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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-617895.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-151441.tab
A         obsoleted-entries/OMIM-180070.tab
A         obsoleted-entries/OMIM-181515.tab
A         obsoleted-entries/OMIM-189980.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-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 5051
[workspace] $ /bin/sh -xe /tmp/jenkins5489604996866965814.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
--2018-06-13 22:19:02--  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: 27551769 (26M) [text/xml]
Saving to: ‘data/en_product4_HPO.xml’

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 10750K .......... .......... .......... .......... .......... 40% 78.2M 1s
 10800K .......... .......... .......... .......... .......... 40% 13.8M 1s
 10850K .......... .......... .......... .......... .......... 40% 75.6M 1s
 10900K .......... .......... .......... .......... .......... 40% 75.7M 1s
 10950K .......... .......... .......... .......... .......... 40% 96.5M 1s
 11000K .......... .......... .......... .......... .......... 41%  109M 1s
 11050K .......... .......... .......... .......... .......... 41% 90.4M 1s
 11100K .......... .......... .......... .......... .......... 41% 87.0M 1s
 11150K .......... .......... .......... .......... .......... 41% 40.5M 1s
 11200K .......... .......... .......... .......... .......... 41%  101M 1s
 11250K .......... .......... .......... .......... .......... 41%  116M 1s
 11300K .......... .......... .......... .......... .......... 42%  105M 1s
 11350K .......... .......... .......... .......... .......... 42%  121M 1s
 11400K .......... .......... .......... .......... .......... 42%  103M 1s
 11450K .......... .......... .......... .......... .......... 42%  108M 1s
 11500K .......... .......... .......... .......... .......... 42%  111M 1s
 11550K .......... .......... .......... .......... .......... 43%  102M 1s
 11600K .......... .......... .......... .......... .......... 43%  114M 1s
 11650K .......... .......... .......... .......... .......... 43%  103M 1s
 11700K .......... .......... .......... .......... .......... 43%  103M 1s
 11750K .......... .......... .......... .......... .......... 43%  106M 1s
 11800K .......... .......... .......... .......... .......... 44% 96.4M 1s
 11850K .......... .......... .......... .......... .......... 44%  111M 1s
 11900K .......... .......... .......... .......... .......... 44% 98.7M 1s
 11950K .......... .......... .......... .......... .......... 44%  119M 1s
 12000K .......... .......... .......... .......... .......... 44% 99.0M 1s
 12050K .......... .......... .......... .......... .......... 44%  113M 1s
 12100K .......... .......... .......... .......... .......... 45%  113M 1s
 12150K .......... .......... .......... .......... .......... 45%  113M 1s
 12200K .......... .......... .......... .......... .......... 45%  113M 1s
 12250K .......... .......... .......... .......... .......... 45%  104M 1s
 12300K .......... .......... .......... .......... .......... 45% 3.36M 1s
 12350K .......... .......... .......... .......... .......... 46% 93.6M 1s
 12400K .......... .......... .......... .......... .......... 46%  102M 1s
 12450K .......... .......... .......... .......... .......... 46% 93.7M 1s
 12500K .......... .......... .......... .......... .......... 46%  111M 1s
 12550K .......... .......... .......... .......... .......... 46%  105M 1s
 12600K .......... .......... .......... .......... .......... 47%  118M 1s
 12650K .......... .......... .......... .......... .......... 47% 70.1M 1s
 12700K .......... .......... .......... .......... .......... 47% 77.0M 1s
 12750K .......... .......... .......... .......... .......... 47%  101M 1s
 12800K .......... .......... .......... .......... .......... 47% 97.3M 1s
 12850K .......... .......... .......... .......... .......... 47%  119M 1s
 12900K .......... .......... .......... .......... .......... 48% 93.9M 1s
 12950K .......... .......... .......... .......... .......... 48%  106M 1s
 13000K .......... .......... .......... .......... .......... 48%  106M 1s
 13050K .......... .......... .......... .......... .......... 48%  104M 1s
 13100K .......... .......... .......... .......... .......... 48% 99.3M 1s
 13150K .......... .......... .......... .......... .......... 49%  102M 1s
 13200K .......... .......... .......... .......... .......... 49%  106M 1s
 13250K .......... .......... .......... .......... .......... 49%  111M 1s
 13300K .......... .......... .......... .......... .......... 49%  100M 1s
 13350K .......... .......... .......... .......... .......... 49% 98.2M 1s
 13400K .......... .......... .......... .......... .......... 49% 36.8M 1s
 13450K .......... .......... .......... .......... .......... 50% 98.1M 1s
 13500K .......... .......... .......... .......... .......... 50%  111M 1s
 13550K .......... .......... .......... .......... .......... 50%  115M 1s
 13600K .......... .......... .......... .......... .......... 50%  103M 1s
 13650K .......... .......... .......... .......... .......... 50%  118M 1s
 13700K .......... .......... .......... .......... .......... 51%  101M 1s
 13750K .......... .......... .......... .......... .......... 51%  113M 1s
 13800K .......... .......... .......... .......... .......... 51%  106M 1s
 13850K .......... .......... .......... .......... .......... 51%  111M 1s
 13900K .......... .......... .......... .......... .......... 51%  106M 1s
 13950K .......... .......... .......... .......... .......... 52%  112M 1s
 14000K .......... .......... .......... .......... .......... 52%  102M 1s
 14050K .......... .......... .......... .......... .......... 52% 98.9M 1s
 14100K .......... .......... .......... .......... .......... 52%  113M 1s
 14150K .......... .......... .......... .......... .......... 52% 3.20M 1s
 14200K .......... .......... .......... .......... .......... 52% 48.2M 1s
 14250K .......... .......... .......... .......... .......... 53% 50.8M 1s
 14300K .......... .......... .......... .......... .......... 53% 50.1M 1s
 14350K .......... .......... .......... .......... .......... 53% 46.5M 1s
 14400K .......... .......... .......... .......... .......... 53% 32.8M 1s
 14450K .......... .......... .......... .......... .......... 53% 36.1M 1s
 14500K .......... .......... .......... .......... .......... 54% 47.9M 1s
 14550K .......... .......... .......... .......... .......... 54% 50.3M 1s
 14600K .......... .......... .......... .......... .......... 54% 38.9M 1s
 14650K .......... .......... .......... .......... .......... 54% 45.0M 1s
 14700K .......... .......... .......... .......... .......... 54% 38.9M 1s
 14750K .......... .......... .......... .......... .......... 55% 33.1M 1s
 14800K .......... .......... .......... .......... .......... 55% 39.0M 1s
 14850K .......... .......... .......... .......... .......... 55% 15.6M 1s
 14900K .......... .......... .......... .......... .......... 55% 61.1M 1s
 14950K .......... .......... .......... .......... .......... 55% 36.4M 1s
 15000K .......... .......... .......... .......... .......... 55% 41.7M 1s
 15050K .......... .......... .......... .......... .......... 56% 70.8M 1s
 15100K .......... .......... .......... .......... .......... 56% 57.6M 1s
 15150K .......... .......... .......... .......... .......... 56% 75.2M 1s
 15200K .......... .......... .......... .......... .......... 56% 59.6M 1s
 15250K .......... .......... .......... .......... .......... 56% 35.7M 1s
 15300K .......... .......... .......... .......... .......... 57%  115M 1s
 15350K .......... .......... .......... .......... .......... 57% 98.0M 1s
 15400K .......... .......... .......... .......... .......... 57%  103M 1s
 15450K .......... .......... .......... .......... .......... 57%  111M 1s
 15500K .......... .......... .......... .......... .......... 57%  114M 1s
 15550K .......... .......... .......... .......... .......... 57%  115M 1s
 15600K .......... .......... .......... .......... .......... 58%  105M 1s
 15650K .......... .......... .......... .......... .......... 58%  118M 1s
 15700K .......... .......... .......... .......... .......... 58%  107M 1s
 15750K .......... .......... .......... .......... .......... 58%  114M 1s
 15800K .......... .......... .......... .......... .......... 58%  110M 1s
 15850K .......... .......... .......... .......... .......... 59%  114M 1s
 15900K .......... .......... .......... .......... .......... 59% 99.2M 1s
 15950K .......... .......... .......... .......... .......... 59%  117M 1s
 16000K .......... .......... .......... .......... .......... 59%  108M 1s
 16050K .......... .......... .......... .......... .......... 59%  111M 1s
 16100K .......... .......... .......... .......... .......... 60% 99.2M 1s
 16150K .......... .......... .......... .......... .......... 60%  120M 1s
 16200K .......... .......... .......... .......... .......... 60% 97.8M 1s
 16250K .......... .......... .......... .......... .......... 60%  113M 1s
 16300K .......... .......... .......... .......... .......... 60% 24.7M 1s
 16350K .......... .......... .......... .......... .......... 60% 21.8M 1s
 16400K .......... .......... .......... .......... .......... 61% 48.7M 1s
 16450K .......... .......... .......... .......... .......... 61% 37.4M 1s
 16500K .......... .......... .......... .......... .......... 61% 76.8M 1s
 16550K .......... .......... .......... .......... .......... 61%  122M 1s
 16600K .......... .......... .......... .......... .......... 61%  109M 1s
 16650K .......... .......... .......... .......... .......... 62% 93.6M 1s
 16700K .......... .......... .......... .......... .......... 62% 58.9M 1s
 16750K .......... .......... .......... .......... .......... 62%  122M 1s
 16800K .......... .......... .......... .......... .......... 62% 96.4M 1s
 16850K .......... .......... .......... .......... .......... 62%  117M 1s
 16900K .......... .......... .......... .......... .......... 62%  108M 1s
 16950K .......... .......... .......... .......... .......... 63%  109M 1s
 17000K .......... .......... .......... .......... .......... 63%  120M 1s
 17050K .......... .......... .......... .......... .......... 63%  106M 1s
 17100K .......... .......... .......... .......... .......... 63%  117M 1s
 17150K .......... .......... .......... .......... .......... 63% 99.4M 1s
 17200K .......... .......... .......... .......... .......... 64% 98.7M 1s
 17250K .......... .......... .......... .......... .......... 64% 38.5M 1s
 17300K .......... .......... .......... .......... .......... 64% 84.1M 1s
 17350K .......... .......... .......... .......... .......... 64% 35.5M 1s
 17400K .......... .......... .......... .......... .......... 64% 43.5M 1s
 17450K .......... .......... .......... .......... .......... 65% 45.0M 1s
 17500K .......... .......... .......... .......... .......... 65% 57.2M 1s
 17550K .......... .......... .......... .......... .......... 65% 85.5M 1s
 17600K .......... .......... .......... .......... .......... 65%  101M 1s
 17650K .......... .......... .......... .......... .......... 65%  120M 1s
 17700K .......... .......... .......... .......... .......... 65%  102M 1s
 17750K .......... .......... .......... .......... .......... 66%  120M 1s
 17800K .......... .......... .......... .......... .......... 66%  113M 1s
