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A         annotated/OMIM-617187.tab
A         annotated/OMIM-617188.tab
A         annotated/OMIM-617190.tab
A         annotated/OMIM-617193.tab
A         annotated/OMIM-617194.tab
A         annotated/OMIM-617201.tab
A         annotated/OMIM-617205.tab
A         annotated/OMIM-617207.tab
A         annotated/OMIM-617213.tab
A         annotated/OMIM-617214.tab
A         annotated/OMIM-617217.tab
A         annotated/OMIM-617219.tab
A         annotated/OMIM-617222.tab
A         annotated/OMIM-617223.tab
A         annotated/OMIM-617225.tab
A         annotated/OMIM-617228.tab
A         annotated/OMIM-617232.tab
A         annotated/OMIM-617234.tab
A         annotated/OMIM-617235.tab
A         annotated/OMIM-617236.tab
A         annotated/OMIM-617237.tab
A         annotated/OMIM-617238.tab
A         annotated/OMIM-617239.tab
A         annotated/OMIM-617241.tab
A         annotated/OMIM-617243.tab
A         annotated/OMIM-617244.tab
A         annotated/OMIM-617247.tab
A         annotated/OMIM-617248.tab
A         annotated/OMIM-617251.tab
A         annotated/OMIM-617252.tab
A         annotated/OMIM-617253.tab
A         annotated/OMIM-617255.tab
A         annotated/OMIM-617258.tab
A         annotated/OMIM-617260.tab
A         annotated/OMIM-617270.tab
A         annotated/OMIM-617271.tab
A         annotated/OMIM-617272.tab
A         annotated/OMIM-617275.tab
A         annotated/OMIM-617276.tab
A         annotated/OMIM-617280.tab
A         annotated/OMIM-617282.tab
A         annotated/OMIM-617284.tab
A         annotated/OMIM-617290.tab
A         annotated/OMIM-617294.tab
A         annotated/OMIM-617296.tab
A         annotated/OMIM-617297.tab
A         annotated/OMIM-617300.tab
A         annotated/OMIM-617301.tab
A         annotated/OMIM-617302.tab
A         annotated/OMIM-617303.tab
A         annotated/OMIM-617304.tab
A         annotated/OMIM-617306.tab
A         annotated/OMIM-617308.tab
A         annotated/OMIM-617315.tab
A         annotated/OMIM-617319.tab
A         annotated/OMIM-617320.tab
A         annotated/OMIM-617323.tab
A         annotated/OMIM-617330.tab
A         annotated/OMIM-617333.tab
A         annotated/OMIM-617336.tab
A         annotated/OMIM-617337.tab
A         annotated/OMIM-617339.tab
A         annotated/OMIM-617341.tab
A         annotated/OMIM-617343.tab
A         annotated/OMIM-617349.tab
A         annotated/OMIM-617350.tab
A         annotated/OMIM-617360.tab
A         annotated/OMIM-617364.tab
A         annotated/OMIM-617370.tab
A         annotated/OMIM-617383.tab
A         annotated/OMIM-617384.tab
A         annotated/OMIM-617388.tab
A         annotated/OMIM-617389.tab
A         annotated/OMIM-617391.tab
A         annotated/OMIM-617392.tab
A         annotated/OMIM-617393.tab
A         annotated/OMIM-617394.tab
A         annotated/OMIM-617395.tab
A         annotated/OMIM-617396.tab
A         annotated/OMIM-617397.tab
A         annotated/OMIM-617402.tab
A         annotated/OMIM-617404.tab
A         annotated/OMIM-617405.tab
A         annotated/OMIM-617406.tab
A         annotated/OMIM-617408.tab
A         annotated/OMIM-617409.tab
A         annotated/OMIM-617412.tab
A         annotated/OMIM-617425.tab
A         annotated/OMIM-617432.tab
A         annotated/OMIM-617433.tab
A         annotated/OMIM-617439.tab
A         annotated/OMIM-617441.tab
A         annotated/OMIM-617442.tab
A         annotated/OMIM-617450.tab
A         annotated/OMIM-617452.tab
A         annotated/OMIM-617460.tab
A         annotated/OMIM-617466.tab
A         annotated/OMIM-617468.tab
A         annotated/OMIM-617478.tab
A         annotated/OMIM-617506.tab
A         annotated/OMIM-617526.tab
A         annotated/OMIM-617537.tab
A         annotated/OMIM-617784.tab
A         annotated/OMIM-617895.tab
A         annotated/OMIM-617952.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-134700.tab
A         obsoleted-entries/OMIM-144400.tab
A         obsoleted-entries/OMIM-146400.tab
A         obsoleted-entries/OMIM-180070.tab
A         obsoleted-entries/OMIM-181515.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 5022
no change for https://github.com/monarch-initiative/hpo-annotation-data/trunk/rare-diseases since the previous build
[workspace] $ /bin/sh -xe /tmp/jenkins5810405013650124237.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
--2018-05-14 07:50:26--  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: 27154644 (26M) [text/xml]
Saving to: ‘data/en_product4_HPO.xml’

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  9250K .......... .......... .......... .......... .......... 35%  103M 1s
  9300K .......... .......... .......... .......... .......... 35%  125M 1s
  9350K .......... .......... .......... .......... .......... 35%  104M 1s
  9400K .......... .......... .......... .......... .......... 35% 93.4M 1s
  9450K .......... .......... .......... .......... .......... 35%  117M 1s
  9500K .......... .......... .......... .......... .......... 36%  105M 1s
