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A         annotated/OMIM-617235.tab
A         annotated/OMIM-617236.tab
A         annotated/OMIM-617237.tab
A         annotated/OMIM-617238.tab
A         annotated/OMIM-617239.tab
A         annotated/OMIM-617241.tab
A         annotated/OMIM-617243.tab
A         annotated/OMIM-617244.tab
A         annotated/OMIM-617247.tab
A         annotated/OMIM-617248.tab
A         annotated/OMIM-617251.tab
A         annotated/OMIM-617252.tab
A         annotated/OMIM-617253.tab
A         annotated/OMIM-617255.tab
A         annotated/OMIM-617258.tab
A         annotated/OMIM-617260.tab
A         annotated/OMIM-617268.tab
A         annotated/OMIM-617270.tab
A         annotated/OMIM-617271.tab
A         annotated/OMIM-617272.tab
A         annotated/OMIM-617275.tab
A         annotated/OMIM-617276.tab
A         annotated/OMIM-617280.tab
A         annotated/OMIM-617282.tab
A         annotated/OMIM-617284.tab
A         annotated/OMIM-617290.tab
A         annotated/OMIM-617294.tab
A         annotated/OMIM-617296.tab
A         annotated/OMIM-617297.tab
A         annotated/OMIM-617300.tab
A         annotated/OMIM-617301.tab
A         annotated/OMIM-617302.tab
A         annotated/OMIM-617303.tab
A         annotated/OMIM-617304.tab
A         annotated/OMIM-617306.tab
A         annotated/OMIM-617308.tab
A         annotated/OMIM-617315.tab
A         annotated/OMIM-617319.tab
A         annotated/OMIM-617320.tab
A         annotated/OMIM-617321.tab
A         annotated/OMIM-617323.tab
A         annotated/OMIM-617330.tab
A         annotated/OMIM-617333.tab
A         annotated/OMIM-617336.tab
A         annotated/OMIM-617337.tab
A         annotated/OMIM-617339.tab
A         annotated/OMIM-617341.tab
A         annotated/OMIM-617343.tab
A         annotated/OMIM-617349.tab
A         annotated/OMIM-617350.tab
A         annotated/OMIM-617360.tab
A         annotated/OMIM-617364.tab
A         annotated/OMIM-617370.tab
A         annotated/OMIM-617383.tab
A         annotated/OMIM-617384.tab
A         annotated/OMIM-617388.tab
A         annotated/OMIM-617389.tab
A         annotated/OMIM-617391.tab
A         annotated/OMIM-617392.tab
A         annotated/OMIM-617393.tab
A         annotated/OMIM-617394.tab
A         annotated/OMIM-617395.tab
A         annotated/OMIM-617396.tab
A         annotated/OMIM-617397.tab
A         annotated/OMIM-617402.tab
A         annotated/OMIM-617404.tab
A         annotated/OMIM-617405.tab
A         annotated/OMIM-617406.tab
A         annotated/OMIM-617408.tab
A         annotated/OMIM-617409.tab
A         annotated/OMIM-617412.tab
A         annotated/OMIM-617425.tab
A         annotated/OMIM-617432.tab
A         annotated/OMIM-617433.tab
A         annotated/OMIM-617439.tab
A         annotated/OMIM-617441.tab
A         annotated/OMIM-617442.tab
A         annotated/OMIM-617450.tab
A         annotated/OMIM-617452.tab
A         annotated/OMIM-617460.tab
A         annotated/OMIM-617466.tab
A         annotated/OMIM-617468.tab
A         annotated/OMIM-617478.tab
A         annotated/OMIM-617506.tab
A         annotated/OMIM-617526.tab
A         annotated/OMIM-617537.tab
A         annotated/OMIM-617694.tab
A         annotated/OMIM-617751.tab
A         annotated/OMIM-617784.tab
A         annotated/OMIM-617808.tab
A         annotated/OMIM-617836.tab
A         annotated/OMIM-617875.tab
A         annotated/OMIM-617895.tab
A         annotated/OMIM-617925.tab
A         annotated/OMIM-617926.tab
A         annotated/OMIM-617952.tab
A         annotated/OMIM-618011.tab
A         annotated/omit-list.txt
A         ignore_for_annotation.txt
A         misc
A         misc/.gitignore
A         misc/cataract
A         misc/cataract/MIM-107250.tab
A         misc/cataract/MIM-115650.tab
A         misc/cataract/MIM-115665.tab
A         misc/cataract/MIM-116600.tab
A         misc/cataract/MIM-116800.tab
A         misc/cataract/MIM-123680.tab
A         misc/cataract/MIM-123730.tab
A         misc/cataract/MIM-154050.tab
A         misc/cataract/MIM-600897.tab
A         misc/cataract/MIM-601885.tab
A         misc/cataract/MIM-604307.tab
A         misc/cataract/MIM-607304.tab
A         misc/cataract/MIM-608810-AR.tab
A         misc/cataract/MIM-608810.tab
A         misc/cataract/MIM-610634.tab
A         misc/cataract/MIM-611597.tab
A         misc/excelfiles
A         misc/excelfiles/Analysis_Table.xls
A         misc/excelfiles/Analysis_Table_NEW_13-09-11.xls
A         misc/excelfiles/Analysis_novel_18-09-11.xls
A         misc/excelfiles/Prioritized DECIPHER_for_Annotation.xls
A         misc/excelfiles/Prioritized-Disease-List.xls
A         misc/excelfiles/candidates_alpha-3.xls
A         misc/helpscripts
A         misc/helpscripts/fixDate.pl
A         misc/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
A         obsoleted-entries/OMIM-144400.tab
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 5102
[workspace] $ /bin/sh -xe /tmp/jenkins8410431265709820647.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
--2018-07-25 09:15:59--  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: 28089886 (27M) [text/xml]
Saving to: ‘data/en_product4_HPO.xml’

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  9050K .......... .......... .......... .......... .......... 33%  107M 2s
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  9150K .......... .......... .......... .......... .......... 33% 68.0M 2s
  9200K .......... .......... .......... .......... .......... 33% 79.0M 2s
  9250K .......... .......... .......... .......... .......... 33% 75.5M 2s
  9300K .......... .......... .......... .......... .......... 34% 40.1M 2s
  9350K .......... .......... .......... .......... .......... 34% 56.2M 2s
  9400K .......... .......... .......... .......... .......... 34% 49.0M 2s
  9450K .......... .......... .......... .......... .......... 34%  115M 2s
  9500K .......... .......... .......... .......... .......... 34%  105M 2s
  9550K .......... .......... .......... .......... .......... 34%  106M 2s
  9600K .......... .......... .......... .......... .......... 35%  111M 2s
  9650K .......... .......... .......... .......... .......... 35% 3.32M 2s
