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A         annotated/OMIM-617641.tab
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A         annotated/OMIM-617644.tab
A         annotated/OMIM-617654.tab
A         annotated/OMIM-617660.tab
A         annotated/OMIM-617661.tab
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A         annotated/OMIM-617664.tab
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A         annotated/OMIM-617666.tab
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A         annotated/OMIM-618107.tab
A         annotated/OMIM-618110.tab
A         annotated/OMIM-618115.tab
A         annotated/omit-list.txt
A         misc
A         misc/.gitignore
A         misc/cataract
A         misc/cataract/MIM-107250.tab
A         misc/cataract/MIM-115650.tab
A         misc/cataract/MIM-115665.tab
A         misc/cataract/MIM-116600.tab
A         misc/cataract/MIM-116800.tab
A         misc/cataract/MIM-123680.tab
A         misc/cataract/MIM-123730.tab
A         misc/cataract/MIM-154050.tab
A         misc/cataract/MIM-600897.tab
A         misc/cataract/MIM-601885.tab
A         misc/cataract/MIM-604307.tab
A         misc/cataract/MIM-607304.tab
A         misc/cataract/MIM-608810-AR.tab
A         misc/cataract/MIM-608810.tab
A         misc/cataract/MIM-610634.tab
A         misc/cataract/MIM-611597.tab
A         misc/excelfiles
A         misc/excelfiles/Analysis_Table.xls
A         misc/excelfiles/Analysis_Table_NEW_13-09-11.xls
A         misc/excelfiles/Analysis_novel_18-09-11.xls
A         misc/excelfiles/Prioritized DECIPHER_for_Annotation.xls
A         misc/excelfiles/Prioritized-Disease-List.xls
A         misc/excelfiles/candidates_alpha-3.xls
A         misc/helpscripts
A         misc/helpscripts/fixDate.pl
A         misc/makefile
A         misc_2018
A         misc_2018/.gitignore
A         misc_2018/makefile
A         obsoleted-entries
A         obsoleted-entries/OMIM-100640.tab
AU        obsoleted-entries/OMIM-100650.tab
A         obsoleted-entries/OMIM-100675.tab
A         obsoleted-entries/OMIM-109560.tab
A         obsoleted-entries/OMIM-134700.tab
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A         obsoleted-entries/OMIM-146400.tab
A         obsoleted-entries/OMIM-151440.tab
A         obsoleted-entries/OMIM-151441.tab
A         obsoleted-entries/OMIM-176960.tab
A         obsoleted-entries/OMIM-180070.tab
A         obsoleted-entries/OMIM-181515.tab
A         obsoleted-entries/OMIM-189980.tab
A         obsoleted-entries/OMIM-189990.tab
A         obsoleted-entries/OMIM-191540.tab
A         obsoleted-entries/OMIM-216411.tab
A         obsoleted-entries/OMIM-233500.tab
A         obsoleted-entries/OMIM-271550.tab
A         obsoleted-entries/OMIM-277610.tab
A         obsoleted-entries/OMIM-277970.tab
A         obsoleted-entries/OMIM-300290.tab
A         obsoleted-entries/OMIM-300987.tab
A         obsoleted-entries/OMIM-302300.tab
A         obsoleted-entries/OMIM-306500.tab
A         obsoleted-entries/OMIM-307300.tab
A         obsoleted-entries/OMIM-308930.tab
A         obsoleted-entries/OMIM-311280.tab
A         obsoleted-entries/OMIM-312100.tab
A         obsoleted-entries/OMIM-312530.tab
A         obsoleted-entries/OMIM-312860.tab
A         obsoleted-entries/OMIM-315000.tab
A         obsoleted-entries/OMIM-605685.tab
A         obsoleted-entries/OMIM-608591.tab
A         obsoleted-entries/OMIM-608664.tab
A         obsoleted-entries/OMIM-608967.tab
A         obsoleted-entries/OMIM-610380.tab
A         obsoleted-entries/OMIM-612934.tab
A         obsoleted-entries/OMIM-614253.tab
A         obsoleted-entries/OMIM-615057.tab
A         obsoleted-entries/OMIM-616233.tab
At revision 5340
[workspace] $ /bin/sh -xe /tmp/jenkins3636227174232602858.sh
+ make -C misc_2018
make: Entering directory '/var/lib/jenkins/jobs/hpo.annotations.2018/workspace/misc_2018'
mkdir -p data
# load orphanet data
wget -N -P data http://www.orphadata.org/data/xml/en_product4_HPO.xml
--2018-10-09 09:55:02--  http://www.orphadata.org/data/xml/en_product4_HPO.xml
Resolving proxy.charite.de (proxy.charite.de)... 141.42.1.215
Connecting to proxy.charite.de (proxy.charite.de)|141.42.1.215|:8080... connected.