 17850K .......... .......... .......... .......... .......... 66%  102M 1s
 17900K .......... .......... .......... .......... .......... 66%  116M 1s
 17950K .......... .......... .......... .......... .......... 66%  110M 1s
 18000K .......... .......... .......... .......... .......... 67%  105M 1s
 18050K .......... .......... .......... .......... .......... 67%  115M 1s
 18100K .......... .......... .......... .......... .......... 67%  108M 1s
 18150K .......... .......... .......... .......... .......... 67%  113M 1s
 18200K .......... .......... .......... .......... .......... 67%  108M 0s
 18250K .......... .......... .......... .......... .......... 68%  110M 0s
 18300K .......... .......... .......... .......... .......... 68% 14.5M 0s
 18350K .......... .......... .......... .......... .......... 68% 81.8M 0s
 18400K .......... .......... .......... .......... .......... 68% 98.1M 0s
 18450K .......... .......... .......... .......... .......... 68% 20.3M 0s
 18500K .......... .......... .......... .......... .......... 68% 19.7M 0s
 18550K .......... .......... .......... .......... .......... 69% 76.4M 0s
 18600K .......... .......... .......... .......... .......... 69%  102M 0s
 18650K .......... .......... .......... .......... .......... 69% 94.9M 0s
 18700K .......... .......... .......... .......... .......... 69% 29.3M 0s
 18750K .......... .......... .......... .......... .......... 69% 91.5M 0s
 18800K .......... .......... .......... .......... .......... 70% 61.2M 0s
 18850K .......... .......... .......... .......... .......... 70% 65.8M 0s
 18900K .......... .......... .......... .......... .......... 70% 78.5M 0s
 18950K .......... .......... .......... .......... .......... 70% 70.4M 0s
 19000K .......... .......... .......... .......... .......... 70% 22.9M 0s
 19050K .......... .......... .......... .......... .......... 70% 72.6M 0s
 19100K .......... .......... .......... .......... .......... 71% 68.9M 0s
 19150K .......... .......... .......... .......... .......... 71% 56.8M 0s
 19200K .......... .......... .......... .......... .......... 71% 78.1M 0s
 19250K .......... .......... .......... .......... .......... 71% 65.5M 0s
 19300K .......... .......... .......... .......... .......... 71% 78.7M 0s
 19350K .......... .......... .......... .......... .......... 72% 76.8M 0s
 19400K .......... .......... .......... .......... .......... 72% 32.1M 0s
 19450K .......... .......... .......... .......... .......... 72% 97.2M 0s
 19500K .......... .......... .......... .......... .......... 72%  101M 0s
 19550K .......... .......... .......... .......... .......... 72%  119M 0s
 19600K .......... .......... .......... .......... .......... 73%  113M 0s
 19650K .......... .......... .......... .......... .......... 73%  104M 0s
 19700K .......... .......... .......... .......... .......... 73%  118M 0s
 19750K .......... .......... .......... .......... .......... 73%  107M 0s
 19800K .......... .......... .......... .......... .......... 73%  110M 0s
 19850K .......... .......... .......... .......... .......... 73%  104M 0s
 19900K .......... .......... .......... .......... .......... 74% 91.6M 0s
 19950K .......... .......... .......... .......... .......... 74%  107M 0s
 20000K .......... .......... .......... .......... .......... 74%  105M 0s
 20050K .......... .......... .......... .......... .......... 74%  116M 0s
 20100K .......... .......... .......... .......... .......... 74%  102M 0s
 20150K .......... .......... .......... .......... .......... 75%  108M 0s
 20200K .......... .......... .......... .......... .......... 75%  116M 0s
 20250K .......... .......... .......... .......... .......... 75%  120M 0s
 20300K .......... .......... .......... .......... .......... 75% 94.8M 0s
 20350K .......... .......... .......... .......... .......... 75%  116M 0s
 20400K .......... .......... .......... .......... .......... 76%  105M 0s
 20450K .......... .......... .......... .......... .......... 76% 20.9M 0s
 20500K .......... .......... .......... .......... .......... 76% 53.0M 0s
 20550K .......... .......... .......... .......... .......... 76% 88.4M 0s
 20600K .......... .......... .......... .......... .......... 76%  107M 0s
 20650K .......... .......... .......... .......... .......... 76% 96.1M 0s
 20700K .......... .......... .......... .......... .......... 77% 46.2M 0s
 20750K .......... .......... .......... .......... .......... 77% 58.3M 0s
 20800K .......... .......... .......... .......... .......... 77% 71.2M 0s
 20850K .......... .......... .......... .......... .......... 77% 44.6M 0s
 20900K .......... .......... .......... .......... .......... 77%  113M 0s
 20950K .......... .......... .......... .......... .......... 78% 99.4M 0s
 21000K .......... .......... .......... .......... .......... 78%  113M 0s
 21050K .......... .......... .......... .......... .......... 78% 98.0M 0s
 21100K .......... .......... .......... .......... .......... 78%  121M 0s
 21150K .......... .......... .......... .......... .......... 78%  114M 0s
 21200K .......... .......... .......... .......... .......... 78%  107M 0s
 21250K .......... .......... .......... .......... .......... 79% 82.0M 0s
 21300K .......... .......... .......... .......... .......... 79%  106M 0s
 21350K .......... .......... .......... .......... .......... 79%  105M 0s
 21400K .......... .......... .......... .......... .......... 79% 99.0M 0s
 21450K .......... .......... .......... .......... .......... 79% 34.1M 0s
 21500K .......... .......... .......... .......... .......... 80%  110M 0s
 21550K .......... .......... .......... .......... .......... 80%  100M 0s
 21600K .......... .......... .......... .......... .......... 80%  108M 0s
 21650K .......... .......... .......... .......... .......... 80%  120M 0s
 21700K .......... .......... .......... .......... .......... 80%  110M 0s
 21750K .......... .......... .......... .......... .......... 81%  100M 0s
 21800K .......... .......... .......... .......... .......... 81%  118M 0s
 21850K .......... .......... .......... .......... .......... 81%  105M 0s
 21900K .......... .......... .......... .......... .......... 81% 98.5M 0s
 21950K .......... .......... .......... .......... .......... 81%  110M 0s
 22000K .......... .......... .......... .......... .......... 81% 99.2M 0s
 22050K .......... .......... .......... .......... .......... 82%  100M 0s
 22100K .......... .......... .......... .......... .......... 82%  103M 0s
 22150K .......... .......... .......... .......... .......... 82%  113M 0s
 22200K .......... .......... .......... .......... .......... 82%  112M 0s
 22250K .......... .......... .......... .......... .......... 82%  101M 0s
 22300K .......... .......... .......... .......... .......... 83% 97.8M 0s
 22350K .......... .......... .......... .......... .......... 83%  110M 0s
 22400K .......... .......... .......... .......... .......... 83%  106M 0s
 22450K .......... .......... .......... .......... .......... 83% 93.1M 0s
 22500K .......... .......... .......... .......... .......... 83%  120M 0s
 22550K .......... .......... .......... .......... .......... 83%  113M 0s
 22600K .......... .......... .......... .......... .......... 84% 86.8M 0s
 22650K .......... .......... .......... .......... .......... 84%  120M 0s
 22700K .......... .......... .......... .......... .......... 84% 99.1M 0s
 22750K .......... .......... .......... .......... .......... 84%  104M 0s
 22800K .......... .......... .......... .......... .......... 84% 6.25M 0s
 22850K .......... .......... .......... .......... .......... 85% 60.1M 0s
 22900K .......... .......... .......... .......... .......... 85% 66.8M 0s
 22950K .......... .......... .......... .......... .......... 85%  109M 0s
 23000K .......... .......... .......... .......... .......... 85% 94.5M 0s
 23050K .......... .......... .......... .......... .......... 85% 38.6M 0s
 23100K .......... .......... .......... .......... .......... 86% 89.6M 0s
 23150K .......... .......... .......... .......... .......... 86%  103M 0s
 23200K .......... .......... .......... .......... .......... 86% 68.6M 0s
 23250K .......... .......... .......... .......... .......... 86% 55.0M 0s
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 23350K .......... .......... .......... .......... .......... 86%  106M 0s
 23400K .......... .......... .......... .......... .......... 87%  116M 0s
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 23750K .......... .......... .......... .......... .......... 88%  116M 0s
 23800K .......... .......... .......... .......... .......... 88%  104M 0s
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 23900K .......... .......... .......... .......... .......... 89%  117M 0s
 23950K .......... .......... .......... .......... .......... 89% 99.6M 0s
 24000K .......... .......... .......... .......... .......... 89%  112M 0s
 24050K .......... .......... .......... .......... .......... 89%  108M 0s
 24100K .......... .......... .......... .......... .......... 89%  116M 0s
 24150K .......... .......... .......... .......... .......... 89% 37.6M 0s
 24200K .......... .......... .......... .......... .......... 90% 93.1M 0s
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 24300K .......... .......... .......... .......... .......... 90%  111M 0s
 24350K .......... .......... .......... .......... .......... 90%  112M 0s
 24400K .......... .......... .......... .......... .......... 90%  104M 0s
 24450K .......... .......... .......... .......... .......... 91% 95.3M 0s
 24500K .......... .......... .......... .......... .......... 91%  109M 0s
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 24600K .......... .......... .......... .......... .......... 91%  115M 0s
 24650K .......... .......... .......... .......... .......... 91% 98.3M 0s
 24700K .......... .......... .......... .......... .......... 91%  106M 0s
 24750K .......... .......... .......... .......... .......... 92%  113M 0s
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 24850K .......... .......... .......... .......... .......... 92%  114M 0s
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 25050K .......... .......... .......... .......... .......... 93% 96.9M 0s
 25100K .......... .......... .......... .......... .......... 93%  112M 0s
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 25200K .......... .......... .......... .......... .......... 93% 92.4M 0s
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 25300K .......... .......... .......... .......... .......... 94% 99.5M 0s
 25350K .......... .......... .......... .......... .......... 94%  113M 0s
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 25450K .......... .......... .......... .......... .......... 94% 89.2M 0s
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 26900K ......                                                100% 11491G=1.2s

2018-06-13 22:19:03 (22.6 MB/s) - ‘data/en_product4_HPO.xml’ saved [27551769/27551769]

# loads the HPO
wget -N -P data http://purl.obolibrary.org/obo/hp.obo
--2018-06-13 22:19:03--  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]
--2018-06-13 22:19:04--  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: 6004703 (5.7M) [text/plain]
Saving to: ‘data/hp.obo’

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  5850K .......... ...                                        100%  282M=0.5s

Last-modified header missing -- time-stamps turned off.