  9700K .......... .......... .......... .......... .......... 35% 77.9M 2s
  9750K .......... .......... .......... .......... .......... 35% 51.9M 2s
  9800K .......... .......... .......... .......... .......... 35% 9.64M 2s
  9850K .......... .......... .......... .......... .......... 36% 84.7M 2s
  9900K .......... .......... .......... .......... .......... 36%  103M 2s
  9950K .......... .......... .......... .......... .......... 36% 6.51M 2s
 10000K .......... .......... .......... .......... .......... 36% 92.3M 2s
 10050K .......... .......... .......... .......... .......... 36% 29.4M 2s
 10100K .......... .......... .......... .......... .......... 37% 98.1M 2s
 10150K .......... .......... .......... .......... .......... 37% 99.5M 2s
 10200K .......... .......... .......... .......... .......... 37%  117M 2s
 10250K .......... .......... .......... .......... .......... 37% 99.2M 2s
 10300K .......... .......... .......... .......... .......... 37%  111M 2s
 10350K .......... .......... .......... .......... .......... 37% 97.5M 1s
 10400K .......... .......... .......... .......... .......... 38%  116M 1s
 10450K .......... .......... .......... .......... .......... 38%  106M 1s
 10500K .......... .......... .......... .......... .......... 38%  116M 1s
 10550K .......... .......... .......... .......... .......... 38%  113M 1s
 10600K .......... .......... .......... .......... .......... 38%  112M 1s
 10650K .......... .......... .......... .......... .......... 39%  112M 1s
 10700K .......... .......... .......... .......... .......... 39% 12.9M 1s
 10750K .......... .......... .......... .......... .......... 39% 81.5M 1s
 10800K .......... .......... .......... .......... .......... 39% 6.42M 1s
 10850K .......... .......... .......... .......... .......... 39%  115M 1s
 10900K .......... .......... .......... .......... .......... 39% 97.9M 1s
 10950K .......... .......... .......... .......... .......... 40% 8.29M 1s
 11000K .......... .......... .......... .......... .......... 40% 91.0M 1s
 11050K .......... .......... .......... .......... .......... 40%  108M 1s
 11100K .......... .......... .......... .......... .......... 40%  104M 1s
 11150K .......... .......... .......... .......... .......... 40%  119M 1s
 11200K .......... .......... .......... .......... .......... 41% 8.81M 1s
 11250K .......... .......... .......... .......... .......... 41% 9.06M 1s
 11300K .......... .......... .......... .......... .......... 41% 96.6M 1s
 11350K .......... .......... .......... .......... .......... 41% 87.2M 1s
 11400K .......... .......... .......... .......... .......... 41%  116M 1s
 11450K .......... .......... .......... .......... .......... 41% 99.9M 1s
 11500K .......... .......... .......... .......... .......... 42%  123M 1s
 11550K .......... .......... .......... .......... .......... 42%  111M 1s
 11600K .......... .......... .......... .......... .......... 42% 99.9M 1s
 11650K .......... .......... .......... .......... .......... 42%  113M 1s
 11700K .......... .......... .......... .......... .......... 42%  112M 1s
 11750K .......... .......... .......... .......... .......... 43%  103M 1s
 11800K .......... .......... .......... .......... .......... 43%  109M 1s
 11850K .......... .......... .......... .......... .......... 43%  113M 1s
 11900K .......... .......... .......... .......... .......... 43% 90.3M 1s
 11950K .......... .......... .......... .......... .......... 43% 6.13M 1s
 12000K .......... .......... .......... .......... .......... 43% 97.2M 1s
 12050K .......... .......... .......... .......... .......... 44%  111M 1s
 12100K .......... .......... .......... .......... .......... 44%  111M 1s
 12150K .......... .......... .......... .......... .......... 44% 13.7M 1s
 12200K .......... .......... .......... .......... .......... 44% 41.3M 1s
 12250K .......... .......... .......... .......... .......... 44% 83.4M 1s
 12300K .......... .......... .......... .......... .......... 45%  115M 1s
 12350K .......... .......... .......... .......... .......... 45%  112M 1s
 12400K .......... .......... .......... .......... .......... 45% 5.82M 1s
 12450K .......... .......... .......... .......... .......... 45% 82.3M 1s
 12500K .......... .......... .......... .......... .......... 45%  106M 1s
 12550K .......... .......... .......... .......... .......... 45%  101M 1s
 12600K .......... .......... .......... .......... .......... 46%  105M 1s
 12650K .......... .......... .......... .......... .......... 46% 47.9M 1s
 12700K .......... .......... .......... .......... .......... 46%  101M 1s
 12750K .......... .......... .......... .......... .......... 46% 33.8M 1s
 12800K .......... .......... .......... .......... .......... 46% 69.0M 1s
 12850K .......... .......... .......... .......... .......... 47% 82.5M 1s
 12900K .......... .......... .......... .......... .......... 47% 86.7M 1s
 12950K .......... .......... .......... .......... .......... 47%  115M 1s
 13000K .......... .......... .......... .......... .......... 47%  105M 1s
 13050K .......... .......... .......... .......... .......... 47% 21.6M 1s
 13100K .......... .......... .......... .......... .......... 47%  108M 1s
 13150K .......... .......... .......... .......... .......... 48% 95.2M 1s
 13200K .......... .......... .......... .......... .......... 48% 9.99M 1s
 13250K .......... .......... .......... .......... .......... 48% 22.5M 1s
 13300K .......... .......... .......... .......... .......... 48% 91.1M 1s
 13350K .......... .......... .......... .......... .......... 48% 76.6M 1s
 13400K .......... .......... .......... .......... .......... 49%  117M 1s
 13450K .......... .......... .......... .......... .......... 49% 18.1M 1s
 13500K .......... .......... .......... .......... .......... 49% 82.8M 1s
 13550K .......... .......... .......... .......... .......... 49% 95.7M 1s
 13600K .......... .......... .......... .......... .......... 49%  102M 1s
 13650K .......... .......... .......... .......... .......... 49% 91.3M 1s
 13700K .......... .......... .......... .......... .......... 50%  115M 1s