Proxy request sent, awaiting response... 200 OK
Length: 28542549 (27M) [text/xml]
Saving to: ‘data/en_product4_HPO.xml’

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  6650K .......... .......... .......... .......... .......... 24% 64.9M 2s
  6700K .......... .......... .......... .......... .......... 24% 21.7M 2s
  6750K .......... .......... .......... .......... .......... 24% 49.2M 2s
  6800K .......... .......... .......... .......... .......... 24% 16.9M 2s
  6850K .......... .......... .......... .......... .......... 24% 69.0M 2s
  6900K .......... .......... .......... .......... .......... 24% 44.1M 2s
  6950K .......... .......... .......... .......... .......... 25% 54.4M 2s
  7000K .......... .......... .......... .......... .......... 25%  118M 2s
  7050K .......... .......... .......... .......... .......... 25% 60.0M 2s
  7100K .......... .......... .......... .......... .......... 25% 86.9M 2s
  7150K .......... .......... .......... .......... .......... 25% 30.5M 2s
  7200K .......... .......... .......... .......... .......... 26% 61.6M 2s
  7250K .......... .......... .......... .......... .......... 26% 75.3M 2s
  7300K .......... .......... .......... .......... .......... 26%  106M 2s
  7350K .......... .......... .......... .......... .......... 26%  116M 2s
  7400K .......... .......... .......... .......... .......... 26% 82.1M 2s
  7450K .......... .......... .......... .......... .......... 26%  113M 2s
  7500K .......... .......... .......... .......... .......... 27% 3.01M 2s
  7550K .......... .......... .......... .......... .......... 27% 16.3M 2s
  7600K .......... .......... .......... .......... .......... 27% 18.2M 2s
  7650K .......... .......... .......... .......... .......... 27% 21.8M 2s
  7700K .......... .......... .......... .......... .......... 27% 44.1M 2s
  7750K .......... .......... .......... .......... .......... 27% 97.9M 2s
  7800K .......... .......... .......... .......... .......... 28% 60.3M 2s
  7850K .......... .......... .......... .......... .......... 28% 85.3M 2s
  7900K .......... .......... .......... .......... .......... 28% 6.70M 2s
  7950K .......... .......... .......... .......... .......... 28% 55.6M 2s
  8000K .......... .......... .......... .......... .......... 28% 24.3M 2s
  8050K .......... .......... .......... .......... .......... 29% 98.1M 2s
  8100K .......... .......... .......... .......... .......... 29% 66.1M 2s
  8150K .......... .......... .......... .......... .......... 29% 81.7M 2s
  8200K .......... .......... .......... .......... .......... 29% 52.6M 2s
  8250K .......... .......... .......... .......... .......... 29% 88.0M 2s
  8300K .......... .......... .......... .......... .......... 29% 73.1M 2s
  8350K .......... .......... .......... .......... .......... 30% 84.5M 2s
  8400K .......... .......... .......... .......... .......... 30% 66.8M 2s
  8450K .......... .......... .......... .......... .......... 30% 95.6M 2s
  8500K .......... .......... .......... .......... .......... 30% 20.4M 2s
  8550K .......... .......... .......... .......... .......... 30% 25.6M 2s
  8600K .......... .......... .......... .......... .......... 31% 39.0M 2s
  8650K .......... .......... .......... .......... .......... 31% 93.7M 2s
  8700K .......... .......... .......... .......... .......... 31% 47.9M 2s
  8750K .......... .......... .......... .......... .......... 31% 87.0M 2s
  8800K .......... .......... .......... .......... .......... 31% 35.3M 2s
  8850K .......... .......... .......... .......... .......... 31% 9.48M 2s
  8900K .......... .......... .......... .......... .......... 32% 43.6M 2s
  8950K .......... .......... .......... .......... .......... 32% 88.9M 2s
  9000K .......... .......... .......... .......... .......... 32% 77.0M 2s
  9050K .......... .......... .......... .......... .......... 32% 58.5M 2s
  9100K .......... .......... .......... .......... .......... 32% 94.4M 2s
  9150K .......... .......... .......... .......... .......... 33% 62.1M 2s
  9200K .......... .......... .......... .......... .......... 33% 17.0M 2s
  9250K .......... .......... .......... .......... .......... 33% 94.8M 2s
  9300K .......... .......... .......... .......... .......... 33% 57.0M 2s
  9350K .......... .......... .......... .......... .......... 33% 72.8M 2s
  9400K .......... .......... .......... .......... .......... 33% 69.3M 2s
  9450K .......... .......... .......... .......... .......... 34% 44.1M 2s
  9500K .......... .......... .......... .......... .......... 34% 80.9M 2s
  9550K .......... .......... .......... .......... .......... 34% 80.8M 2s
  9600K .......... .......... .......... .......... .......... 34%  103M 2s
  9650K .......... .......... .......... .......... .......... 34% 77.6M 2s
  9700K .......... .......... .......... .......... .......... 34%  112M 2s
  9750K .......... .......... .......... .......... .......... 35% 7.88M 2s
  9800K .......... .......... .......... .......... .......... 35% 38.1M 2s
  9850K .......... .......... .......... .......... .......... 35% 44.3M 2s
  9900K .......... .......... .......... .......... .......... 35% 37.7M 2s
  9950K .......... .......... .......... .......... .......... 35% 71.5M 2s
 10000K .......... .......... .......... .......... .......... 36% 51.3M 2s