2018-06-13 22:19:04 (12.3 MB/s) - ‘data/hp.obo’ saved [6004703/6004703]

mkdir -p jar
wget -N -P jar https://github.com/monarch-initiative/hpoannotqc/releases/download/v0.2.3/HpoAnnotQc.jar
--2018-06-13 22:19:04--  https://github.com/monarch-initiative/hpoannotqc/releases/download/v0.2.3/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/a146bd18-3000-11e8-81cb-af4b1ecb3ea5?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180613%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180613T201931Z&X-Amz-Expires=300&X-Amz-Signature=48066a2417f538921ff3c9ad5da7e9f68bb6b95051f6932d98fcd2abfe2a5123&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DHpoAnnotQc.jar&response-content-type=application%2Foctet-stream [following]
--2018-06-13 22:19:05--  https://github-production-release-asset-2e65be.s3.amazonaws.com/120038140/a146bd18-3000-11e8-81cb-af4b1ecb3ea5?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180613%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180613T201931Z&X-Amz-Expires=300&X-Amz-Signature=48066a2417f538921ff3c9ad5da7e9f68bb6b95051f6932d98fcd2abfe2a5123&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: 17649361 (17M) [application/octet-stream]
Saving to: ‘jar/HpoAnnotQc.jar’

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  4900K .......... .......... .......... .......... .......... 28% 80.2M 6s
  4950K .......... .......... .......... .......... .......... 29%  113M 6s
  5000K .......... .......... .......... .......... .......... 29%  101M 6s
  5050K .......... .......... .......... .......... .......... 29%  131M 6s
  5100K .......... .......... .......... .......... .......... 29%  128M 6s
  5150K .......... .......... .......... .......... .......... 30% 1.47M 6s
  5200K .......... .......... .......... .......... .......... 30% 56.9M 6s
  5250K .......... .......... .......... .......... .......... 30%  755K 6s
  5300K .......... .......... .......... .......... .......... 31% 92.1M 6s
  5350K .......... .......... .......... .......... .......... 31% 94.1M 5s
  5400K .......... .......... .......... .......... .......... 31% 74.0M 5s
  5450K .......... .......... .......... .......... .......... 31% 88.6M 5s
  5500K .......... .......... .......... .......... .......... 32% 32.2M 5s
  5550K .......... .......... .......... .......... .......... 32%  103M 5s
  5600K .......... .......... .......... .......... .......... 32% 62.3M 5s
  5650K .......... .......... .......... .......... .......... 33% 99.5M 5s
  5700K .......... .......... .......... .......... .......... 33% 90.6M 5s
  5750K .......... .......... .......... .......... .......... 33%  101M 5s
  5800K .......... .......... .......... .......... .......... 33% 85.1M 5s
  5850K .......... .......... .......... .......... .......... 34% 94.5M 5s
  5900K .......... .......... .......... .......... .......... 34% 98.2M 5s
  5950K .......... .......... .......... .......... .......... 34% 96.4M 5s
  6000K .......... .......... .......... .......... .......... 35% 95.6M 5s
  6050K .......... .......... .......... .......... .......... 35%  100M 5s
  6100K .......... .......... .......... .......... .......... 35%  105M 4s
  6150K .......... .......... .......... .......... .......... 35% 1.60M 4s
  6200K .......... .......... .......... .......... .......... 36% 55.1M 4s
  6250K .......... .......... .......... .......... .......... 36%  108M 4s
  6300K .......... .......... .......... .......... .......... 36%  751K 4s
  6350K .......... .......... .......... .......... .......... 37%  105M 4s
  6400K .......... .......... .......... .......... .......... 37% 97.4M 4s
  6450K .......... .......... .......... .......... .......... 37% 85.6M 4s
  6500K .......... .......... .......... .......... .......... 38% 98.8M 4s
  6550K .......... .......... .......... .......... .......... 38%  115M 4s
  6600K .......... .......... .......... .......... .......... 38% 63.5M 4s
  6650K .......... .......... .......... .......... .......... 38%  104M 4s
  6700K .......... .......... .......... .......... .......... 39%  110M 4s
  6750K .......... .......... .......... .......... .......... 39%  114M 4s
  6800K .......... .......... .......... .......... .......... 39%  107M 4s
  6850K .......... .......... .......... .......... .......... 40%  113M 4s
  6900K .......... .......... .......... .......... .......... 40%  112M 4s
  6950K .......... .......... .......... .......... .......... 40%  116M 4s
  7000K .......... .......... .......... .......... .......... 40% 74.7M 4s
  7050K .......... .......... .......... .......... .......... 41%  110M 4s
  7100K .......... .......... .......... .......... .......... 41%  112M 4s
  7150K .......... .......... .......... .......... .......... 41%  102M 4s
  7200K .......... .......... .......... .......... .......... 42%  109M 4s
  7250K .......... .......... .......... .......... .......... 42%  112M 4s
  7300K .......... .......... .......... .......... .......... 42% 1.58M 4s
  7350K .......... .......... .......... .......... .......... 42% 76.6M 3s
  7400K .......... .......... .......... .......... .......... 43% 91.2M 3s
  7450K .......... .......... .......... .......... .......... 43%  755K 3s
  7500K .......... .......... .......... .......... .......... 43% 93.0M 3s
  7550K .......... .......... .......... .......... .......... 44%  106M 3s
  7600K .......... .......... .......... .......... .......... 44%  108M 3s
  7650K .......... .......... .......... .......... .......... 44%  115M 3s
  7700K .......... .......... .......... .......... .......... 44%  101M 3s
  7750K .......... .......... .......... .......... .......... 45%  111M 3s
  7800K .......... .......... .......... .......... .......... 45% 91.0M 3s
  7850K .......... .......... .......... .......... .......... 45% 99.4M 3s
  7900K .......... .......... .......... .......... .......... 46%  114M 3s
  7950K .......... .......... .......... .......... .......... 46%  116M 3s
  8000K .......... .......... .......... .......... .......... 46% 56.2M 3s
  8050K .......... .......... .......... .......... .......... 46%  108M 3s
  8100K .......... .......... .......... .......... .......... 47%  105M 3s
  8150K .......... .......... .......... .......... .......... 47%  114M 3s
  8200K .......... .......... .......... .......... .......... 47% 89.1M 3s
  8250K .......... .......... .......... .......... .......... 48%  109M 3s
  8300K .......... .......... .......... .......... .......... 48%  107M 3s
  8350K .......... .......... .......... .......... .......... 48%  111M 3s
  8400K .......... .......... .......... .......... .......... 49%  108M 3s
  8450K .......... .......... .......... .......... .......... 49%  116M 3s
  8500K .......... .......... .......... .......... .......... 49%  107M 3s
  8550K .......... .......... .......... .......... .......... 49% 1.63M 3s
  8600K .......... .......... .......... .......... .......... 50% 72.0M 3s
  8650K .......... .......... .......... .......... .......... 50% 91.2M 3s
  8700K .......... .......... .......... .......... .......... 50% 92.1M 3s
  8750K .......... .......... .......... .......... .......... 51%  757K 3s
  8800K .......... .......... .......... .......... .......... 51% 76.6M 3s
  8850K .......... .......... .......... .......... .......... 51%  100M 3s
  8900K .......... .......... .......... .......... .......... 51%  100M 3s
  8950K .......... .......... .......... .......... .......... 52% 94.9M 3s
  9000K .......... .......... .......... .......... .......... 52% 69.6M 3s
  9050K .......... .......... .......... .......... .......... 52% 92.7M 3s
  9100K .......... .......... .......... .......... .......... 53% 93.0M 2s
  9150K .......... .......... .......... .......... .......... 53% 90.4M 2s
  9200K .......... .......... .......... .......... .......... 53% 88.3M 2s
  9250K .......... .......... .......... .......... .......... 53% 91.5M 2s
  9300K .......... .......... .......... .......... .......... 54% 87.2M 2s
  9350K .......... .......... .......... .......... .......... 54% 91.2M 2s
  9400K .......... .......... .......... .......... .......... 54% 73.6M 2s
  9450K .......... .......... .......... .......... .......... 55%  103M 2s
  9500K .......... .......... .......... .......... .......... 55% 88.9M 2s
  9550K .......... .......... .......... .......... .......... 55% 84.5M 2s
  9600K .......... .......... .......... .......... .......... 55% 87.0M 2s
  9650K .......... .......... .......... .......... .......... 56% 90.9M 2s
  9700K .......... .......... .......... .......... .......... 56% 75.5M 2s
  9750K .......... .......... .......... .......... .......... 56%  106M 2s
  9800K .......... .......... .......... .......... .......... 57% 85.1M 2s
  9850K .......... .......... .......... .......... .......... 57%  112M 2s
  9900K .......... .......... .......... .......... .......... 57%  114M 2s
  9950K .......... .......... .......... .......... .......... 58%  114M 2s
 10000K .......... .......... .......... .......... .......... 58%  108M 2s
 10050K .......... .......... .......... .......... .......... 58% 1.85M 2s
 10100K .......... .......... .......... .......... .......... 58% 78.5M 2s
 10150K .......... .......... .......... .......... .......... 59% 92.2M 2s
 10200K .......... .......... .......... .......... .......... 59% 74.5M 2s
 10250K .......... .......... .......... .......... .......... 59% 90.6M 2s
 10300K .......... .......... .......... .......... .......... 60%  766K 2s
 10350K .......... .......... .......... .......... .......... 60% 66.7M 2s
 10400K .......... .......... .......... .......... .......... 60% 86.8M 2s
 10450K .......... .......... .......... .......... .......... 60% 91.7M 2s
 10500K .......... .......... .......... .......... .......... 61% 92.3M 2s
 10550K .......... .......... .......... .......... .......... 61% 84.2M 2s
 10600K .......... .......... .......... .......... .......... 61% 73.7M 2s
 10650K .......... .......... .......... .......... .......... 62% 95.8M 2s
 10700K .......... .......... .......... .......... .......... 62% 94.2M 2s
 10750K .......... .......... .......... .......... .......... 62% 94.9M 2s
 10800K .......... .......... .......... .......... .......... 62% 83.7M 2s
 10850K .......... .......... .......... .......... .......... 63% 96.5M 2s
 10900K .......... .......... .......... .......... .......... 63% 89.2M 2s
 10950K .......... .......... .......... .......... .......... 63% 94.8M 2s
 11000K .......... .......... .......... .......... .......... 64% 76.9M 2s