 13750K .......... .......... .......... .......... .......... 50%  100M 1s
 13800K .......... .......... .......... .......... .......... 50% 6.10M 1s
 13850K .......... .......... .......... .......... .......... 50% 90.5M 1s
 13900K .......... .......... .......... .......... .......... 50%  103M 1s
 13950K .......... .......... .......... .......... .......... 51%  121M 1s
 14000K .......... .......... .......... .......... .......... 51%  104M 1s
 14050K .......... .......... .......... .......... .......... 51%  116M 1s
 14100K .......... .......... .......... .......... .......... 51% 68.6M 1s
 14150K .......... .......... .......... .......... .......... 51% 74.2M 1s
 14200K .......... .......... .......... .......... .......... 51% 26.1M 1s
 14250K .......... .......... .......... .......... .......... 52% 25.0M 1s
 14300K .......... .......... .......... .......... .......... 52% 94.7M 1s
 14350K .......... .......... .......... .......... .......... 52% 80.4M 1s
 14400K .......... .......... .......... .......... .......... 52%  116M 1s
 14450K .......... .......... .......... .......... .......... 52%  104M 1s
 14500K .......... .......... .......... .......... .......... 53%  116M 1s
 14550K .......... .......... .......... .......... .......... 53%  117M 1s
 14600K .......... .......... .......... .......... .......... 53%  110M 1s
 14650K .......... .......... .......... .......... .......... 53% 12.0M 1s
 14700K .......... .......... .......... .......... .......... 53% 44.3M 1s
 14750K .......... .......... .......... .......... .......... 53% 82.6M 1s
 14800K .......... .......... .......... .......... .......... 54%  100M 1s
 14850K .......... .......... .......... .......... .......... 54%  104M 1s
 14900K .......... .......... .......... .......... .......... 54% 15.1M 1s
 14950K .......... .......... .......... .......... .......... 54% 43.4M 1s
 15000K .......... .......... .......... .......... .......... 54% 54.8M 1s
 15050K .......... .......... .......... .......... .......... 55% 52.5M 1s
 15100K .......... .......... .......... .......... .......... 55%  113M 1s
 15150K .......... .......... .......... .......... .......... 55% 71.4M 1s
 15200K .......... .......... .......... .......... .......... 55% 81.0M 1s
 15250K .......... .......... .......... .......... .......... 55% 61.5M 1s
 15300K .......... .......... .......... .......... .......... 55% 8.34M 1s
 15350K .......... .......... .......... .......... .......... 56% 66.2M 1s
 15400K .......... .......... .......... .......... .......... 56% 24.2M 1s
 15450K .......... .......... .......... .......... .......... 56% 85.2M 1s
 15500K .......... .......... .......... .......... .......... 56% 96.6M 1s
 15550K .......... .......... .......... .......... .......... 56%  100M 1s
 15600K .......... .......... .......... .......... .......... 57%  108M 1s
 15650K .......... .......... .......... .......... .......... 57%  119M 1s
 15700K .......... .......... .......... .......... .......... 57%  105M 1s
 15750K .......... .......... .......... .......... .......... 57%  100M 1s
 15800K .......... .......... .......... .......... .......... 57%  107M 1s
 15850K .......... .......... .......... .......... .......... 57%  108M 1s
 15900K .......... .......... .......... .......... .......... 58%  104M 1s
 15950K .......... .......... .......... .......... .......... 58%  109M 1s
 16000K .......... .......... .......... .......... .......... 58% 92.2M 1s
 16050K .......... .......... .......... .......... .......... 58% 45.4M 1s
 16100K .......... .......... .......... .......... .......... 58% 96.6M 1s
 16150K .......... .......... .......... .......... .......... 59% 43.2M 1s
 16200K .......... .......... .......... .......... .......... 59% 66.1M 1s
 16250K .......... .......... .......... .......... .......... 59%  107M 1s
 16300K .......... .......... .......... .......... .......... 59%  104M 1s
 16350K .......... .......... .......... .......... .......... 59% 20.0M 1s
 16400K .......... .......... .......... .......... .......... 59% 30.7M 1s
 16450K .......... .......... .......... .......... .......... 60%  103M 1s
 16500K .......... .......... .......... .......... .......... 60% 31.4M 1s
 16550K .......... .......... .......... .......... .......... 60% 37.2M 1s
 16600K .......... .......... .......... .......... .......... 60%  112M 1s
 16650K .......... .......... .......... .......... .......... 60%  104M 1s
 16700K .......... .......... .......... .......... .......... 61% 17.3M 1s
 16750K .......... .......... .......... .......... .......... 61% 40.7M 1s
 16800K .......... .......... .......... .......... .......... 61% 31.2M 1s
 16850K .......... .......... .......... .......... .......... 61% 38.5M 1s
 16900K .......... .......... .......... .......... .......... 61% 62.2M 1s
 16950K .......... .......... .......... .......... .......... 61% 65.4M 1s
 17000K .......... .......... .......... .......... .......... 62% 60.7M 1s
 17050K .......... .......... .......... .......... .......... 62% 16.8M 1s
 17100K .......... .......... .......... .......... .......... 62% 7.83M 1s
 17150K .......... .......... .......... .......... .......... 62% 1.36M 1s
 17200K .......... .......... .......... .......... .......... 62%  103M 1s
 17250K .......... .......... .......... .......... .......... 63%  100M 1s
 17300K .......... .......... .......... .......... .......... 63%  120M 1s
 17350K .......... .......... .......... .......... .......... 63% 87.0M 1s
 17400K .......... .......... .......... .......... .......... 63%  108M 1s
 17450K .......... .......... .......... .......... .......... 63%  104M 1s
 17500K .......... .......... .......... .......... .......... 63% 66.4M 1s
 17550K .......... .......... .......... .......... .......... 64% 99.2M 1s
 17600K .......... .......... .......... .......... .......... 64% 79.4M 1s
 17650K .......... .......... .......... .......... .......... 64%  101M 1s
 17700K .......... .......... .......... .......... .......... 64%  103M 1s
 17750K .......... .......... .......... .......... .......... 64%  121M 1s