 10050K .......... .......... .......... .......... .......... 36% 78.3M 2s
 10100K .......... .......... .......... .......... .......... 36% 8.83M 2s
 10150K .......... .......... .......... .......... .......... 36% 34.9M 2s
 10200K .......... .......... .......... .......... .......... 36% 56.8M 2s
 10250K .......... .......... .......... .......... .......... 36% 50.3M 2s
 10300K .......... .......... .......... .......... .......... 37% 51.1M 1s
 10350K .......... .......... .......... .......... .......... 37% 27.2M 1s
 10400K .......... .......... .......... .......... .......... 37% 23.8M 1s
 10450K .......... .......... .......... .......... .......... 37% 20.9M 1s
 10500K .......... .......... .......... .......... .......... 37% 26.3M 1s
 10550K .......... .......... .......... .......... .......... 38% 30.6M 1s
 10600K .......... .......... .......... .......... .......... 38% 60.5M 1s
 10650K .......... .......... .......... .......... .......... 38% 59.9M 1s
 10700K .......... .......... .......... .......... .......... 38% 32.6M 1s
 10750K .......... .......... .......... .......... .......... 38% 39.7M 1s
 10800K .......... .......... .......... .......... .......... 38% 28.7M 1s
 10850K .......... .......... .......... .......... .......... 39% 75.5M 1s
 10900K .......... .......... .......... .......... .......... 39% 22.9M 1s
 10950K .......... .......... .......... .......... .......... 39%  105M 1s
 11000K .......... .......... .......... .......... .......... 39% 98.6M 1s
 11050K .......... .......... .......... .......... .......... 39% 39.9M 1s
 11100K .......... .......... .......... .......... .......... 40% 58.4M 1s
 11150K .......... .......... .......... .......... .......... 40% 71.3M 1s
 11200K .......... .......... .......... .......... .......... 40% 67.6M 1s
 11250K .......... .......... .......... .......... .......... 40% 99.4M 1s
 11300K .......... .......... .......... .......... .......... 40%  108M 1s
 11350K .......... .......... .......... .......... .......... 40% 80.9M 1s
 11400K .......... .......... .......... .......... .......... 41% 56.4M 1s
 11450K .......... .......... .......... .......... .......... 41% 73.3M 1s
 11500K .......... .......... .......... .......... .......... 41% 71.1M 1s
 11550K .......... .......... .......... .......... .......... 41% 40.7M 1s
 11600K .......... .......... .......... .......... .......... 41% 85.3M 1s
 11650K .......... .......... .......... .......... .......... 41% 93.0M 1s
 11700K .......... .......... .......... .......... .......... 42% 41.9M 1s
 11750K .......... .......... .......... .......... .......... 42% 53.4M 1s
 11800K .......... .......... .......... .......... .......... 42% 80.0M 1s
 11850K .......... .......... .......... .......... .......... 42% 83.0M 1s
 11900K .......... .......... .......... .......... .......... 42% 70.5M 1s
 11950K .......... .......... .......... .......... .......... 43% 74.1M 1s
 12000K .......... .......... .......... .......... .......... 43% 71.0M 1s
 12050K .......... .......... .......... .......... .......... 43% 52.6M 1s
 12100K .......... .......... .......... .......... .......... 43%  109M 1s
 12150K .......... .......... .......... .......... .......... 43% 82.0M 1s
 12200K .......... .......... .......... .......... .......... 43% 31.4M 1s
 12250K .......... .......... .......... .......... .......... 44% 97.7M 1s
 12300K .......... .......... .......... .......... .......... 44% 28.7M 1s
 12350K .......... .......... .......... .......... .......... 44% 70.2M 1s
 12400K .......... .......... .......... .......... .......... 44% 77.0M 1s
 12450K .......... .......... .......... .......... .......... 44%  120M 1s
 12500K .......... .......... .......... .......... .......... 45% 75.8M 1s
 12550K .......... .......... .......... .......... .......... 45% 93.7M 1s
 12600K .......... .......... .......... .......... .......... 45%  105M 1s
 12650K .......... .......... .......... .......... .......... 45% 78.2M 1s
 12700K .......... .......... .......... .......... .......... 45% 31.3M 1s
 12750K .......... .......... .......... .......... .......... 45% 24.7M 1s
 12800K .......... .......... .......... .......... .......... 46% 85.4M 1s
 12850K .......... .......... .......... .......... .......... 46% 98.8M 1s
 12900K .......... .......... .......... .......... .......... 46% 56.5M 1s
 12950K .......... .......... .......... .......... .......... 46%  110M 1s
 13000K .......... .......... .......... .......... .......... 46% 51.1M 1s
 13050K .......... .......... .......... .......... .......... 46% 43.8M 1s
 13100K .......... .......... .......... .......... .......... 47%  101M 1s
 13150K .......... .......... .......... .......... .......... 47% 44.6M 1s
 13200K .......... .......... .......... .......... .......... 47% 15.2M 1s
 13250K .......... .......... .......... .......... .......... 47% 60.0M 1s
 13300K .......... .......... .......... .......... .......... 47% 36.8M 1s
 13350K .......... .......... .......... .......... .......... 48% 77.6M 1s
 13400K .......... .......... .......... .......... .......... 48% 70.2M 1s
 13450K .......... .......... .......... .......... .......... 48% 68.1M 1s
 13500K .......... .......... .......... .......... .......... 48% 85.5M 1s
 13550K .......... .......... .......... .......... .......... 48% 82.5M 1s