 11050K .......... .......... .......... .......... .......... 64% 89.8M 2s
 11100K .......... .......... .......... .......... .......... 64% 93.9M 2s
 11150K .......... .......... .......... .......... .......... 64% 94.5M 2s
 11200K .......... .......... .......... .......... .......... 65% 90.8M 2s
 11250K .......... .......... .......... .......... .......... 65% 90.5M 2s
 11300K .......... .......... .......... .......... .......... 65% 91.6M 2s
 11350K .......... .......... .......... .......... .......... 66% 89.9M 1s
 11400K .......... .......... .......... .......... .......... 66% 75.7M 1s
 11450K .......... .......... .......... .......... .......... 66% 98.7M 1s
 11500K .......... .......... .......... .......... .......... 67%  110M 1s
 11550K .......... .......... .......... .......... .......... 67% 93.8M 1s
 11600K .......... .......... .......... .......... .......... 67% 82.9M 1s
 11650K .......... .......... .......... .......... .......... 67% 95.7M 1s
 11700K .......... .......... .......... .......... .......... 68% 97.7M 1s
 11750K .......... .......... .......... .......... .......... 68%  121M 1s
 11800K .......... .......... .......... .......... .......... 68% 1.96M 1s
 11850K .......... .......... .......... .......... .......... 69% 89.1M 1s
 11900K .......... .......... .......... .......... .......... 69% 98.3M 1s
 11950K .......... .......... .......... .......... .......... 69% 99.2M 1s
 12000K .......... .......... .......... .......... .......... 69% 89.3M 1s
 12050K .......... .......... .......... .......... .......... 70%  113M 1s
 12100K .......... .......... .......... .......... .......... 70%  769K 1s
 12150K .......... .......... .......... .......... .......... 70% 90.9M 1s
 12200K .......... .......... .......... .......... .......... 71% 73.9M 1s
 12250K .......... .......... .......... .......... .......... 71% 92.8M 1s
 12300K .......... .......... .......... .......... .......... 71% 91.6M 1s
 12350K .......... .......... .......... .......... .......... 71% 88.4M 1s
 12400K .......... .......... .......... .......... .......... 72%  115M 1s
 12450K .......... .......... .......... .......... .......... 72%  132M 1s
 12500K .......... .......... .......... .......... .......... 72% 97.6M 1s
 12550K .......... .......... .......... .......... .......... 73% 43.9M 1s
 12600K .......... .......... .......... .......... .......... 73% 61.0M 1s
 12650K .......... .......... .......... .......... .......... 73% 39.3M 1s
 12700K .......... .......... .......... .......... .......... 73%  102M 1s
 12750K .......... .......... .......... .......... .......... 74% 77.7M 1s
 12800K .......... .......... .......... .......... .......... 74% 92.1M 1s
 12850K .......... .......... .......... .......... .......... 74% 95.3M 1s
 12900K .......... .......... .......... .......... .......... 75%  101M 1s
 12950K .......... .......... .......... .......... .......... 75% 98.2M 1s
 13000K .......... .......... .......... .......... .......... 75% 76.9M 1s
 13050K .......... .......... .......... .......... .......... 76%  101M 1s
 13100K .......... .......... .......... .......... .......... 76% 94.5M 1s
 13150K .......... .......... .......... .......... .......... 76% 99.7M 1s
 13200K .......... .......... .......... .......... .......... 76% 92.9M 1s
 13250K .......... .......... .......... .......... .......... 77%  101M 1s
 13300K .......... .......... .......... .......... .......... 77%  100M 1s
 13350K .......... .......... .......... .......... .......... 77% 84.3M 1s
 13400K .......... .......... .......... .......... .......... 78% 79.4M 1s
 13450K .......... .......... .......... .......... .......... 78%  109M 1s
 13500K .......... .......... .......... .......... .......... 78%  109M 1s
 13550K .......... .......... .......... .......... .......... 78%  112M 1s
 13600K .......... .......... .......... .......... .......... 79%  104M 1s
 13650K .......... .......... .......... .......... .......... 79%  108M 1s
 13700K .......... .......... .......... .......... .......... 79%  114M 1s
 13750K .......... .......... .......... .......... .......... 80%  109M 1s
 13800K .......... .......... .......... .......... .......... 80% 2.26M 1s
 13850K .......... .......... .......... .......... .......... 80% 99.6M 1s
 13900K .......... .......... .......... .......... .......... 80% 97.4M 1s
 13950K .......... .......... .......... .......... .......... 81%  103M 1s
 14000K .......... .......... .......... .......... .......... 81% 96.6M 1s
 14050K .......... .......... .......... .......... .......... 81%  104M 1s
 14100K .......... .......... .......... .......... .......... 82%  118M 1s
 14150K .......... .......... .......... .......... .......... 82% 94.3M 1s
 14200K .......... .......... .......... .......... .......... 82%  775K 1s
 14250K .......... .......... .......... .......... .......... 82%  108M 1s
 14300K .......... .......... .......... .......... .......... 83%  108M 1s
 14350K .......... .......... .......... .......... .......... 83%  107M 1s
 14400K .......... .......... .......... .......... .......... 83%  100M 1s
 14450K .......... .......... .......... .......... .......... 84% 88.3M 1s
 14500K .......... .......... .......... .......... .......... 84%  104M 1s
 14550K .......... .......... .......... .......... .......... 84% 91.6M 1s
 14600K .......... .......... .......... .......... .......... 84% 74.5M 1s
 14650K .......... .......... .......... .......... .......... 85% 89.6M 1s
 14700K .......... .......... .......... .......... .......... 85% 98.7M 1s
 14750K .......... .......... .......... .......... .......... 85% 94.2M 1s
 14800K .......... .......... .......... .......... .......... 86% 92.7M 1s
 14850K .......... .......... .......... .......... .......... 86% 52.9M 0s
 14900K .......... .......... .......... .......... .......... 86% 87.6M 0s
 14950K .......... .......... .......... .......... .......... 87% 43.6M 0s
 15000K .......... .......... .......... .......... .......... 87% 74.8M 0s
 15050K .......... .......... .......... .......... .......... 87% 94.1M 0s
 15100K .......... .......... .......... .......... .......... 87% 94.7M 0s
 15150K .......... .......... .......... .......... .......... 88% 84.8M 0s
 15200K .......... .......... .......... .......... .......... 88%  134M 0s
 15250K .......... .......... .......... .......... .......... 88%  146M 0s
 15300K .......... .......... .......... .......... .......... 89%  147M 0s
 15350K .......... .......... .......... .......... .......... 89%  150M 0s
 15400K .......... .......... .......... .......... .......... 89% 70.9M 0s
 15450K .......... .......... .......... .......... .......... 89% 93.3M 0s
 15500K .......... .......... .......... .......... .......... 90% 95.0M 0s
 15550K .......... .......... .......... .......... .......... 90% 90.3M 0s
 15600K .......... .......... .......... .......... .......... 90% 77.8M 0s
 15650K .......... .......... .......... .......... .......... 91%  108M 0s
 15700K .......... .......... .......... .......... .......... 91%  105M 0s
 15750K .......... .......... .......... .......... .......... 91%  114M 0s
 15800K .......... .......... .......... .......... .......... 91% 89.4M 0s
 15850K .......... .......... .......... .......... .......... 92%  110M 0s
 15900K .......... .......... .......... .......... .......... 92%  111M 0s
 15950K .......... .......... .......... .......... .......... 92%  109M 0s
 16000K .......... .......... .......... .......... .......... 93% 99.3M 0s
 16050K .......... .......... .......... .......... .......... 93%  114M 0s
 16100K .......... .......... .......... .......... .......... 93%  112M 0s
 16150K .......... .......... .......... .......... .......... 93%  113M 0s
 16200K .......... .......... .......... .......... .......... 94% 2.41M 0s
 16250K .......... .......... .......... .......... .......... 94%  101M 0s
 16300K .......... .......... .......... .......... .......... 94%  103M 0s
 16350K .......... .......... .......... .......... .......... 95% 99.0M 0s
 16400K .......... .......... .......... .......... .......... 95% 95.5M 0s
 16450K .......... .......... .......... .......... .......... 95% 84.8M 0s
 16500K .......... .......... .......... .......... .......... 96%  106M 0s
 16550K .......... .......... .......... .......... .......... 96%  109M 0s
 16600K .......... .......... .......... .......... .......... 96%  790K 0s
 16650K .......... .......... .......... .......... .......... 96% 56.9M 0s
 16700K .......... .......... .......... .......... .......... 97% 98.2M 0s
 16750K .......... .......... .......... .......... .......... 97%  101M 0s
 16800K .......... .......... .......... .......... .......... 97% 92.8M 0s
 16850K .......... .......... .......... .......... .......... 98%  107M 0s
 16900K .......... .......... .......... .......... .......... 98% 87.8M 0s
 16950K .......... .......... .......... .......... .......... 98% 79.1M 0s
 17000K .......... .......... .......... .......... .......... 98% 54.6M 0s
 17050K .......... .......... .......... .......... .......... 99% 91.4M 0s
 17100K .......... .......... .......... .......... .......... 99% 93.9M 0s
 17150K .......... .......... .......... .......... .......... 99% 98.1M 0s
 17200K .......... .......... .......... .....                100%  104M=3.2s

2018-06-13 22:19:09 (5.19 MB/s) - ‘jar/HpoAnnotQc.jar’ saved [17649361/17649361]

java -Xmx1G -jar jar/HpoAnnotQc.jar big-file --orphadata "data/en_product4_HPO.xml"  --hpo "data/hp.obo" --small-files "../annotated/" --out "phenotype.hpoa"
2018-06-13 22:19:10,170 main ERROR File contains an invalid element or attribute "maxFileSize"
log4j:WARN No appenders could be found for logger (org.monarchinitiative.phenol.io.obo.OboParser).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
We finished with the input of 7267 V2 small files with a total of 92324 annotation lines
2018-06-13 22:19:13.392 ERROR main [main] (OrphanetXML2HpoDiseaseModelParser.java:92) - [ERROR] Could not find TermId for Orphanet HPO ID "HP:0001676"
2018-06-13 22:19:13.444 ERROR main [main] (OrphanetXML2HpoDiseaseModelParser.java:92) - [ERROR] Could not find TermId for Orphanet HPO ID "HP:0011607"
2018-06-13 22:19:13.542 ERROR main [main] (OrphanetXML2HpoDiseaseModelParser.java:92) - [ERROR] Could not find TermId for Orphanet HPO ID "HP:0002755"
We extracted 3159 orphanet disorders with 66273 annotations 
We output a total of 92324 big file lines