 17800K .......... .......... .......... .......... .......... 65% 93.9M 1s
 17850K .......... .......... .......... .......... .......... 65% 41.0M 1s
 17900K .......... .......... .......... .......... .......... 65% 18.0M 1s
 17950K .......... .......... .......... .......... .......... 65% 67.6M 1s
 18000K .......... .......... .......... .......... .......... 65%  108M 1s
 18050K .......... .......... .......... .......... .......... 65% 31.4M 1s
 18100K .......... .......... .......... .......... .......... 66%  104M 1s
 18150K .......... .......... .......... .......... .......... 66%  106M 1s
 18200K .......... .......... .......... .......... .......... 66%  118M 1s
 18250K .......... .......... .......... .......... .......... 66% 97.8M 1s
 18300K .......... .......... .......... .......... .......... 66%  116M 1s
 18350K .......... .......... .......... .......... .......... 67%  115M 1s
 18400K .......... .......... .......... .......... .......... 67%  112M 1s
 18450K .......... .......... .......... .......... .......... 67%  103M 1s
 18500K .......... .......... .......... .......... .......... 67%  119M 1s
 18550K .......... .......... .......... .......... .......... 67% 85.1M 1s
 18600K .......... .......... .......... .......... .......... 67%  117M 1s
 18650K .......... .......... .......... .......... .......... 68%  115M 1s
 18700K .......... .......... .......... .......... .......... 68%  110M 1s
 18750K .......... .......... .......... .......... .......... 68%  114M 1s
 18800K .......... .......... .......... .......... .......... 68% 36.3M 1s
 18850K .......... .......... .......... .......... .......... 68%  109M 1s
 18900K .......... .......... .......... .......... .......... 69%  101M 1s
 18950K .......... .......... .......... .......... .......... 69%  103M 1s
 19000K .......... .......... .......... .......... .......... 69%  108M 1s
 19050K .......... .......... .......... .......... .......... 69% 2.93M 1s
 19100K .......... .......... .......... .......... .......... 69% 71.9M 1s
 19150K .......... .......... .......... .......... .......... 69%  119M 0s
 19200K .......... .......... .......... .......... .......... 70%  113M 0s
 19250K .......... .......... .......... .......... .......... 70%  105M 0s
 19300K .......... .......... .......... .......... .......... 70%  112M 0s
 19350K .......... .......... .......... .......... .......... 70%  106M 0s
 19400K .......... .......... .......... .......... .......... 70%  120M 0s
 19450K .......... .......... .......... .......... .......... 71% 40.3M 0s
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 19550K .......... .......... .......... .......... .......... 71%  120M 0s
 19600K .......... .......... .......... .......... .......... 71% 98.8M 0s
 19650K .......... .......... .......... .......... .......... 71%  121M 0s
 19700K .......... .......... .......... .......... .......... 71%  107M 0s
 19750K .......... .......... .......... .......... .......... 72%  106M 0s
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 19850K .......... .......... .......... .......... .......... 72% 34.6M 0s
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 20500K .......... .......... .......... .......... .......... 74% 48.0M 0s
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 20700K .......... .......... .......... .......... .......... 75%  119M 0s
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 20800K .......... .......... .......... .......... .......... 76% 94.7M 0s
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 20900K .......... .......... .......... .......... .......... 76% 89.1M 0s
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 22100K .......... .......... .......... .......... .......... 80%  111M 0s
 22150K .......... .......... .......... .......... .......... 80%  103M 0s
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 22450K .......... .......... .......... .......... .......... 82% 96.4M 0s
 22500K .......... .......... .......... .......... .......... 82% 39.0M 0s
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 22600K .......... .......... .......... .......... .......... 82% 79.9M 0s
 22650K .......... .......... .......... .......... .......... 82% 99.2M 0s
 22700K .......... .......... .......... .......... .......... 82% 95.9M 0s
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 22800K .......... .......... .......... .......... .......... 83% 82.6M 0s
 22850K .......... .......... .......... .......... .......... 83% 91.2M 0s
 22900K .......... .......... .......... .......... .......... 83%  107M 0s
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 23050K .......... .......... .......... .......... .......... 84%  103M 0s
 23100K .......... .......... .......... .......... .......... 84% 82.3M 0s
 23150K .......... .......... .......... .......... .......... 84% 99.0M 0s
 23200K .......... .......... .......... .......... .......... 84% 76.6M 0s
 23250K .......... .......... .......... .......... .......... 84% 91.5M 0s
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 26100K .......... .......... .......... .......... .......... 95%  116M 0s
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 26400K .......... .......... .......... .......... .......... 96%  123M 0s
 26450K .......... .......... .......... .......... .......... 96% 6.89M 0s
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 26550K .......... .......... .......... .......... .......... 96% 73.0M 0s
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 26650K .......... .......... .......... .......... .......... 97% 17.7M 0s
 26700K .......... .......... .......... .......... .......... 97% 17.7M 0s
 26750K .......... .......... .......... .......... .......... 97% 62.2M 0s
 26800K .......... .......... .......... .......... .......... 97% 81.4M 0s
 26850K .......... .......... .......... .......... .......... 98%  116M 0s
 26900K .......... .......... .......... .......... .......... 98%  103M 0s
 26950K .......... .......... .......... .......... .......... 98% 66.1M 0s
 27000K .......... .......... .......... .......... .......... 98% 90.5M 0s
