tRNA: 599
  rRNA: 59
  scRNA: 4
  biological-region: 4143
  protein-coding: 19990
  ncRNA: 17267
  pseudo: 16492
  snRNA: 71
  snoRNA: 541
  unknown: 1377
entrez2symbol size: 43526
there were 2 unidentified gene-IDs: [107305681, 2439]
diseaseid-to-entrezid: 5424
ORPHANETPARSING: orphadisease2HGNCgenes:3789
ORPHANETPARSING: hgncid2entrez:27978
there were 31 unmappable HGNC-IDs: [3082, 14252, 37475, 21340, 3101, 33472, 30161, 22993, 34382, 22433, 35416, 31376, 32780, 39436, 32944, 17204, 3777, 12599, 26071, 20684, 14260, 33240, 43726, 25855, 8141, 43724, 32314, 33445, 16706, 33485, 13730]
diseaseId2entry.size(): 11576
 omim: 7758
 orphanet: 3771
 others: 47
Disease entries with at least one known disease gene: 7209
Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 11535
parse NCBI
summary of gene_info-file
  other: 852
  tRNA: 599
  rRNA: 59
  scRNA: 4
  biological-region: 4143
  protein-coding: 19990
  ncRNA: 17267
  pseudo: 16492
  snRNA: 71
  snoRNA: 541
  unknown: 1377
entrez2symbol size: 43526
there were 2 unidentified gene-IDs: [107305681, 2439]
diseaseid-to-entrezid: 5424
ORPHANETPARSING: orphadisease2HGNCgenes:3789
ORPHANETPARSING: hgncid2entrez:27978
there were 31 unmappable HGNC-IDs: [3082, 14252, 37475, 21340, 3101, 33472, 30161, 22993, 34382, 22433, 35416, 31376, 32780, 39436, 32944, 17204, 3777, 12599, 26071, 20684, 14260, 33240, 43726, 25855, 8141, 43724, 32314, 33445, 16706, 33485, 13730]
diseaseId2entry.size(): 11576
 omim: 7758
 orphanet: 3771
 others: 47
Disease entries with at least one known disease gene: 7209
Disease entries with at least 1 HPO term(s) (from phenotypic abn.): 11535
generating files for source-filter: OMIM and frequency-filter: FREQUENT_FEATURES
debug disease = AnnotatedItem [itemId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0]
annotations did not contain debug disease
generating files for source-filter: OMIM and frequency-filter: ALL_FREQUENCIES
debug disease = AnnotatedItem [itemId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0]
annotations did not contain debug disease
generating files for source-filter: ORPHA and frequency-filter: FREQUENT_FEATURES
annotation: Sensorineural hearing impairment (HP:0000407) orphadata 1.0
filters: true/true
annotation: Conjunctivitis (HP:0000509) orphadata 1.0
filters: true/true
annotation: Hyperhidrosis (HP:0000975) orphadata 1.0
filters: true/true
annotation: Pruritus (HP:0000989) orphadata 1.0
filters: true/true
annotation: Urticaria (HP:0001025) orphadata 1.0
filters: true/true
annotation: Arthritis (HP:0001369) orphadata 1.0
filters: true/true
annotation: Dehydration (HP:0001944) orphadata 1.0
filters: true/true
annotation: Fever (HP:0001945) orphadata 1.0
filters: true/true
annotation: Polydipsia (HP:0001959) orphadata 1.0
filters: true/true
annotation: Nausea and vomiting (HP:0002017) orphadata 1.0
filters: true/true
annotation: Abdominal pain (HP:0002027) orphadata 1.0
filters: true/true
annotation: Headache (HP:0002315) orphadata 1.0
filters: true/true
annotation: Arthralgia (HP:0002829) orphadata 1.0
filters: true/true
annotation: Myalgia (HP:0003326) orphadata 1.0
filters: true/true
annotation: Erythema (HP:0010783) orphadata 1.0
filters: true/true
annotation: Fatigue (HP:0012378) orphadata 1.0
filters: true/true
annotation: Dysesthesia (HP:0012534) orphadata 1.0
filters: true/true
debug disease = AnnotatedItem [itemId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0]
annotations did not contain debug disease
generating files for source-filter: ORPHA and frequency-filter: ALL_FREQUENCIES
annotation: Sensorineural hearing impairment (HP:0000407) orphadata 1.0
filters: true/true
annotation: Conjunctivitis (HP:0000509) orphadata 1.0
filters: true/true
annotation: Hyperhidrosis (HP:0000975) orphadata 1.0
filters: true/true
annotation: Pruritus (HP:0000989) orphadata 1.0
filters: true/true
annotation: Urticaria (HP:0001025) orphadata 1.0
filters: true/true
annotation: Arthritis (HP:0001369) orphadata 1.0