2018-06-13 22:19:14.880 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating high-density lipoprotein levels instead of Decreased HDL cholesterol concentration for Decreased HDL cholesterol concentration: see following line
2018-06-13 22:19:14.880 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:245900	LECITHIN:CHOLESTEROL ACYLTRANSFERASE DEFICIENCY	HP:0003233	Decreased circulating high-density lipoprotein levels								OMIM:245900	TAS	HPO:probinson	2009-02-17
2018-06-13 22:19:14.880 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of B cell count instead of Abnormal B cell count for Abnormal B cell count: see following line
2018-06-13 22:19:14.880 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:613495	#613495 IMMUNODEFICIENCY, COMMON VARIABLE, 5; CVID5;;ANTIBODY DEFICIENCY DUE TO CD20 DEFECT	HP:0010975	Abnormality of B cell count					NOT		OMIM-CS:IMMUNOLOGY > NORMAL NUMBERS OF B CELLS	OMIM:613495	TAS	HPO:skoehler	2014-11-27
2018-06-13 22:19:14.881 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Reduced factor V activity instead of Reduced coagulation factor V activity for Reduced coagulation factor V activity: see following line
2018-06-13 22:19:14.881 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:613625	#613625 FACTOR V AND FACTOR VIII, COMBINED DEFICIENCY OF, 2; F5F8D2	HP:0003225	Reduced factor V activity								OMIM:613625	TAS	HPO:probinson	2013-02-22
2018-06-13 22:19:14.881 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating low-density lipoprotein levels instead of Increased LDL cholesterol concentration for Increased LDL cholesterol concentration: see following line
2018-06-13 22:19:14.881 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:607616	NIEMANN-PICK DISEASE, TYPE B	HP:0003141	Increased circulating low-density lipoprotein levels								OMIM:607616	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.881 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating high-density lipoprotein levels instead of Decreased HDL cholesterol concentration for Decreased HDL cholesterol concentration: see following line
2018-06-13 22:19:14.882 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:607616	NIEMANN-PICK DISEASE, TYPE B	HP:0003233	Decreased circulating high-density lipoprotein levels								OMIM:607616	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.882 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increase in B cell count instead of Increased B cell count for Increased B cell count: see following line
2018-06-13 22:19:14.882 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:603909	AUTOIMMUNE LYMPHOPROLIFERATIVE SYNDROME, TYPE IIA	HP:0005404	Increase in B cell count								OMIM:603909	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.882 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating low-density lipoprotein levels instead of Decreased LDL cholesterol conncentration for Decreased LDL cholesterol conncentration: see following line
2018-06-13 22:19:14.882 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:256840	NEUROPATHY, HEREDITARY SENSORY, WITH SPASTIC PARAPLEGIA, AUTOSOMAL	HP:0003563	Decreased circulating low-density lipoprotein levels								OMIM:256840	TAS	HPO:probinson	2012-09-20
2018-06-13 22:19:14.883 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating low-density lipoprotein levels instead of Decreased LDL cholesterol conncentration for Decreased LDL cholesterol conncentration: see following line
2018-06-13 22:19:14.883 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:616834	MICROCEPHALY, CONGENITAL CATARACT, AND PSORIASIFORM DERMATITIS	HP:0003563	Decreased circulating low-density lipoprotein levels								PMID:21285510	PCS	HPO:probinson	2017-06-17
2018-06-13 22:19:14.883 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Capillary hemangiomas instead of Capillary hemangioma for Capillary hemangioma: see following line
2018-06-13 22:19:14.883 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:607812	CRANIOLENTICULOSUTURAL DYSPLASIA	HP:0005306	Capillary hemangiomas								OMIM:607812	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.884 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of the conjunctiva instead of Abnormal conjunctiva morphology for Abnormal conjunctiva morphology: see following line
2018-06-13 22:19:14.884 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:193900	WHITE SPONGE NEVUS OF CANNON	HP:0000502	Abnormality of the conjunctiva					NOT			OMIM:193900	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.884 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Aplastic clavicles instead of Aplastic clavicle for Aplastic clavicle: see following line
2018-06-13 22:19:14.884 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:119600	CLEIDOCRANIAL DYSPLASIA	HP:0006660	Aplastic clavicles								OMIM:119600	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.885 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of the lip instead of Abnormal lip morphology for Abnormal lip morphology: see following line
2018-06-13 22:19:14.885 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:171450	PHLEBECTASIA OF LIPS	HP:0000159	Abnormality of the lip								OMIM:171450	IEA	HPO:iea	2012-07-24
2018-06-13 22:19:14.885 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Chewing difficulties instead of Impaired mastication for Impaired mastication: see following line
2018-06-13 22:19:14.885 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:602483	AURICULOCONDYLAR SYNDROME 1	HP:0005216	Chewing difficulties								OMIM:602483	PCS	HPO:probinson	2012-03-31
2018-06-13 22:19:14.885 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of eosinophils instead of Abnormal eosinophil morphology for Abnormal eosinophil morphology: see following line
2018-06-13 22:19:14.886 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:261500	EOSINOPHIL PEROXIDASE DEFICIENCY; EPXD	HP:0001879	Abnormality of eosinophils								OMIM:261500	TAS	HPO:iea	2009-02-17
2018-06-13 22:19:14.886 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating very-low-density lipoprotein levels instead of Increased VLDL cholesterol concentration for Increased VLDL cholesterol concentration: see following line
2018-06-13 22:19:14.886 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:136120	FISH-EYE DISEASE	HP:0003362	Increased circulating very-low-density lipoprotein levels								OMIM:136120	TAS	HPO:probinson	2009-02-17
2018-06-13 22:19:14.886 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating high-density lipoprotein levels instead of Decreased HDL cholesterol concentration for Decreased HDL cholesterol concentration: see following line
2018-06-13 22:19:14.887 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:136120	#136120 FISH-EYE DISEASE; FED;;DYSLIPOPROTEINEMIC CORNEAL DYSTROPHY;;ALPHA-LECITHIN:CHOLESTEROL ACYLTRANSFERASE DEFICIENCY;;ALPHA-LCAT DEFICIENCY;;LCATA DEFICIENCY	HP:0003233	Decreased circulating high-density lipoprotein levels								OMIM:136120	TAS	HPO:skoehler	2013-02-25
2018-06-13 22:19:14.887 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating low-density lipoprotein levels instead of Increased LDL cholesterol concentration for Increased LDL cholesterol concentration: see following line
2018-06-13 22:19:14.887 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:136120	FISH-EYE DISEASE	HP:0003141	Increased circulating low-density lipoprotein levels								OMIM:136120	TAS	HPO:probinson	2013-12-15
2018-06-13 22:19:14.888 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating low-density lipoprotein levels instead of Increased LDL cholesterol concentration for Increased LDL cholesterol concentration: see following line
2018-06-13 22:19:14.888 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:616516	#616516 EMERY-DREIFUSS MUSCULAR DYSTROPHY 3, AUTOSOMAL RECESSIVE; EDMD3	HP:0003141	Increased circulating low-density lipoprotein levels			HP:0040283				OMIM-CS:LABORATORY ABNORMALITIES > INCREASED LDL CHOLESTEROL (1 FAMILY)	OMIM:616516	TAS	HPO:skoehler	2015-12-30
2018-06-13 22:19:14.888 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of the conjunctiva instead of Abnormal conjunctiva morphology for Abnormal conjunctiva morphology: see following line
2018-06-13 22:19:14.888 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:125595	DERMATOPATHIA PIGMENTOSA RETICULARIS	HP:0000502	Abnormality of the conjunctiva								OMIM:125595	IEA	HPO:iea	2015-02-01
2018-06-13 22:19:14.889 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating low-density lipoprotein levels instead of Decreased LDL cholesterol conncentration for Decreased LDL cholesterol conncentration: see following line
2018-06-13 22:19:14.889 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:246700	CHYLOMICRON RETENTION DISEASE	HP:0003563	Decreased circulating low-density lipoprotein levels								OMIM:246700	IEA	HPO:skoehler	2010-06-18
2018-06-13 22:19:14.889 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of B cell count instead of Abnormal B cell count for Abnormal B cell count: see following line
2018-06-13 22:19:14.889 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:312863	#312863 COMBINED IMMUNODEFICIENCY, X-LINKED; CIDX;;XCID;;IMMUNODEFICIENCY 6; IMD6	HP:0010975	Abnormality of B cell count					NOT		OMIM-CS:IMMUNOLOGY > NORMAL NUMBER OF B CELLS	OMIM:312863	TAS	HPO:skoehler	2015-01-04
2018-06-13 22:19:14.890 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Aplastic clavicles instead of Aplastic clavicle for Aplastic clavicle: see following line
2018-06-13 22:19:14.890 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:616546	#616546 SHORT-RIB THORACIC DYSPLASIA 14 WITH POLYDACTYLY; SRTD14	HP:0006660	Aplastic clavicles							OMIM-CS:CHEST_RIBS, STERNUM, CLAVICLES, AND SCAPULAE > ABSENT CLAVICLES	OMIM:616546	TAS	HPO:skoehler	2015-12-30
2018-06-13 22:19:14.890 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of the conjunctiva instead of Abnormal conjunctiva morphology for Abnormal conjunctiva morphology: see following line
2018-06-13 22:19:14.890 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:180550	#180550 RING DERMOID OF CORNEA; RDC	HP:0000502	Abnormality of the conjunctiva							OMIM-CS:EYES > ANNULAR LIMBAL DERMOIDS EXTENDING ONTO CORNEA AND CONJUNCTIVA	OMIM:180550	TAS	HPO:skoehler	2012-10-16
2018-06-13 22:19:14.891 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating high-density lipoprotein levels instead of Decreased HDL cholesterol concentration for Decreased HDL cholesterol concentration: see following line