 27050K .......... .......... .......... .......... .......... 98% 59.2M 0s
 27100K .......... .......... .......... .......... .......... 98%  107M 0s
 27150K .......... .......... .......... .......... .......... 99%  120M 0s
 27200K .......... .......... .......... .......... .......... 99%  108M 0s
 27250K .......... .......... .......... .......... .......... 99% 95.6M 0s
 27300K .......... .......... .......... .......... .......... 99%  108M 0s
 27350K .......... .......... .......... .......... .......... 99%  108M 0s
 27400K .......... .......... .......... .                    100%  133M=1.4s

2018-07-25 09:16:01 (19.5 MB/s) - ‘data/en_product4_HPO.xml’ saved [28089886/28089886]

# loads the HPO
wget -N -P data http://purl.obolibrary.org/obo/hp.obo
--2018-07-25 09:16:01--  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]
--2018-07-25 09:16:01--  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: 6004703 (5.7M) [text/plain]
Saving to: ‘data/hp.obo’

     0K .......... .......... .......... .......... ..........  0% 1.47M 4s
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  4850K .......... .......... .......... .......... .......... 83% 18.2M 0s
  4900K .......... .......... .......... .......... .......... 84% 38.3M 0s
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  5000K .......... .......... .......... .......... .......... 86% 22.6M 0s
  5050K .......... .......... .......... .......... .......... 86% 14.2M 0s
  5100K .......... .......... .......... .......... .......... 87% 27.6M 0s
  5150K .......... .......... .......... .......... .......... 88% 27.5M 0s
  5200K .......... .......... .......... .......... .......... 89% 16.4M 0s
  5250K .......... .......... .......... .......... .......... 90% 37.9M 0s
  5300K .......... .......... .......... .......... .......... 91% 17.7M 0s
  5350K .......... .......... .......... .......... .......... 92% 39.7M 0s
  5400K .......... .......... .......... .......... .......... 92% 12.9M 0s
  5450K .......... .......... .......... .......... .......... 93% 34.0M 0s
  5500K .......... .......... .......... .......... .......... 94% 26.7M 0s
  5550K .......... .......... .......... .......... .......... 95% 31.8M 0s
  5600K .......... .......... .......... .......... .......... 96% 19.3M 0s
  5650K .......... .......... .......... .......... .......... 97% 22.8M 0s
  5700K .......... .......... .......... .......... .......... 98% 40.2M 0s
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  5800K .......... .......... .......... .......... .......... 99% 25.1M 0s
  5850K .......... ...                                        100%  260M=0.5s

Last-modified header missing -- time-stamps turned off.
2018-07-25 09:16:06 (12.1 MB/s) - ‘data/hp.obo’ saved [6004703/6004703]

mkdir -p jar
wget -N -P jar https://github.com/monarch-initiative/hpoannotqc/releases/download/v1.2.2/HpoAnnotQc.jar
--2018-07-25 09:16:06--  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%2F20180725%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180725T071635Z&X-Amz-Expires=300&X-Amz-Signature=5ec198ee9c29eb5653e9b4b955f399299eaa37ba3224786dcbccd0507ab286fe&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DHpoAnnotQc.jar&response-content-type=application%2Foctet-stream [following]
--2018-07-25 09:16:06--  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%2F20180725%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180725T071635Z&X-Amz-Expires=300&X-Amz-Signature=5ec198ee9c29eb5653e9b4b955f399299eaa37ba3224786dcbccd0507ab286fe&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’

     0K .......... .......... .......... .......... ..........  0%  161K 1m47s
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   850K .......... .......... .......... .......... ..........  5% 88.9M 26s
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  2700K .......... .......... .......... .......... .......... 15% 79.5M 11s
  2750K .......... .......... .......... .......... .......... 16% 80.8M 11s
  2800K .......... .......... .......... .......... .......... 16% 86.2M 10s
  2850K .......... .......... .......... .......... .......... 16% 14.4M 10s
  2900K .......... .......... .......... .......... .......... 17% 81.7M 10s
  2950K .......... .......... .......... .......... .......... 17% 87.8M 10s
  3000K .......... .......... .......... .......... .......... 17% 82.5M 10s
  3050K .......... .......... .......... .......... .......... 17% 1.64M 10s
  3100K .......... .......... .......... .......... .......... 18%  756K 10s
  3150K .......... .......... .......... .......... .......... 18% 69.7M 10s
  3200K .......... .......... .......... .......... .......... 18% 79.5M 9s
  3250K .......... .......... .......... .......... .......... 19% 83.6M 9s
  3300K .......... .......... .......... .......... .......... 19% 79.7M 9s
  3350K .......... .......... .......... .......... .......... 19% 95.4M 9s
  3400K .......... .......... .......... .......... .......... 20% 15.5M 9s
  3450K .......... .......... .......... .......... .......... 20% 12.5M 9s
  3500K .......... .......... .......... .......... .......... 20% 85.8M 8s
  3550K .......... .......... .......... .......... .......... 20% 97.4M 8s
  3600K .......... .......... .......... .......... .......... 21% 27.7M 8s
  3650K .......... .......... .......... .......... .......... 21% 1.92M 8s
  3700K .......... .......... .......... .......... .......... 21%  744K 8s
  3750K .......... .......... .......... .......... .......... 22% 75.9M 8s
  3800K .......... .......... .......... .......... .......... 22% 86.1M 8s
  3850K .......... .......... .......... .......... .......... 22% 92.0M 8s
  3900K .......... .......... .......... .......... .......... 22% 90.9M 8s
  3950K .......... .......... .......... .......... .......... 23% 92.0M 8s
  4000K .......... .......... .......... .......... .......... 23% 67.6M 7s
  4050K .......... .......... .......... .......... .......... 23% 29.5M 7s
  4100K .......... .......... .......... .......... .......... 24% 75.4M 7s