  9550K .......... .......... .......... .......... .......... 36%  107M 1s
  9600K .......... .......... .......... .......... .......... 36%  107M 1s
  9650K .......... .......... .......... .......... .......... 36%  116M 1s
  9700K .......... .......... .......... .......... .......... 36%  119M 1s
  9750K .......... .......... .......... .......... .......... 36% 84.0M 1s
  9800K .......... .......... .......... .......... .......... 37%  127M 1s
  9850K .......... .......... .......... .......... .......... 37%  106M 1s
  9900K .......... .......... .......... .......... .......... 37% 64.3M 1s
  9950K .......... .......... .......... .......... .......... 37% 88.7M 1s
 10000K .......... .......... .......... .......... .......... 37%  104M 1s
 10050K .......... .......... .......... .......... .......... 38%  117M 1s
 10100K .......... .......... .......... .......... .......... 38% 60.2M 1s
 10150K .......... .......... .......... .......... .......... 38%  117M 1s
 10200K .......... .......... .......... .......... .......... 38%  104M 1s
 10250K .......... .......... .......... .......... .......... 38%  109M 1s
 10300K .......... .......... .......... .......... .......... 39%  104M 1s
 10350K .......... .......... .......... .......... .......... 39%  119M 1s
 10400K .......... .......... .......... .......... .......... 39%  105M 1s
 10450K .......... .......... .......... .......... .......... 39%  118M 1s
 10500K .......... .......... .......... .......... .......... 39% 3.16M 1s
 10550K .......... .......... .......... .......... .......... 39% 98.2M 1s
 10600K .......... .......... .......... .......... .......... 40%  113M 1s
 10650K .......... .......... .......... .......... .......... 40%  110M 1s
 10700K .......... .......... .......... .......... .......... 40%  106M 1s
 10750K .......... .......... .......... .......... .......... 40% 64.4M 1s
 10800K .......... .......... .......... .......... .......... 40%  105M 1s
 10850K .......... .......... .......... .......... .......... 41% 64.3M 1s
 10900K .......... .......... .......... .......... .......... 41% 92.8M 1s
 10950K .......... .......... .......... .......... .......... 41%  105M 1s
 11000K .......... .......... .......... .......... .......... 41%  117M 1s
 11050K .......... .......... .......... .......... .......... 41%  109M 1s
 11100K .......... .......... .......... .......... .......... 42%  119M 1s
 11150K .......... .......... .......... .......... .......... 42%  104M 1s
 11200K .......... .......... .......... .......... .......... 42%  117M 1s
 11250K .......... .......... .......... .......... .......... 42% 49.7M 1s
 11300K .......... .......... .......... .......... .......... 42%  117M 1s
 11350K .......... .......... .......... .......... .......... 42%  103M 1s
 11400K .......... .......... .......... .......... .......... 43%  118M 1s
 11450K .......... .......... .......... .......... .......... 43%  105M 1s
 11500K .......... .......... .......... .......... .......... 43%  110M 1s
 11550K .......... .......... .......... .......... .......... 43%  107M 1s
 11600K .......... .......... .......... .......... .......... 43%  118M 1s
 11650K .......... .......... .......... .......... .......... 44%  106M 1s
 11700K .......... .......... .......... .......... .......... 44%  118M 1s
 11750K .......... .......... .......... .......... .......... 44%  109M 1s
 11800K .......... .......... .......... .......... .......... 44% 50.9M 1s
 11850K .......... .......... .......... .......... .......... 44%  120M 1s
 11900K .......... .......... .......... .......... .......... 45%  104M 1s
 11950K .......... .......... .......... .......... .......... 45%  116M 1s
 12000K .......... .......... .......... .......... .......... 45%  118M 1s
 12050K .......... .......... .......... .......... .......... 45%  103M 1s
 12100K .......... .......... .......... .......... .......... 45%  119M 1s
 12150K .......... .......... .......... .......... .......... 46%  107M 1s
 12200K .......... .......... .......... .......... .......... 46%  116M 1s
 12250K .......... .......... .......... .......... .......... 46%  117M 1s
 12300K .......... .......... .......... .......... .......... 46% 98.8M 1s
 12350K .......... .......... .......... .......... .......... 46%  122M 1s
 12400K .......... .......... .......... .......... .......... 46%  118M 1s
 12450K .......... .......... .......... .......... .......... 47%  104M 1s
 12500K .......... .......... .......... .......... .......... 47% 3.66M 1s
 12550K .......... .......... .......... .......... .......... 47% 69.1M 1s
 12600K .......... .......... .......... .......... .......... 47%  114M 1s
 12650K .......... .......... .......... .......... .......... 47%  103M 1s
 12700K .......... .......... .......... .......... .......... 48%  114M 1s
 12750K .......... .......... .......... .......... .......... 48% 65.9M 1s
 12800K .......... .......... .......... .......... .......... 48% 61.3M 1s