2018-06-13 22:19:14.891 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:604367	LIPODYSTROPHY, FAMILIAL PARTIAL, TYPE 3	HP:0003233	Decreased circulating high-density lipoprotein levels								OMIM:604367	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.891 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating very-low-density lipoprotein levels instead of Increased VLDL cholesterol concentration for Increased VLDL cholesterol concentration: see following line
2018-06-13 22:19:14.891 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:603813	#603813 HYPERCHOLESTEROLEMIA, AUTOSOMAL RECESSIVE; ARH;;HYPERCHOLESTEROLEMIA, AUTOSOMAL RECESSIVE, 1, FORMERLY; ARH1, FORMERLY;;FHCB1, FORMERLY;;HYPERCHOLESTEROLEMIA, AUTOSOMAL RECESSIVE, 2, FORMERLY; ARH2, FORMERLY;;FHCB2, FORMERLY	HP:0003362	Increased circulating very-low-density lipoprotein levels								OMIM:603813	IEA	HPO:skoehler	2013-01-14
2018-06-13 22:19:14.892 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating high-density lipoprotein levels instead of Decreased HDL cholesterol concentration for Decreased HDL cholesterol concentration: see following line
2018-06-13 22:19:14.892 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:615703	MORBID OBESITY AND SPERMATOGENIC FAILURE; MOSPGF	HP:0003233	Decreased circulating high-density lipoprotein levels			6/11			HP:0012828		PMID:24268657	IEA	HPO:probinson	2015-05-10
2018-06-13 22:19:14.892 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating low-density lipoprotein levels instead of Increased LDL cholesterol concentration for Increased LDL cholesterol concentration: see following line
2018-06-13 22:19:14.893 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:615703	MORBID OBESITY AND SPERMATOGENIC FAILURE; MOSPGF	HP:0003141	Increased circulating low-density lipoprotein levels			2/11			HP:0012828		PMID:24268657	IEA	HPO:probinson	2015-05-10
2018-06-13 22:19:14.893 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating high-density lipoprotein levels instead of Decreased HDL cholesterol concentration for Decreased HDL cholesterol concentration: see following line
2018-06-13 22:19:14.893 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:203800	ALSTROM SYNDROME	HP:0003233	Decreased circulating high-density lipoprotein levels								OMIM:203800	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.893 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Reduced factor V activity instead of Reduced coagulation factor V activity for Reduced coagulation factor V activity: see following line
2018-06-13 22:19:14.894 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:227310	FACTOR V AND FACTOR VIII, COMBINED DEFICIENCY OF, WITH NORMAL PROTEINC AND PROTEIN C INHIBITOR	HP:0003225	Reduced factor V activity								OMIM:227310	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.894 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Lipomas of upper eyelids instead of Lipomas of eyelids for Lipomas of eyelids: see following line
2018-06-13 22:19:14.894 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:167730	%167730 PALPEBRAL COLOBOMA-LIPOMA SYNDROME;;NASOPALPEBRAL LIPOMA-COLOBOMA SYNDROME	HP:0040164	Lipomas of upper eyelids							OMIM-CS:EYES > LIPOMAS OF UPPER LIDS	OMIM:167730	TAS	HPO:skoehler	2015-08-02
2018-06-13 22:19:14.894 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of the large intestine instead of Abnormal large intestine morphology for Abnormal large intestine morphology: see following line
2018-06-13 22:19:14.895 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:107700	APPENDICITIS, PRONENESS TO	HP:0002250	Abnormality of the large intestine								OMIM:107700	IEA	HPO:skoehler	2009-02-17
2018-06-13 22:19:14.895 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating high-density lipoprotein levels instead of Decreased HDL cholesterol concentration for Decreased HDL cholesterol concentration: see following line
2018-06-13 22:19:14.895 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:108725	ATHEROSCLEROSIS SUSCEPTIBILITY	HP:0003233	Decreased circulating high-density lipoprotein levels								OMIM:108725	TAS	HPO:probinson	2012-10-20
2018-06-13 22:19:14.896 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating low-density lipoprotein levels instead of Increased LDL cholesterol concentration for Increased LDL cholesterol concentration: see following line
2018-06-13 22:19:14.896 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:144300	HYPERLIPOPROTEINEMIA, TYPE II, AND DEAFNESS	HP:0003141	Increased circulating low-density lipoprotein levels								OMIM:144300	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.896 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Chewing difficulties instead of Impaired mastication for Impaired mastication: see following line
2018-06-13 22:19:14.896 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:607225	SPASTIC PARALYSIS, INFANTILE-ONSET ASCENDING	HP:0005216	Chewing difficulties								OMIM:607225	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.897 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating low-density lipoprotein levels instead of Increased LDL cholesterol concentration for Increased LDL cholesterol concentration: see following line
2018-06-13 22:19:14.897 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:144250	HYPERLIPIDEMIA, FAMILIAL COMBINED	HP:0003141	Increased circulating low-density lipoprotein levels								PMID:4718953	PCS	HPO:probinson	2017-08-27
2018-06-13 22:19:14.897 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating very-low-density lipoprotein levels instead of Increased VLDL cholesterol concentration for Increased VLDL cholesterol concentration: see following line
2018-06-13 22:19:14.897 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:144250	HYPERLIPIDEMIA, FAMILIAL COMBINED	HP:0003362	Increased circulating very-low-density lipoprotein levels								PMID:4718953	PCS	HPO:probinson	2017-08-27
2018-06-13 22:19:14.897 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating high-density lipoprotein levels instead of Decreased HDL cholesterol concentration for Decreased HDL cholesterol concentration: see following line
2018-06-13 22:19:14.898 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:151660	LIPODYSTROPHY, FAMILIAL PARTIAL, TYPE 2	HP:0003233	Decreased circulating high-density lipoprotein levels								OMIM:151660	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.898 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Capillary hemangiomas instead of Capillary hemangioma for Capillary hemangioma: see following line
2018-06-13 22:19:14.898 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:605321	FRONTOOCULAR SYNDROME	HP:0005306	Capillary hemangiomas								OMIM:605321	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.898 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of B cell count instead of Abnormal B cell count for Abnormal B cell count: see following line
2018-06-13 22:19:14.898 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:613493	#613493 IMMUNODEFICIENCY, COMMON VARIABLE, 3; CVID3;;ANTIBODY DEFICIENCY DUE TO CD19 DEFECT	HP:0010975	Abnormality of B cell count					NOT		OMIM-CS:IMMUNOLOGY > NORMAL NUMBERS OF B CELLS	OMIM:613493	TAS	HPO:skoehler	2014-11-27
2018-06-13 22:19:14.899 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating high-density lipoprotein levels instead of Decreased HDL cholesterol concentration for Decreased HDL cholesterol concentration: see following line
2018-06-13 22:19:14.899 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:205400	TANGIER DISEASE	HP:0003233	Decreased circulating high-density lipoprotein levels								OMIM:205400	PCS	HPO:probinson	2012-04-11
2018-06-13 22:19:14.899 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating low-density lipoprotein levels instead of Increased LDL cholesterol concentration for Increased LDL cholesterol concentration: see following line
2018-06-13 22:19:14.899 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:616828	CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIo	HP:0003141	Increased circulating low-density lipoprotein levels			5/5					PMID:26833332	PCS	HPO:probinson	2017-06-17
2018-06-13 22:19:14.899 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Chewing difficulties instead of Impaired mastication for Impaired mastication: see following line
2018-06-13 22:19:14.899 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:614688	Pontine tegmental cap dysplasia	HP:0005216	Chewing difficulties							OMIM-CS:HEAD AND NECK_MOUTH > CHEWING DIFFICULTIES	OMIM:614688	TAS	HPO:skoehler	2012-10-17
2018-06-13 22:19:14.900 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of parotid gland instead of Abnormal parotid gland morphology for Abnormal parotid gland morphology: see following line
2018-06-13 22:19:14.900 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:154500	TREACHER COLLINS-FRANCESCHETTI SYNDROME	HP:0000197	Abnormality of parotid gland								OMIM:154500	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.900 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of the lip instead of Abnormal lip morphology for Abnormal lip morphology: see following line
2018-06-13 22:19:14.900 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:247150	247150 LIP PRINTS	HP:0000159	Abnormality of the lip							OMIM-CS:HEENT > LIP PRINTS	OMIM:247150	TAS	HPO:skoehler	2012-10-16
2018-06-13 22:19:14.901 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of the conjunctiva instead of Abnormal conjunctiva morphology for Abnormal conjunctiva morphology: see following line
2018-06-13 22:19:14.901 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:602248	MALIGNANT ATROPHIC PAPULOSIS	HP:0000502	Abnormality of the conjunctiva								OMIM:602248	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.901 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating low-density lipoprotein levels instead of Decreased LDL cholesterol conncentration for Decreased LDL cholesterol conncentration: see following line
2018-06-13 22:19:14.901 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:605019	#605019 HYPOBETALIPOPROTEINEMIA, FAMILIAL, 2; FHBL2;;HYPOLIPIDEMIA, FAMILIAL, COMBINED	HP:0003563	Decreased circulating low-density lipoprotein levels								PMID:20942659	IEA	HPO:probinson	2013-01-09
2018-06-13 22:19:14.901 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating very-low-density lipoprotein levels instead of Increased VLDL cholesterol concentration for Increased VLDL cholesterol concentration: see following line