  4150K .......... .......... .......... .......... .......... 24% 89.2M 7s
  4200K .......... .......... .......... .......... .......... 24% 22.5M 7s
  4250K .......... .......... .......... .......... .......... 24% 1.69M 7s
  4300K .......... .......... .......... .......... .......... 25% 19.2M 7s
  4350K .......... .......... .......... .......... .......... 25%  777K 7s
  4400K .......... .......... .......... .......... .......... 25% 73.3M 7s
  4450K .......... .......... .......... .......... .......... 26% 89.3M 7s
  4500K .......... .......... .......... .......... .......... 26% 92.3M 7s
  4550K .......... .......... .......... .......... .......... 26% 55.2M 7s
  4600K .......... .......... .......... .......... .......... 26% 79.2M 6s
  4650K .......... .......... .......... .......... .......... 27% 89.7M 6s
  4700K .......... .......... .......... .......... .......... 27% 91.1M 6s
  4750K .......... .......... .......... .......... .......... 27% 88.2M 6s
  4800K .......... .......... .......... .......... .......... 28% 89.0M 6s
  4850K .......... .......... .......... .......... .......... 28% 24.2M 6s
  4900K .......... .......... .......... .......... .......... 28% 1.82M 6s
  4950K .......... .......... .......... .......... .......... 29% 12.1M 6s
  5000K .......... .......... .......... .......... .......... 29%  767K 6s
  5050K .......... .......... .......... .......... .......... 29% 94.4M 6s
  5100K .......... .......... .......... .......... .......... 29% 98.4M 6s
  5150K .......... .......... .......... .......... .......... 30%  102M 6s
  5200K .......... .......... .......... .......... .......... 30% 95.2M 6s
  5250K .......... .......... .......... .......... .......... 30%  103M 6s
  5300K .......... .......... .......... .......... .......... 31% 96.3M 6s
  5350K .......... .......... .......... .......... .......... 31%  109M 5s
  5400K .......... .......... .......... .......... .......... 31% 81.8M 5s
  5450K .......... .......... .......... .......... .......... 31%  103M 5s
  5500K .......... .......... .......... .......... .......... 32%  103M 5s
  5550K .......... .......... .......... .......... .......... 32%  100M 5s
  5600K .......... .......... .......... .......... .......... 32% 19.5M 5s
  5650K .......... .......... .......... .......... .......... 33%  105M 5s
  5700K .......... .......... .......... .......... .......... 33% 1.87M 5s
  5750K .......... .......... .......... .......... .......... 33% 13.1M 5s
  5800K .......... .......... .......... .......... .......... 33%  765K 5s
  5850K .......... .......... .......... .......... .......... 34% 76.8M 5s
  5900K .......... .......... .......... .......... .......... 34% 88.2M 5s
  5950K .......... .......... .......... .......... .......... 34% 92.9M 5s
  6000K .......... .......... .......... .......... .......... 35% 97.7M 5s
  6050K .......... .......... .......... .......... .......... 35% 97.4M 5s
  6100K .......... .......... .......... .......... .......... 35%  103M 5s
  6150K .......... .......... .......... .......... .......... 35%  103M 5s
  6200K .......... .......... .......... .......... .......... 36% 81.8M 5s
  6250K .......... .......... .......... .......... .......... 36%  102M 5s
  6300K .......... .......... .......... .......... .......... 36% 94.8M 4s
  6350K .......... .......... .......... .......... .......... 37%  103M 4s
  6400K .......... .......... .......... .......... .......... 37%  106M 4s
  6450K .......... .......... .......... .......... .......... 37%  124M 4s
  6500K .......... .......... .......... .......... .......... 37% 43.0M 4s
  6550K .......... .......... .......... .......... .......... 38% 1.89M 4s
  6600K .......... .......... .......... .......... .......... 38% 11.9M 4s
  6650K .......... .......... .......... .......... .......... 38% 83.3M 4s
  6700K .......... .......... .......... .......... .......... 39%  761K 4s
  6750K .......... .......... .......... .......... .......... 39% 91.9M 4s
  6800K .......... .......... .......... .......... .......... 39% 81.2M 4s
  6850K .......... .......... .......... .......... .......... 40% 96.8M 4s
  6900K .......... .......... .......... .......... .......... 40%  104M 4s
  6950K .......... .......... .......... .......... .......... 40%  117M 4s
  7000K .......... .......... .......... .......... .......... 40% 45.7M 4s
  7050K .......... .......... .......... .......... .......... 41% 95.4M 4s
  7100K .......... .......... .......... .......... .......... 41%  104M 4s
  7150K .......... .......... .......... .......... .......... 41%  103M 4s
  7200K .......... .......... .......... .......... .......... 42% 89.5M 4s
  7250K .......... .......... .......... .......... .......... 42%  102M 4s
  7300K .......... .......... .......... .......... .......... 42%  103M 4s
  7350K .......... .......... .......... .......... .......... 42% 97.6M 4s
  7400K .......... .......... .......... .......... .......... 43% 82.4M 4s
  7450K .......... .......... .......... .......... .......... 43%  102M 4s
  7500K .......... .......... .......... .......... .......... 43%  111M 3s
  7550K .......... .......... .......... .......... .......... 44% 1.99M 3s
  7600K .......... .......... .......... .......... .......... 44% 77.9M 3s
  7650K .......... .......... .......... .......... .......... 44% 11.9M 3s
  7700K .......... .......... .......... .......... .......... 44%  727K 3s
  7750K .......... .......... .......... .......... .......... 45% 92.9M 3s
  7800K .......... .......... .......... .......... .......... 45% 76.2M 3s
  7850K .......... .......... .......... .......... .......... 45% 91.1M 3s
  7900K .......... .......... .......... .......... .......... 46% 93.0M 3s
  7950K .......... .......... .......... .......... .......... 46% 91.3M 3s
  8000K .......... .......... .......... .......... .......... 46% 87.1M 3s
  8050K .......... .......... .......... .......... .......... 46% 95.7M 3s
  8100K .......... .......... .......... .......... .......... 47% 93.1M 3s
  8150K .......... .......... .......... .......... .......... 47%  112M 3s
  8200K .......... .......... .......... .......... .......... 47% 67.3M 3s