 13600K .......... .......... .......... .......... .......... 48% 75.0M 1s
 13650K .......... .......... .......... .......... .......... 49% 83.8M 1s
 13700K .......... .......... .......... .......... .......... 49% 65.4M 1s
 13750K .......... .......... .......... .......... .......... 49% 31.9M 1s
 13800K .......... .......... .......... .......... .......... 49% 40.2M 1s
 13850K .......... .......... .......... .......... .......... 49% 32.7M 1s
 13900K .......... .......... .......... .......... .......... 50% 69.7M 1s
 13950K .......... .......... .......... .......... .......... 50% 83.4M 1s
 14000K .......... .......... .......... .......... .......... 50%  118M 1s
 14050K .......... .......... .......... .......... .......... 50% 52.6M 1s
 14100K .......... .......... .......... .......... .......... 50% 72.9M 1s
 14150K .......... .......... .......... .......... .......... 50% 88.6M 1s
 14200K .......... .......... .......... .......... .......... 51% 58.9M 1s
 14250K .......... .......... .......... .......... .......... 51%  101M 1s
 14300K .......... .......... .......... .......... .......... 51% 69.5M 1s
 14350K .......... .......... .......... .......... .......... 51% 42.6M 1s
 14400K .......... .......... .......... .......... .......... 51%  103M 1s
 14450K .......... .......... .......... .......... .......... 52%  106M 1s
 14500K .......... .......... .......... .......... .......... 52% 14.6M 1s
 14550K .......... .......... .......... .......... .......... 52% 32.6M 1s
 14600K .......... .......... .......... .......... .......... 52% 55.4M 1s
 14650K .......... .......... .......... .......... .......... 52% 66.1M 1s
 14700K .......... .......... .......... .......... .......... 52% 43.7M 1s
 14750K .......... .......... .......... .......... .......... 53% 56.5M 1s
 14800K .......... .......... .......... .......... .......... 53% 38.8M 1s
 14850K .......... .......... .......... .......... .......... 53% 29.7M 1s
 14900K .......... .......... .......... .......... .......... 53% 61.6M 1s
 14950K .......... .......... .......... .......... .......... 53%  117M 1s
 15000K .......... .......... .......... .......... .......... 53% 87.5M 1s
 15050K .......... .......... .......... .......... .......... 54%  103M 1s
 15100K .......... .......... .......... .......... .......... 54% 42.3M 1s
 15150K .......... .......... .......... .......... .......... 54% 68.7M 1s
 15200K .......... .......... .......... .......... .......... 54% 97.3M 1s
 15250K .......... .......... .......... .......... .......... 54% 78.0M 1s
 15300K .......... .......... .......... .......... .......... 55% 60.6M 1s
 15350K .......... .......... .......... .......... .......... 55% 89.0M 1s
 15400K .......... .......... .......... .......... .......... 55% 56.2M 1s
 15450K .......... .......... .......... .......... .......... 55% 31.4M 1s
 15500K .......... .......... .......... .......... .......... 55% 52.4M 1s
 15550K .......... .......... .......... .......... .......... 55% 70.3M 1s
 15600K .......... .......... .......... .......... .......... 56% 48.2M 1s
 15650K .......... .......... .......... .......... .......... 56% 61.8M 1s
 15700K .......... .......... .......... .......... .......... 56% 70.2M 1s
 15750K .......... .......... .......... .......... .......... 56% 79.6M 1s
 15800K .......... .......... .......... .......... .......... 56%  128M 1s
 15850K .......... .......... .......... .......... .......... 57% 95.7M 1s
 15900K .......... .......... .......... .......... .......... 57% 48.8M 1s
 15950K .......... .......... .......... .......... .......... 57%  107M 1s
 16000K .......... .......... .......... .......... .......... 57% 94.6M 1s
 16050K .......... .......... .......... .......... .......... 57%  107M 1s
 16100K .......... .......... .......... .......... .......... 57% 59.7M 1s
 16150K .......... .......... .......... .......... .......... 58% 83.9M 1s
 16200K .......... .......... .......... .......... .......... 58% 62.4M 1s
 16250K .......... .......... .......... .......... .......... 58% 35.9M 1s
 16300K .......... .......... .......... .......... .......... 58% 97.4M 1s
 16350K .......... .......... .......... .......... .......... 58% 46.6M 1s
 16400K .......... .......... .......... .......... .......... 59% 48.3M 1s
 16450K .......... .......... .......... .......... .......... 59% 66.5M 1s
 16500K .......... .......... .......... .......... .......... 59% 56.9M 1s
 16550K .......... .......... .......... .......... .......... 59% 78.3M 1s
 16600K .......... .......... .......... .......... .......... 59% 66.2M 1s
 16650K .......... .......... .......... .......... .......... 59% 88.5M 1s
 16700K .......... .......... .......... .......... .......... 60% 55.4M 1s
 16750K .......... .......... .......... .......... .......... 60% 68.3M 1s
 16800K .......... .......... .......... .......... .......... 60% 65.8M 1s
 16850K .......... .......... .......... .......... .......... 60% 86.9M 1s
 16900K .......... .......... .......... .......... .......... 60% 74.8M 1s
 16950K .......... .......... .......... .......... .......... 60% 90.1M 1s
 17000K .......... .......... .......... .......... .......... 61% 99.1M 1s
 17050K .......... .......... .......... .......... .......... 61% 78.9M 1s