2018-06-13 22:19:14.902 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:145750	HYPERTRIGLYCERIDEMIA, FAMILIAL	HP:0003362	Increased circulating very-low-density lipoprotein levels								OMIM:145750	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.902 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating low-density lipoprotein levels instead of Decreased LDL cholesterol conncentration for Decreased LDL cholesterol conncentration: see following line
2018-06-13 22:19:14.902 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:615558	#615558 HYPOBETALIPOPROTEINEMIA, FAMILIAL, 1; FHBL1;;HYPOBETALIPOPROTEINEMIA, FAMILIAL; FHBL;;ACANTHOCYTOSIS WITH HYPOBETALIPOPROTEINEMIA;;HYPOBETALIPOPROTEINEMIA, NORMOTRIGLYCERIDEMIC	HP:0003563	Decreased circulating low-density lipoprotein levels							OMIM-CS:LABORATORY ABNORMALITIES > HYPOBETALIPOPROTEINEMIA	OMIM:615558	TAS	HPO:skoehler	2014-01-28
2018-06-13 22:19:14.902 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of the conjunctiva instead of Abnormal conjunctiva morphology for Abnormal conjunctiva morphology: see following line
2018-06-13 22:19:14.902 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:178000	PTERYGIUM OF CONJUNCTIVA AND CORNEA	HP:0000502	Abnormality of the conjunctiva								OMIM:178000	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.902 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Elevated factor V activity instead of Elevated coagulation factor V activity for Elevated coagulation factor V activity: see following line
2018-06-13 22:19:14.903 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:134400	FACTOR V EXCESS WITH SPONTANEOUS THROMBOSIS	HP:0011996	Elevated factor V activity								OMIM:134400	TAS	HPO:iea	2012-07-21
2018-06-13 22:19:14.903 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating high-density lipoprotein levels instead of Increased HDL cholesterol concentration for Increased HDL cholesterol concentration: see following line
2018-06-13 22:19:14.903 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:143470	HYPERALPHALIPOPROTEINEMIA	HP:0012184	Increased circulating high-density lipoprotein levels								OMIM:143470	TAS	HPO:probinson	2014-05-24
2018-06-13 22:19:14.903 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating very-low-density lipoprotein levels instead of Increased VLDL cholesterol concentration for Increased VLDL cholesterol concentration: see following line
2018-06-13 22:19:14.903 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:144600	HYPERLIPOPROTEINEMIA, TYPE IV	HP:0003362	Increased circulating very-low-density lipoprotein levels								OMIM:144600	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.904 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating very-low-density lipoprotein levels instead of Increased VLDL cholesterol concentration for Increased VLDL cholesterol concentration: see following line
2018-06-13 22:19:14.904 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:243800	JOHANSON-BLIZZARD SYNDROME	HP:0003362	Increased circulating very-low-density lipoprotein levels								OMIM:243800	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.904 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of B cell count instead of Abnormal B cell count for Abnormal B cell count: see following line
2018-06-13 22:19:14.904 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:208900	#208900 ATAXIA-TELANGIECTASIA; AT;;AT1;;LOUIS-BAR SYNDROMEAT, COMPLEMENTATION GROUP A, INCLUDED; ATA, INCLUDED;;AT, COMPLEMENTATION GROUP C, INCLUDED; ATC, INCLUDED;;AT, COMPLEMENTATION GROUP D, INCLUDED; ATD, INCLUDED;;AT, COMPLEMENTATION GROUP E, INCLUDED; ATE, INCLUDED;;ATAXIA-TELANGIECTASIA VARIANT, INCLUDED	HP:0010975	Abnormality of B cell count					NOT		OMIM-CS:IMMUNOLOGY > NORMAL NUMBERS OF B CELLS	OMIM:208900	TAS	HPO:skoehler	2014-11-27
2018-06-13 22:19:14.904 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormal morphology of the nasolacrimal system instead of Abnormal nasolacrimal system morphology for Abnormal nasolacrimal system morphology: see following line
2018-06-13 22:19:14.904 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:101400	SAETHRE-CHOTZEN SYNDROME	HP:0000614	Abnormal morphology of the nasolacrimal system								OMIM:101400	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.905 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Capillary hemangiomas instead of Capillary hemangioma for Capillary hemangioma: see following line
2018-06-13 22:19:14.905 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:180849	RUBINSTEIN-TAYBI SYNDROME 1	HP:0005306	Capillary hemangiomas								ISBN-13:978-0721606156	PCS	HPO:iea	2009-02-17
2018-06-13 22:19:14.905 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of oral mucosa instead of Abnormal oral mucosa morphology for Abnormal oral mucosa morphology: see following line
2018-06-13 22:19:14.905 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:305100	#305100 ECTODERMAL DYSPLASIA 1, HYPOHIDROTIC, X-LINKED; XHED;;ECTODERMAL DYSPLASIA 1, HYPOHIDROTIC/HAIR/TOOTH TYPE, X-LINKED; ECTD1;;XLHED;;ECTODERMAL DYSPLASIA, ANHIDROTIC, X-LINKED; EDA;;EDA1;;ECTODERMAL DYSPLASIA, HYPOHIDROTIC, 1; HED1;;ECTODERMAL DYSPLASIA 1; ED1;;CHRIST-SIEMENS-TOURAINE SYNDROME;;CST SYNDROME	HP:0011830	Abnormality of oral mucosa							OMIM-CS:RESPIRATORY_LARYNX > ATROPHIC MUCOSA CAUSING DYSPHONIA	OMIM:305100	TAS	HPO:skoehler	2012-11-26
2018-06-13 22:19:14.905 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of B cell count instead of Abnormal B cell count for Abnormal B cell count: see following line
2018-06-13 22:19:14.906 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:269840	#269840 SELECTIVE T-CELL DEFECT; STCD	HP:0010975	Abnormality of B cell count					NOT		OMIM-CS:IMMUNOLOGY > NORMAL NUMBER OF B CELLS	OMIM:269840	TAS	HPO:skoehler	2015-01-04
2018-06-13 22:19:14.906 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating low-density lipoprotein levels instead of Increased LDL cholesterol concentration for Increased LDL cholesterol concentration: see following line
2018-06-13 22:19:14.906 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:277460	VITAMIN E, FAMILIAL ISOLATED DEFICIENCY OF	HP:0003141	Increased circulating low-density lipoprotein levels								OMIM:277460	TAS	HPO:probinson	2013-12-15
2018-06-13 22:19:14.906 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Reduced factor V activity instead of Reduced coagulation factor V activity for Reduced coagulation factor V activity: see following line
2018-06-13 22:19:14.906 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:227300	FACTOR V AND FACTOR VIII, COMBINED DEFICIENCY OF	HP:0003225	Reduced factor V activity								OMIM:227300	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.907 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating low-density lipoprotein levels instead of Increased LDL cholesterol concentration for Increased LDL cholesterol concentration: see following line
2018-06-13 22:19:14.907 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:616829	CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIp	HP:0003141	Increased circulating low-density lipoprotein levels			4/4					PMID:26833330	PCS	HPO:probinson	2017-06-17
2018-06-13 22:19:14.907 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating low-density lipoprotein levels instead of Increased LDL cholesterol concentration for Increased LDL cholesterol concentration: see following line
2018-06-13 22:19:14.907 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:267700	%267700 HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL, 1; FHL1;;HPLH1;;HLH1;;HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL; FHL; FHLH; HPLH;;RETICULOSIS, FAMILIAL HISTIOCYTIC;;HEMOPHAGOCYTIC RETICULOSIS, FAMILIAL;;ERYTHROPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL; FEL	HP:0003141	Increased circulating low-density lipoprotein levels								OMIM:267700	TAS	HPO:probinson	2013-01-07
2018-06-13 22:19:14.907 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating very-low-density lipoprotein levels instead of Increased VLDL cholesterol concentration for Increased VLDL cholesterol concentration: see following line
2018-06-13 22:19:14.908 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:267700	%267700 HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL, 1; FHL1;;HPLH1;;HLH1;;HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL; FHL; FHLH; HPLH;;RETICULOSIS, FAMILIAL HISTIOCYTIC;;HEMOPHAGOCYTIC RETICULOSIS, FAMILIAL;;ERYTHROPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL; FEL	HP:0003362	Increased circulating very-low-density lipoprotein levels								OMIM:267700	TAS	HPO:probinson	2013-01-07
2018-06-13 22:19:14.908 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating high-density lipoprotein levels instead of Decreased HDL cholesterol concentration for Decreased HDL cholesterol concentration: see following line
2018-06-13 22:19:14.908 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:267700	%267700 HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL, 1; FHL1;;HPLH1;;HLH1;;HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL; FHL; FHLH; HPLH;;RETICULOSIS, FAMILIAL HISTIOCYTIC;;HEMOPHAGOCYTIC RETICULOSIS, FAMILIAL;;ERYTHROPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL; FEL	HP:0003233	Decreased circulating high-density lipoprotein levels								OMIM:267700	TAS	HPO:probinson	2013-01-07
2018-06-13 22:19:14.908 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label decreased biotinidase activity instead of Decreased biotinidase activity for Decreased biotinidase activity: see following line
2018-06-13 22:19:14.908 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:253260	BIOTINIDASE DEFICIENCYMULTIPLE CARBOXYLASE DEFICIENCY, LATE-ONSET	HP:0410145	decreased biotinidase activity								PMID:3930842	PCS	HPO:nvasilevsky	2018-03-12
2018-06-13 22:19:14.908 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Capillary hemangiomas instead of Capillary hemangioma for Capillary hemangioma: see following line
2018-06-13 22:19:14.908 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:602089	HEMANGIOMA, CAPILLARY INFANTILE	HP:0005306	Capillary hemangiomas								OMIM:602089	TAS	HPO:probinson	2009-02-17
2018-06-13 22:19:14.909 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating high-density lipoprotein levels instead of Decreased HDL cholesterol concentration for Decreased HDL cholesterol concentration: see following line
2018-06-13 22:19:14.909 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:605814	CITRULLINEMIA, TYPE II, NEONATAL-ONSET	HP:0003233	Decreased circulating high-density lipoprotein levels								OMIM:605814	TAS	HPO:probinson	2012-07-16