  8250K .......... .......... .......... .......... .......... 48% 94.5M 3s
  8300K .......... .......... .......... .......... .......... 48% 92.9M 3s
  8350K .......... .......... .......... .......... .......... 48% 91.0M 3s
  8400K .......... .......... .......... .......... .......... 49% 89.0M 3s
  8450K .......... .......... .......... .......... .......... 49% 95.4M 3s
  8500K .......... .......... .......... .......... .......... 49% 94.2M 3s
  8550K .......... .......... .......... .......... .......... 49% 94.8M 3s
  8600K .......... .......... .......... .......... .......... 50% 77.0M 3s
  8650K .......... .......... .......... .......... .......... 50%  113M 3s
  8700K .......... .......... .......... .......... .......... 50% 2.48M 3s
  8750K .......... .......... .......... .......... .......... 51% 12.6M 3s
  8800K .......... .......... .......... .......... .......... 51% 78.0M 3s
  8850K .......... .......... .......... .......... .......... 51%  731K 3s
  8900K .......... .......... .......... .......... .......... 51% 73.4M 3s
  8950K .......... .......... .......... .......... .......... 52% 95.0M 3s
  9000K .......... .......... .......... .......... .......... 52% 75.6M 3s
  9050K .......... .......... .......... .......... .......... 52% 95.7M 3s
  9100K .......... .......... .......... .......... .......... 53% 89.0M 3s
  9150K .......... .......... .......... .......... .......... 53% 95.2M 3s
  9200K .......... .......... .......... .......... .......... 53% 86.1M 3s
  9250K .......... .......... .......... .......... .......... 53% 95.2M 2s
  9300K .......... .......... .......... .......... .......... 54%  101M 2s
  9350K .......... .......... .......... .......... .......... 54% 88.6M 2s
  9400K .......... .......... .......... .......... .......... 54% 78.3M 2s
  9450K .......... .......... .......... .......... .......... 55% 93.2M 2s
  9500K .......... .......... .......... .......... .......... 55% 94.1M 2s
  9550K .......... .......... .......... .......... .......... 55% 93.5M 2s
  9600K .......... .......... .......... .......... .......... 55% 87.8M 2s
  9650K .......... .......... .......... .......... .......... 56% 88.6M 2s
  9700K .......... .......... .......... .......... .......... 56% 94.4M 2s
  9750K .......... .......... .......... .......... .......... 56%  103M 2s
  9800K .......... .......... .......... .......... .......... 57% 85.6M 2s
  9850K .......... .......... .......... .......... .......... 57%  114M 2s
  9900K .......... .......... .......... .......... .......... 57% 2.56M 2s
  9950K .......... .......... .......... .......... .......... 58% 71.5M 2s
 10000K .......... .......... .......... .......... .......... 58% 9.93M 2s
 10050K .......... .......... .......... .......... .......... 58% 91.9M 2s
 10100K .......... .......... .......... .......... .......... 58%  100M 2s
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 10300K .......... .......... .......... .......... .......... 60% 23.1M 2s
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 10400K .......... .......... .......... .......... .......... 60% 90.3M 2s
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 11150K .......... .......... .......... .......... .......... 64% 94.6M 2s
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 12150K .......... .......... .......... .......... .......... 70% 94.8M 1s
 12200K .......... .......... .......... .......... .......... 71% 72.1M 1s
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 12400K .......... .......... .......... .......... .......... 72% 84.5M 1s
 12450K .......... .......... .......... .......... .......... 72% 95.9M 1s
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 13050K .......... .......... .......... .......... .......... 75% 93.5M 1s
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 13600K .......... .......... .......... .......... .......... 79% 86.1M 1s
 13650K .......... .......... .......... .......... .......... 79% 89.8M 1s
 13700K .......... .......... .......... .......... .......... 79% 92.0M 1s
 13750K .......... .......... .......... .......... .......... 80% 89.3M 1s
 13800K .......... .......... .......... .......... .......... 80% 31.2M 1s
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 15300K .......... .......... .......... .......... .......... 89% 93.4M 0s
 15350K .......... .......... .......... .......... .......... 89% 91.4M 0s
 15400K .......... .......... .......... .......... .......... 89% 75.5M 0s
 15450K .......... .......... .......... .......... .......... 89% 98.3M 0s
 15500K .......... .......... .......... .......... .......... 90% 23.5M 0s
 15550K .......... .......... .......... .......... .......... 90% 17.6M 0s
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 15700K .......... .......... .......... .......... .......... 91% 93.8M 0s
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 15800K .......... .......... .......... .......... .......... 91% 74.9M 0s
 15850K .......... .......... .......... .......... .......... 92%  102M 0s
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 15950K .......... .......... .......... .......... .......... 92%  106M 0s
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 16350K .......... .......... .......... .......... .......... 95%  767K 0s
 16400K .......... .......... .......... .......... .......... 95% 46.0M 0s
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 16700K .......... .......... .......... .......... .......... 97% 87.7M 0s
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 16850K .......... .......... .......... .......... .......... 98% 89.8M 0s
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 17050K .......... .......... .......... .......... .......... 99% 89.5M 0s
 17100K .......... .......... .......... .......... .......... 99% 91.3M 0s
 17150K .......... .......... .......... .......... .......... 99% 95.7M 0s
 17200K .......... .......... .......... .........            100%  120M=3.4s

2018-07-25 09:16:11 (4.91 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.