filters: true/true
annotation: Dehydration (HP:0001944) orphadata 1.0
filters: true/true
annotation: Fever (HP:0001945) orphadata 1.0
filters: true/true
annotation: Polydipsia (HP:0001959) orphadata 1.0
filters: true/true
annotation: Nausea and vomiting (HP:0002017) orphadata 1.0
filters: true/true
annotation: Abdominal pain (HP:0002027) orphadata 1.0
filters: true/true
annotation: Headache (HP:0002315) orphadata 1.0
filters: true/true
annotation: Arthralgia (HP:0002829) orphadata 1.0
filters: true/true
annotation: Myalgia (HP:0003326) orphadata 1.0
filters: true/true
annotation: Erythema (HP:0010783) orphadata 1.0
filters: true/true
annotation: Fatigue (HP:0012378) orphadata 1.0
filters: true/true
annotation: Dysesthesia (HP:0012534) orphadata 1.0
filters: true/true
debug disease = AnnotatedItem [itemId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0]
annotations did not contain debug disease
generating files for source-filter: ALL_SOURCES and frequency-filter: FREQUENT_FEATURES
annotation: Sensorineural hearing impairment (HP:0000407) orphadata 1.0
filters: true/true
annotation: Conjunctivitis (HP:0000509) orphadata 1.0
filters: true/true
annotation: Hyperhidrosis (HP:0000975) orphadata 1.0
filters: true/true
annotation: Pruritus (HP:0000989) orphadata 1.0
filters: true/true
annotation: Urticaria (HP:0001025) orphadata 1.0
filters: true/true
annotation: Arthritis (HP:0001369) orphadata 1.0
filters: true/true
annotation: Dehydration (HP:0001944) orphadata 1.0
filters: true/true
annotation: Fever (HP:0001945) orphadata 1.0
filters: true/true
annotation: Polydipsia (HP:0001959) orphadata 1.0
filters: true/true
annotation: Nausea and vomiting (HP:0002017) orphadata 1.0
filters: true/true
annotation: Abdominal pain (HP:0002027) orphadata 1.0
filters: true/true
annotation: Headache (HP:0002315) orphadata 1.0
filters: true/true
annotation: Arthralgia (HP:0002829) orphadata 1.0
filters: true/true
annotation: Myalgia (HP:0003326) orphadata 1.0
filters: true/true
annotation: Erythema (HP:0010783) orphadata 1.0
filters: true/true
annotation: Fatigue (HP:0012378) orphadata 1.0
filters: true/true
annotation: Dysesthesia (HP:0012534) orphadata 1.0
filters: true/true
debug disease = AnnotatedItem [itemId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0]
annotations did not contain debug disease
generating files for source-filter: ALL_SOURCES and frequency-filter: ALL_FREQUENCIES
annotation: Sensorineural hearing impairment (HP:0000407) orphadata 1.0
filters: true/true
annotation: Conjunctivitis (HP:0000509) orphadata 1.0
filters: true/true
annotation: Hyperhidrosis (HP:0000975) orphadata 1.0
filters: true/true
annotation: Pruritus (HP:0000989) orphadata 1.0
filters: true/true
annotation: Urticaria (HP:0001025) orphadata 1.0
filters: true/true
annotation: Arthritis (HP:0001369) orphadata 1.0
filters: true/true
annotation: Dehydration (HP:0001944) orphadata 1.0
filters: true/true
annotation: Fever (HP:0001945) orphadata 1.0
filters: true/true
annotation: Polydipsia (HP:0001959) orphadata 1.0
filters: true/true
annotation: Nausea and vomiting (HP:0002017) orphadata 1.0
filters: true/true
annotation: Abdominal pain (HP:0002027) orphadata 1.0
filters: true/true
annotation: Headache (HP:0002315) orphadata 1.0
filters: true/true
annotation: Arthralgia (HP:0002829) orphadata 1.0
filters: true/true
annotation: Myalgia (HP:0003326) orphadata 1.0
filters: true/true
annotation: Erythema (HP:0010783) orphadata 1.0
filters: true/true
annotation: Fatigue (HP:0012378) orphadata 1.0
filters: true/true
annotation: Dysesthesia (HP:0012534) orphadata 1.0
filters: true/true
debug disease = AnnotatedItem [itemId=ORPHA:1326, name=Camptodactyly syndrome, Guadalajara type 2, positiveAnnotations=13, negativeAnnotations=0]
annotations did not contain debug disease
make: Leaving directory '/var/lib/jenkins/jobs/hpo.annotations.monthly/workspace/annotation'
Archiving artifacts
Finished: SUCCESS