 17100K .......... .......... .......... .......... .......... 61%  113M 1s
 17150K .......... .......... .......... .......... .......... 61% 97.7M 1s
 17200K .......... .......... .......... .......... .......... 61% 60.8M 1s
 17250K .......... .......... .......... .......... .......... 62% 86.1M 1s
 17300K .......... .......... .......... .......... .......... 62% 28.6M 1s
 17350K .......... .......... .......... .......... .......... 62% 56.1M 1s
 17400K .......... .......... .......... .......... .......... 62% 63.3M 1s
 17450K .......... .......... .......... .......... .......... 62% 86.6M 1s
 17500K .......... .......... .......... .......... .......... 62% 99.1M 1s
 17550K .......... .......... .......... .......... .......... 63% 52.7M 1s
 17600K .......... .......... .......... .......... .......... 63% 65.4M 1s
 17650K .......... .......... .......... .......... .......... 63% 88.0M 1s
 17700K .......... .......... .......... .......... .......... 63% 53.6M 1s
 17750K .......... .......... .......... .......... .......... 63% 88.7M 1s
 17800K .......... .......... .......... .......... .......... 64% 71.8M 1s
 17850K .......... .......... .......... .......... .......... 64% 82.5M 1s
 17900K .......... .......... .......... .......... .......... 64% 96.3M 1s
 17950K .......... .......... .......... .......... .......... 64%  105M 1s
 18000K .......... .......... .......... .......... .......... 64% 63.0M 1s
 18050K .......... .......... .......... .......... .......... 64% 98.9M 1s
 18100K .......... .......... .......... .......... .......... 65% 95.5M 1s
 18150K .......... .......... .......... .......... .......... 65% 79.1M 1s
 18200K .......... .......... .......... .......... .......... 65% 65.4M 1s
 18250K .......... .......... .......... .......... .......... 65% 65.7M 1s
 18300K .......... .......... .......... .......... .......... 65% 86.1M 1s
 18350K .......... .......... .......... .......... .......... 66% 97.2M 1s
 18400K .......... .......... .......... .......... .......... 66% 86.4M 1s
 18450K .......... .......... .......... .......... .......... 66% 77.7M 1s
 18500K .......... .......... .......... .......... .......... 66% 15.1M 1s
 18550K .......... .......... .......... .......... .......... 66% 23.2M 1s
 18600K .......... .......... .......... .......... .......... 66% 30.6M 1s
 18650K .......... .......... .......... .......... .......... 67% 39.1M 1s
 18700K .......... .......... .......... .......... .......... 67% 30.6M 1s
 18750K .......... .......... .......... .......... .......... 67% 39.3M 0s
 18800K .......... .......... .......... .......... .......... 67% 17.4M 0s
 18850K .......... .......... .......... .......... .......... 67% 87.6M 0s
 18900K .......... .......... .......... .......... .......... 67% 42.4M 0s
 18950K .......... .......... .......... .......... .......... 68% 62.3M 0s
 19000K .......... .......... .......... .......... .......... 68% 70.1M 0s
 19050K .......... .......... .......... .......... .......... 68% 75.6M 0s
 19100K .......... .......... .......... .......... .......... 68% 86.2M 0s
 19150K .......... .......... .......... .......... .......... 68% 60.7M 0s
 19200K .......... .......... .......... .......... .......... 69% 66.2M 0s
 19250K .......... .......... .......... .......... .......... 69% 98.0M 0s
 19300K .......... .......... .......... .......... .......... 69% 48.5M 0s
 19350K .......... .......... .......... .......... .......... 69%  109M 0s
 19400K .......... .......... .......... .......... .......... 69% 68.8M 0s
 19450K .......... .......... .......... .......... .......... 69% 61.0M 0s
 19500K .......... .......... .......... .......... .......... 70% 58.2M 0s
 19550K .......... .......... .......... .......... .......... 70% 68.7M 0s
 19600K .......... .......... .......... .......... .......... 70% 65.0M 0s
 19650K .......... .......... .......... .......... .......... 70%  102M 0s
 19700K .......... .......... .......... .......... .......... 70% 60.0M 0s
 19750K .......... .......... .......... .......... .......... 71%  101M 0s
 19800K .......... .......... .......... .......... .......... 71% 98.3M 0s
 19850K .......... .......... .......... .......... .......... 71% 70.6M 0s
 19900K .......... .......... .......... .......... .......... 71% 79.2M 0s
 19950K .......... .......... .......... .......... .......... 71% 86.0M 0s
 20000K .......... .......... .......... .......... .......... 71% 73.1M 0s
 20050K .......... .......... .......... .......... .......... 72%  113M 0s
 20100K .......... .......... .......... .......... .......... 72% 83.6M 0s
 20150K .......... .......... .......... .......... .......... 72% 79.1M 0s
 20200K .......... .......... .......... .......... .......... 72% 60.4M 0s
 20250K .......... .......... .......... .......... .......... 72% 63.7M 0s
 20300K .......... .......... .......... .......... .......... 73% 42.5M 0s
 20350K .......... .......... .......... .......... .......... 73% 44.9M 0s
 20400K .......... .......... .......... .......... .......... 73% 32.4M 0s
 20450K .......... .......... .......... .......... .......... 73% 73.0M 0s
 20500K .......... .......... .......... .......... .......... 73% 85.6M 0s
 20550K .......... .......... .......... .......... .......... 73% 86.0M 0s