2018-07-25 09:16:15.345 ERROR main [main] (V2SmallFileIngestor.java:69) - Finished with input of 7189 files with 92520 annotations
2018-07-25 09:16:15.346 ERROR main [main] (V2SmallFileIngestor.java:70) - A total of 83 entries found in the small file directory were omitted.
2018-07-25 09:16:15.857 ERROR main [main] (OrphanetXML2HpoDiseaseModelParser.java:89) - [ERROR] Could not find TermId for Orphanet HPO ID "HP:0001676"
2018-07-25 09:16:15.907 ERROR main [main] (OrphanetXML2HpoDiseaseModelParser.java:89) - [ERROR] Could not find TermId for Orphanet HPO ID "HP:0011607"
2018-07-25 09:16:15.976 ERROR main [main] (OrphanetXML2HpoDiseaseModelParser.java:89) - [ERROR] Could not find TermId for Orphanet HPO ID "HP:0002755"
We extracted 3193 orphanet disorders with 67571 annotations 
We output a total of 92520 big file lines
2018-07-25 09:16:16.814 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0200027] for TermId [prefix=TermPrefix [value=HP], id=0005830] (Flexion contracture of toe): see following line
2018-07-25 09:16:16.814 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:300373	OSTEOPATHIA STRIATA WITH CRANIAL SCLEROSIS	HP:0200027	Contractures of the toes								OMIM:300373	TAS	HPO:skoehler[2010-06-18]
2018-07-25 09:16:16.814 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Contractures of the toes instead of Flexion contracture of toe for Flexion contracture of toe: see following line
2018-07-25 09:16:16.814 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:300373	OSTEOPATHIA STRIATA WITH CRANIAL SCLEROSIS	HP:0200027	Contractures of the toes								OMIM:300373	TAS	HPO:skoehler[2010-06-18]
2018-07-25 09:16:16.814 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Defect in the atrial septum instead of Atrial septal defect for Atrial septal defect: see following line
2018-07-25 09:16:16.815 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:300373	OSTEOPATHIA STRIATA WITH CRANIAL SCLEROSIS	HP:0001631	Defect in the atrial septum								OMIM:300373	TAS	HPO:probinson[2009-02-21]
2018-07-25 09:16:16.815 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0000156] for TermId [prefix=TermPrefix [value=HP], id=0000218] (High palate): see following line
2018-07-25 09:16:16.815 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:300373	OSTEOPATHIA STRIATA WITH CRANIAL SCLEROSIS	HP:0000156	High-arched palate			15%					OMIM:300373	TAS	HPO:skoehler[2010-06-20]
2018-07-25 09:16:16.815 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label High-arched palate instead of High palate for High palate: see following line
2018-07-25 09:16:16.815 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:300373	OSTEOPATHIA STRIATA WITH CRANIAL SCLEROSIS	HP:0000156	High-arched palate			15%					OMIM:300373	TAS	HPO:skoehler[2010-06-20]
V2 orph about to write this many od3193
2018-07-25 09:16:17.016 ERROR main [main] (Orphanet2BigFile.java:57) - Could not make annotation for term HP:0000118 of disorder Leydig cell hypoplasia 
2018-07-25 09:16:17.016 ERROR main [main] (Orphanet2BigFile.java:58) - Will skip this line: Could not get aspect for term Phenotypic abnormality [HP:0000118]
2018-07-25 09:16:17.320 ERROR main [main] (Orphanet2BigFile.java:57) - Could not make annotation for term HP:0000118 of disorder Male infertility with teratozoospermia due to single gene mutation 
2018-07-25 09:16:17.320 ERROR main [main] (Orphanet2BigFile.java:58) - Will skip this line: Could not get aspect for term Phenotypic abnormality [HP:0000118]
2018-07-25 09:16:17.320 ERROR main [main] (Orphanet2BigFile.java:57) - Could not make annotation for term HP:0000118 of disorder Male infertility with azoospermia or oligozoospermia due to single gene mutation 
2018-07-25 09:16:17.320 ERROR main [main] (Orphanet2BigFile.java:58) - Will skip this line: Could not get aspect for term Phenotypic abnormality [HP:0000118]
2018-07-25 09:16:17.334 ERROR main [main] (Orphanet2BigFile.java:57) - Could not make annotation for term HP:0000118 of disorder Normosmic congenital hypogonadotropic hypogonadism 
2018-07-25 09:16:17.335 ERROR main [main] (Orphanet2BigFile.java:58) - Will skip this line: Could not get aspect for term Phenotypic abnormality [HP:0000118]
2018-07-25 09:16:17.455 ERROR main [main] (Orphanet2BigFile.java:57) - Could not make annotation for term HP:0000118 of disorder Autosomal recessive spastic paraplegia type 15 
2018-07-25 09:16:17.456 ERROR main [main] (Orphanet2BigFile.java:58) - Will skip this line: Could not get aspect for term Phenotypic abnormality [HP:0000118]
We output a total of 67566 orphanet annotations from 3193 diseases
#cat phenotype_annotation.tab negative_phenotype_annotation.tab | awk -F'\t' '{print $14}'  | sort | uniq -c | sort -nr > curator-statistics.tab
make: Leaving directory '/var/lib/jenkins/jobs/hpo.annotations.2018/workspace/misc_2018'
Archiving artifacts
Finished: SUCCESS