2018-06-13 22:19:14.909 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Absent gonadal tissue instead of Agonadism for Agonadism: see following line
2018-06-13 22:19:14.909 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:600908	AGONADISM, XY, WITH MENTAL RETARDATION, SHORT STATURE, RETARDED BONE AGE, AND MULTIPLE EXTRAGENITAL MALFORMATIONS	HP:0008633	Absent gonadal tissue								OMIM:600908	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.909 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of B cell count instead of Abnormal B cell count for Abnormal B cell count: see following line
2018-06-13 22:19:14.909 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:308240	#308240 LYMPHOPROLIFERATIVE SYNDROME, X-LINKED, 1; XLP1;;XLP;;LYMPHOPROLIFERATIVE DISEASE, X-LINKED; XLPD;;LYP;;DUNCAN DISEASE;;EPSTEIN-BARR VIRUS INFECTION, FAMILIAL FATAL;;EBV INFECTION, SEVERE, SUSCEPTIBILITY TO; EBVS;;INFECTIOUS MONONUCLEOSIS, SEVERE, SUSCEPTIBILITY TO;;IMMUNODEFICIENCY, X-LINKED PROGRESSIVE COMBINED VARIABLE;;IMMUNODEFICIENCY 5; IMD5;;PURTILO SYNDROME	HP:0010975	Abnormality of B cell count					NOT		OMIM-CS:IMMUNOLOGY > NORMAL NUMBER OF B CELLS	OMIM:308240	TAS	HPO:skoehler	2015-01-04
2018-06-13 22:19:14.909 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Abnormality of B cell count instead of Abnormal B cell count for Abnormal B cell count: see following line
2018-06-13 22:19:14.910 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:613496	#613496 IMMUNODEFICIENCY, COMMON VARIABLE, 6; CVID6;;ANTIBODY DEFICIENCY DUE TO CD81 DEFECT	HP:0010975	Abnormality of B cell count					NOT		OMIM-CS:IMMUNOLOGY > NORMAL NUMBERS OF B CELLS	OMIM:613496	TAS	HPO:skoehler	2014-11-27
2018-06-13 22:19:14.910 ERROR main [main] (V2LineQualityController.java:429) - Bad disease name: OMIM:615413		HP:0000027	Azoospermia								PMID:23315541	PCS	HPO:skoehler	2013-09-30
2018-06-13 22:19:14.910 ERROR main [main] (V2LineQualityController.java:429) - Bad disease name: OMIM:615413		HP:0000789	Infertility								PMID:23315541	PCS	HPO:skoehler	2013-09-30
2018-06-13 22:19:14.910 ERROR main [main] (V2LineQualityController.java:429) - Bad disease name: OMIM:615413		HP:0000006	Autosomal dominant inheritance								PMID:23315541	PCS	HPO:skoehler	2013-09-30
2018-06-13 22:19:14.910 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Capillary hemangiomas instead of Capillary hemangioma for Capillary hemangioma: see following line
2018-06-13 22:19:14.910 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:608354	#608354 CAPILLARY MALFORMATION-ARTERIOVENOUS MALFORMATION;;CMAVMCAPILLARY MALFORMATION WITHOUT ARTERIOVENOUS MALFORMATION, INCLUDED	HP:0005306	Capillary hemangiomas								PMID:14639529	IEA	HPO:probinson	2013-01-09
2018-06-13 22:19:14.910 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Reduced factor V activity instead of Reduced coagulation factor V activity for Reduced coagulation factor V activity: see following line
2018-06-13 22:19:14.910 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:227400	FACTOR V DEFICIENCY	HP:0003225	Reduced factor V activity								OMIM:227400	IEA	HPO:iea	2009-02-17
2018-06-13 22:19:14.911 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating high-density lipoprotein levels instead of Decreased HDL cholesterol concentration for Decreased HDL cholesterol concentration: see following line
2018-06-13 22:19:14.911 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:604091	HYPOALPHALIPOPROTEINEMIA, PRIMARY	HP:0003233	Decreased circulating high-density lipoprotein levels								PMID:9888879	PCS	HPO:probinson	2013-12-15
2018-06-13 22:19:14.911 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating very-low-density lipoprotein levels instead of Increased VLDL cholesterol concentration for Increased VLDL cholesterol concentration: see following line
2018-06-13 22:19:14.911 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:144650	HYPERLIPOPROTEINEMIA, TYPE V	HP:0003362	Increased circulating very-low-density lipoprotein levels								OMIM:144650	TAS	HPO:probinson	2013-03-12
2018-06-13 22:19:14.911 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating high-density lipoprotein levels instead of Decreased HDL cholesterol concentration for Decreased HDL cholesterol concentration: see following line
2018-06-13 22:19:14.911 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:144650	HYPERLIPOPROTEINEMIA, TYPE V	HP:0003233	Decreased circulating high-density lipoprotein levels								OMIM:144650	TAS	HPO:probinson	2013-03-12
2018-06-13 22:19:14.911 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating low-density lipoprotein levels instead of Decreased LDL cholesterol conncentration for Decreased LDL cholesterol conncentration: see following line
2018-06-13 22:19:14.911 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:144650	HYPERLIPOPROTEINEMIA, TYPE V	HP:0003563	Decreased circulating low-density lipoprotein levels								OMIM:144650	TAS	HPO:probinson	2013-03-31
2018-06-13 22:19:14.912 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating chylomicron levels instead of Increased circulating chylomicron concentration for Increased circulating chylomicron concentration: see following line
2018-06-13 22:19:14.912 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:144650	HYPERLIPOPROTEINEMIA, TYPE V	HP:0012238	Increased circulating chylomicron levels								OMIM:144650	TAS	HPO:probinson	2013-04-01
2018-06-13 22:19:14.912 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Aplastic clavicles instead of Aplastic clavicle for Aplastic clavicle: see following line
2018-06-13 22:19:14.912 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:216340	#216340 YUNIS-VARON SYNDROME; YVS;;CLEIDOCRANIAL DYSPLASIA WITH MICROGNATHIA, ABSENT THUMBS, AND DISTALAPHALANGIA	HP:0006660	Aplastic clavicles							OMIM-CS:CHEST_RIBS, STERNUM, CLAVICLES, AND SCAPULAE > ABSENT CLAVICLES	OMIM:216340	TAS	HPO:skoehler	2013-10-22
2018-06-13 22:19:14.912 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Capillary hemangiomas instead of Capillary hemangioma for Capillary hemangioma: see following line
2018-06-13 22:19:14.912 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:612713	KAHRIZI SYNDROME	HP:0005306	Capillary hemangiomas								OMIM:612713	IEA	HPO:skoehler	2010-06-20
2018-06-13 22:19:14.912 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating chylomicron levels instead of Increased circulating chylomicron concentration for Increased circulating chylomicron concentration: see following line
2018-06-13 22:19:14.912 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:238600	#238600 HYPERLIPOPROTEINEMIA, TYPE I;;LIPOPROTEIN LIPASE DEFICIENCY;;LPL DEFICIENCY;;HYPERCHYLOMICRONEMIA, FAMILIAL;;HYPERLIPEMIA, IDIOPATHIC, BURGER-GRUTZ TYPE;;HYPERLIPEMIA, ESSENTIAL FAMILIAL;;LIPASE D DEFICIENCY;;LIPD DEFICIENCY;;HYPERLIPOPROTEINEMIA, TYPE IA;;CHYLOMICRONEMIA, FAMILIAL	HP:0012238	Increased circulating chylomicron levels							OMIM-CS:LAB > HYPERCHYLOMICRONEMIA	OMIM:238600	TAS	HPO:skoehler	2013-04-02
2018-06-13 22:19:14.912 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Increased circulating high-density lipoprotein levels instead of Increased HDL cholesterol concentration for Increased HDL cholesterol concentration: see following line
2018-06-13 22:19:14.913 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:614028	#614028 HYPERALPHALIPOPROTEINEMIA 2; HALP2;;APOLIPOPROTEIN C-III DEFICIENCY	HP:0012184	Increased circulating high-density lipoprotein levels								PMID:19074352	IEA	HPO:probinson	2013-01-09
2018-06-13 22:19:14.913 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating low-density lipoprotein levels instead of Decreased LDL cholesterol conncentration for Decreased LDL cholesterol conncentration: see following line
2018-06-13 22:19:14.913 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:614028	#614028 HYPERALPHALIPOPROTEINEMIA 2; HALP2;;APOLIPOPROTEIN C-III DEFICIENCY	HP:0003563	Decreased circulating low-density lipoprotein levels								PMID:19074352	IEA	HPO:probinson	2013-02-25
2018-06-13 22:19:14.913 ERROR main [main] (V2LineQualityController.java:429) - Found usage of wrong term label Decreased circulating low-density lipoprotein levels instead of Decreased LDL cholesterol conncentration for Decreased LDL cholesterol conncentration: see following line
2018-06-13 22:19:14.913 ERROR main [main] (V2LineQualityController.java:429) - Bad phenotype label: OMIM:607236	HYPOPREBETALIPOPROTEINEMIA, ACANTHOCYTOSIS, RETINITIS PIGMENTOSA,AND PALLIDAL DEGENERATION	HP:0003563	Decreased circulating low-density lipoprotein levels							Hypoprebetalipoproteinemia 	OMIM:607236	TAS	HPO:probinson	2012-07-16
V2 orph about to write this many od3159
2018-06-13 22:19:15.108 ERROR main [main] (Orphanet2BigFile.java:82) - Could not make annotation for term HP:0000118 of disorder Leydig cell hypoplasia 
2018-06-13 22:19:15.108 ERROR main [main] (Orphanet2BigFile.java:83) - Will skip this line: Could not get aspect for term Phenotypic abnormality [HP:0000118]
2018-06-13 22:19:15.487 ERROR main [main] (Orphanet2BigFile.java:82) - Could not make annotation for term HP:0000118 of disorder Male infertility with teratozoospermia due to single gene mutation 
2018-06-13 22:19:15.488 ERROR main [main] (Orphanet2BigFile.java:83) - Will skip this line: Could not get aspect for term Phenotypic abnormality [HP:0000118]
2018-06-13 22:19:15.488 ERROR main [main] (Orphanet2BigFile.java:82) - Could not make annotation for term HP:0000118 of disorder Male infertility with azoospermia or oligozoospermia due to single gene mutation 
2018-06-13 22:19:15.488 ERROR main [main] (Orphanet2BigFile.java:83) - Will skip this line: Could not get aspect for term Phenotypic abnormality [HP:0000118]
2018-06-13 22:19:15.508 ERROR main [main] (Orphanet2BigFile.java:82) - Could not make annotation for term HP:0000118 of disorder Normosmic congenital hypogonadotropic hypogonadism 
2018-06-13 22:19:15.509 ERROR main [main] (Orphanet2BigFile.java:83) - Will skip this line: Could not get aspect for term Phenotypic abnormality [HP:0000118]
2018-06-13 22:19:15.661 ERROR main [main] (Orphanet2BigFile.java:82) - Could not make annotation for term HP:0000118 of disorder Autosomal recessive spastic paraplegia type 15 
2018-06-13 22:19:15.661 ERROR main [main] (Orphanet2BigFile.java:83) - Will skip this line: Could not get aspect for term Phenotypic abnormality [HP:0000118]
We output a total of 66268 orphanet annotations from 3159 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