 20600K .......... .......... .......... .......... .......... 74% 49.1M 0s
 20650K .......... .......... .......... .......... .......... 74% 46.0M 0s
 20700K .......... .......... .......... .......... .......... 74% 85.3M 0s
 20750K .......... .......... .......... .......... .......... 74% 71.0M 0s
 20800K .......... .......... .......... .......... .......... 74%  119M 0s
 20850K .......... .......... .......... .......... .......... 74% 72.5M 0s
 20900K .......... .......... .......... .......... .......... 75%  104M 0s
 20950K .......... .......... .......... .......... .......... 75% 89.6M 0s
 21000K .......... .......... .......... .......... .......... 75% 72.0M 0s
 21050K .......... .......... .......... .......... .......... 75% 88.7M 0s
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 27000K .......... .......... .......... .......... .......... 97% 70.9M 0s
 27050K .......... .......... .......... .......... .......... 97%  109M 0s
 27100K .......... .......... .......... .......... .......... 97%  103M 0s
 27150K .......... .......... .......... .......... .......... 97% 73.6M 0s
 27200K .......... .......... .......... .......... .......... 97% 95.6M 0s
 27250K .......... .......... .......... .......... .......... 97% 73.6M 0s
 27300K .......... .......... .......... .......... .......... 98%  111M 0s
 27350K .......... .......... .......... .......... .......... 98% 73.2M 0s
 27400K .......... .......... .......... .......... .......... 98% 97.9M 0s
 27450K .......... .......... .......... .......... .......... 98% 58.7M 0s
 27500K .......... .......... .......... .......... .......... 98%  111M 0s
 27550K .......... .......... .......... .......... .......... 99%  112M 0s
 27600K .......... .......... .......... .......... .......... 99% 62.1M 0s
 27650K .......... .......... .......... .......... .......... 99% 69.2M 0s
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 27800K .......... .......... .......... .......... .......... 99%  105M 0s
 27850K .......... .......... ...                             100% 29.7M=1.2s

2018-10-09 09:55:03 (23.2 MB/s) - ‘data/en_product4_HPO.xml’ saved [28542549/28542549]

# loads the HPO
wget -N -P data http://purl.obolibrary.org/obo/hp.obo
--2018-10-09 09:55:03--  http://purl.obolibrary.org/obo/hp.obo
Resolving proxy.charite.de (proxy.charite.de)... 141.42.1.215
Connecting to proxy.charite.de (proxy.charite.de)|141.42.1.215|:8080... connected.
Proxy request sent, awaiting response... 302 Found
Location: https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo [following]
--2018-10-09 09:55:04--  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: 6192170 (5.9M) [text/plain]
Saving to: ‘data/hp.obo’

     0K .......... .......... .......... .......... ..........  0% 1.49M 4s
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  3150K .......... .......... .......... .......... .......... 52% 10.1M 0s
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  4500K .......... .......... .......... .......... .......... 75% 14.7M 0s
  4550K .......... .......... .......... .......... .......... 76% 19.7M 0s
  4600K .......... .......... .......... .......... .......... 76% 32.3M 0s
  4650K .......... .......... .......... .......... .......... 77% 17.0M 0s
  4700K .......... .......... .......... .......... .......... 78% 21.2M 0s
  4750K .......... .......... .......... .......... .......... 79% 22.6M 0s
  4800K .......... .......... .......... .......... .......... 80% 13.7M 0s
  4850K .......... .......... .......... .......... .......... 81% 18.0M 0s
  4900K .......... .......... .......... .......... .......... 81% 21.8M 0s
  4950K .......... .......... .......... .......... .......... 82% 31.7M 0s
  5000K .......... .......... .......... .......... .......... 83% 26.9M 0s
  5050K .......... .......... .......... .......... .......... 84% 23.0M 0s
  5100K .......... .......... .......... .......... .......... 85% 13.8M 0s
  5150K .......... .......... .......... .......... .......... 85% 14.2M 0s
  5200K .......... .......... .......... .......... .......... 86% 50.4M 0s
  5250K .......... .......... .......... .......... .......... 87% 28.2M 0s
  5300K .......... .......... .......... .......... .......... 88% 20.4M 0s
  5350K .......... .......... .......... .......... .......... 89% 29.0M 0s
  5400K .......... .......... .......... .......... .......... 90% 14.8M 0s
  5450K .......... .......... .......... .......... .......... 90% 43.0M 0s
  5500K .......... .......... .......... .......... .......... 91% 13.2M 0s
  5550K .......... .......... .......... .......... .......... 92% 26.8M 0s
  5600K .......... .......... .......... .......... .......... 93% 28.0M 0s
  5650K .......... .......... .......... .......... .......... 94% 31.2M 0s
  5700K .......... .......... .......... .......... .......... 95% 34.6M 0s
  5750K .......... .......... .......... .......... .......... 95% 12.6M 0s
  5800K .......... .......... .......... .......... .......... 96% 33.5M 0s
  5850K .......... .......... .......... .......... .......... 97% 21.4M 0s
  5900K .......... .......... .......... .......... .......... 98% 17.2M 0s
  5950K .......... .......... .......... .......... .......... 99% 58.5M 0s
  6000K .......... .......... .......... .......... .......   100% 35.0M=0.5s

Last-modified header missing -- time-stamps turned off.
2018-10-09 09:55:04 (11.6 MB/s) - ‘data/hp.obo’ saved [6192170/6192170]

mkdir -p jar
wget -N -P jar https://github.com/monarch-initiative/hpoannotqc/releases/download/v1.2.2/HpoAnnotQc.jar
--2018-10-09 09:55:04--  https://github.com/monarch-initiative/hpoannotqc/releases/download/v1.2.2/HpoAnnotQc.jar
Resolving proxy.charite.de (proxy.charite.de)... 141.42.1.215
Connecting to proxy.charite.de (proxy.charite.de)|141.42.1.215|:8080... connected.
Proxy request sent, awaiting response... 302 Found
Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/120038140/fb1f44d6-8f3c-11e8-9f06-df962ed60c03?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20181009%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20181009T075537Z&X-Amz-Expires=300&X-Amz-Signature=88d2faf6e06e77a32f89a5e2967648ffbe7d7182806413ecd98e6cb81cf7d07e&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DHpoAnnotQc.jar&response-content-type=application%2Foctet-stream [following]
--2018-10-09 09:55:05--  https://github-production-release-asset-2e65be.s3.amazonaws.com/120038140/fb1f44d6-8f3c-11e8-9f06-df962ed60c03?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20181009%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20181009T075537Z&X-Amz-Expires=300&X-Amz-Signature=88d2faf6e06e77a32f89a5e2967648ffbe7d7182806413ecd98e6cb81cf7d07e&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DHpoAnnotQc.jar&response-content-type=application%2Foctet-stream
Connecting to proxy.charite.de (proxy.charite.de)|141.42.1.215|:8080... connected.
Proxy request sent, awaiting response... 200 OK
Length: 17653504 (17M) [application/octet-stream]
Saving to: ‘jar/HpoAnnotQc.jar’

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 13300K .......... .......... .......... .......... .......... 77% 99.1M 0s
 13350K .......... .......... .......... .......... .......... 77% 85.2M 0s
 13400K .......... .......... .......... .......... .......... 78% 83.3M 0s
 13450K .......... .......... .......... .......... .......... 78% 78.7M 0s
 13500K .......... .......... .......... .......... .......... 78%  105M 0s
 13550K .......... .......... .......... .......... .......... 78% 92.7M 0s
 13600K .......... .......... .......... .......... .......... 79% 78.4M 0s
 13650K .......... .......... .......... .......... .......... 79%  108M 0s
 13700K .......... .......... .......... .......... .......... 79% 74.2M 0s
 13750K .......... .......... .......... .......... .......... 80%  106M 0s
 13800K .......... .......... .......... .......... .......... 80% 72.9M 0s
 13850K .......... .......... .......... .......... .......... 80% 90.6M 0s
 13900K .......... .......... .......... .......... .......... 80% 67.5M 0s
 13950K .......... .......... .......... .......... .......... 81%  107M 0s
 14000K .......... .......... .......... .......... .......... 81% 76.5M 0s
 14050K .......... .......... .......... .......... .......... 81%  110M 0s
 14100K .......... .......... .......... .......... .......... 82% 69.8M 0s
 14150K .......... .......... .......... .......... .......... 82%  108M 0s
 14200K .......... .......... .......... .......... .......... 82% 77.8M 0s
 14250K .......... .......... .......... .......... .......... 82%  106M 0s
 14300K .......... .......... .......... .......... .......... 83% 86.3M 0s
 14350K .......... .......... .......... .......... .......... 83% 89.0M 0s
 14400K .......... .......... .......... .......... .......... 83% 78.4M 0s
 14450K .......... .......... .......... .......... .......... 84%  106M 0s
 14500K .......... .......... .......... .......... .......... 84% 76.0M 0s
 14550K .......... .......... .......... .......... .......... 84% 88.7M 0s
 14600K .......... .......... .......... .......... .......... 84% 79.9M 0s
 14650K .......... .......... .......... .......... .......... 85%  103M 0s
 14700K .......... .......... .......... .......... .......... 85%  114M 0s
 14750K .......... .......... .......... .......... .......... 85% 89.6M 0s
 14800K .......... .......... .......... .......... .......... 86% 98.5M 0s
 14850K .......... .......... .......... .......... .......... 86% 79.8M 0s
 14900K .......... .......... .......... .......... .......... 86%  117M 0s
 14950K .......... .......... .......... .......... .......... 87%  107M 0s
 15000K .......... .......... .......... .......... .......... 87% 70.8M 0s
 15050K .......... .......... .......... .......... .......... 87% 86.4M 0s
 15100K .......... .......... .......... .......... .......... 87%  102M 0s
 15150K .......... .......... .......... .......... .......... 88%  107M 0s
 15200K .......... .......... .......... .......... .......... 88% 72.1M 0s
 15250K .......... .......... .......... .......... .......... 88%  114M 0s
 15300K .......... .......... .......... .......... .......... 89%  113M 0s
 15350K .......... .......... .......... .......... .......... 89%  110M 0s
 15400K .......... .......... .......... .......... .......... 89% 74.4M 0s
 15450K .......... .......... .......... .......... .......... 89%  114M 0s
 15500K .......... .......... .......... .......... .......... 90% 74.8M 0s
 15550K .......... .......... .......... .......... .......... 90%  107M 0s
 15600K .......... .......... .......... .......... .......... 90%  105M 0s
 15650K .......... .......... .......... .......... .......... 91% 78.3M 0s
 15700K .......... .......... .......... .......... .......... 91% 91.9M 0s
 15750K .......... .......... .......... .......... .......... 91%  660K 0s
 15800K .......... .......... .......... .......... .......... 91% 80.6M 0s
 15850K .......... .......... .......... .......... .......... 92% 60.8M 0s
 15900K .......... .......... .......... .......... .......... 92% 52.8M 0s
 15950K .......... .......... .......... .......... .......... 92% 61.6M 0s
 16000K .......... .......... .......... .......... .......... 93% 67.4M 0s
 16050K .......... .......... .......... .......... .......... 93% 78.2M 0s
 16100K .......... .......... .......... .......... .......... 93% 37.4M 0s
 16150K .......... .......... .......... .......... .......... 93% 34.0M 0s
 16200K .......... .......... .......... .......... .......... 94% 82.5M 0s
 16250K .......... .......... .......... .......... .......... 94% 93.5M 0s
 16300K .......... .......... .......... .......... .......... 94% 66.9M 0s
 16350K .......... .......... .......... .......... .......... 95% 62.3M 0s
 16400K .......... .......... .......... .......... .......... 95% 87.9M 0s
 16450K .......... .......... .......... .......... .......... 95%  110M 0s
 16500K .......... .......... .......... .......... .......... 95% 33.5M 0s
 16550K .......... .......... .......... .......... .......... 96%  110M 0s
 16600K .......... .......... .......... .......... .......... 96% 25.0M 0s
 16650K .......... .......... .......... .......... .......... 96% 39.6M 0s
 16700K .......... .......... .......... .......... .......... 97%  112M 0s
 16750K .......... .......... .......... .......... .......... 97% 91.6M 0s
 16800K .......... .......... .......... .......... .......... 97%  106M 0s
 16850K .......... .......... .......... .......... .......... 98%  105M 0s
 16900K .......... .......... .......... .......... .......... 98% 98.5M 0s
 16950K .......... .......... .......... .......... .......... 98%  106M 0s
 17000K .......... .......... .......... .......... .......... 98% 61.2M 0s
 17050K .......... .......... .......... .......... .......... 99% 86.3M 0s
 17100K .......... .......... .......... .......... .......... 99% 91.3M 0s
 17150K .......... .......... .......... .......... .......... 99%  101M 0s
 17200K .......... .......... .......... .........            100%  128M=1.4s

2018-10-09 09:55:07 (12.4 MB/s) - ‘jar/HpoAnnotQc.jar’ saved [17653504/17653504]

java -Xmx1G -jar jar/HpoAnnotQc.jar big-file --orphadata "data/en_product4_HPO.xml"  --hpo "data/hp.obo" --small-files "../annotated/" --out "phenotype.hpoa"
log4j:WARN No appenders could be found for logger (org.openrdf.rio.RDFParserRegistry).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
2018-10-09 09:55:11.406 ERROR main [main] (V2SmallFileParser.java:72) - We were expecting 14 fields but got 27 for line OMIM:615612	%615612 DEVELOPMENTAL DYSPLASIA OF THE HIP 2; DDH2	HP:0001369	Arthritis								PMID:23716478	PCS	HPO:nvasilevsky[2018-06-13]OMIM:615612	DEVELOPMENTAL DYSPLASIA OF THE HIP 2; DDH2	HP:0002673	Coxa valga							OMIM-CS:skeletalPelvis > FEMORAL NECK ANGLE GREATER THAN 135 DEGREES (COXA VALGA) OR LESS THAN 127 DEGREES (COXA VARA) SEEN ON X-RAY	OMIM:615612	IEA	HPO:skoehler[2018-10-08]	
makefile:44: recipe for target 'generate-annotation-file' failed
make: *** [generate-annotation-file] Error 1
make: Leaving directory '/var/lib/jenkins/jobs/hpo.annotations.2018/workspace/misc_2018'
Build step 'Execute shell' marked build as failure
Archiving artifacts
Sending e-mails to: sebastian.koehler@charite.de peter.robinson@jax.org
Finished: FAILURE