 12850K .......... .......... .......... .......... .......... 48% 85.1M 1s
 12900K .......... .......... .......... .......... .......... 48%  110M 1s
 12950K .......... .......... .......... .......... .......... 49%  101M 1s
 13000K .......... .......... .......... .......... .......... 49%  103M 1s
 13050K .......... .......... .......... .......... .......... 49%  113M 1s
 13100K .......... .......... .......... .......... .......... 49% 99.9M 1s
 13150K .......... .......... .......... .......... .......... 49%  118M 1s
 13200K .......... .......... .......... .......... .......... 49% 95.6M 1s
 13250K .......... .......... .......... .......... .......... 50%  108M 1s
 13300K .......... .......... .......... .......... .......... 50% 86.7M 1s
 13350K .......... .......... .......... .......... .......... 50%  104M 1s
 13400K .......... .......... .......... .......... .......... 50% 98.8M 1s
 13450K .......... .......... .......... .......... .......... 50%  101M 1s
 13500K .......... .......... .......... .......... .......... 51% 81.1M 1s
 13550K .......... .......... .......... .......... .......... 51%  107M 1s
 13600K .......... .......... .......... .......... .......... 51% 87.0M 1s
 13650K .......... .......... .......... .......... .......... 51% 67.7M 1s
 13700K .......... .......... .......... .......... .......... 51%  103M 1s
 13750K .......... .......... .......... .......... .......... 52%  114M 1s
 13800K .......... .......... .......... .......... .......... 52%  114M 1s
 13850K .......... .......... .......... .......... .......... 52%  118M 1s
 13900K .......... .......... .......... .......... .......... 52%  105M 1s
 13950K .......... .......... .......... .......... .......... 52%  122M 1s
 14000K .......... .......... .......... .......... .......... 52%  102M 1s
 14050K .......... .......... .......... .......... .......... 53%  119M 1s
 14100K .......... .......... .......... .......... .......... 53%  115M 1s
 14150K .......... .......... .......... .......... .......... 53%  104M 1s
 14200K .......... .......... .......... .......... .......... 53% 51.8M 1s
 14250K .......... .......... .......... .......... .......... 53%  115M 1s
 14300K .......... .......... .......... .......... .......... 54%  109M 1s
 14350K .......... .......... .......... .......... .......... 54% 65.5M 1s
 14400K .......... .......... .......... .......... .......... 54%  104M 1s
 14450K .......... .......... .......... .......... .......... 54%  119M 1s
 14500K .......... .......... .......... .......... .......... 54%  103M 1s
 14550K .......... .......... .......... .......... .......... 55%  116M 1s
 14600K .......... .......... .......... .......... .......... 55% 3.74M 1s
 14650K .......... .......... .......... .......... .......... 55%  114M 1s
 14700K .......... .......... .......... .......... .......... 55%  112M 1s
 14750K .......... .......... .......... .......... .......... 55%  102M 1s
 14800K .......... .......... .......... .......... .......... 55%  116M 1s
 14850K .......... .......... .......... .......... .......... 56%  111M 1s
 14900K .......... .......... .......... .......... .......... 56%  122M 1s
 14950K .......... .......... .......... .......... .......... 56%  107M 1s
 15000K .......... .......... .......... .......... .......... 56%  105M 1s
 15050K .......... .......... .......... .......... .......... 56%  126M 1s
 15100K .......... .......... .......... .......... .......... 57% 59.2M 1s
 15150K .......... .......... .......... .......... .......... 57% 54.3M 1s
 15200K .......... .......... .......... .......... .......... 57%  103M 1s
 15250K .......... .......... .......... .......... .......... 57%  114M 1s
 15300K .......... .......... .......... .......... .......... 57%  117M 1s
 15350K .......... .......... .......... .......... .......... 58%  103M 1s
 15400K .......... .......... .......... .......... .......... 58%  120M 1s
 15450K .......... .......... .......... .......... .......... 58%  105M 1s
 15500K .......... .......... .......... .......... .......... 58%  119M 1s
 15550K .......... .......... .......... .......... .......... 58%  106M 1s
 15600K .......... .......... .......... .......... .......... 59%  103M 1s
 15650K .......... .......... .......... .......... .......... 59%  119M 1s
 15700K .......... .......... .......... .......... .......... 59% 98.3M 1s
 15750K .......... .......... .......... .......... .......... 59%  120M 1s
 15800K .......... .......... .......... .......... .......... 59%  105M 1s
 15850K .......... .......... .......... .......... .......... 59%  119M 1s
 15900K .......... .......... .......... .......... .......... 60%  105M 1s
 15950K .......... .......... .......... .......... .......... 60%  115M 1s
 16000K .......... .......... .......... .......... .......... 60%  121M 1s
 16050K .......... .......... .......... .......... .......... 60%  106M 1s
 16100K .......... .......... .......... .......... .......... 60%  112M 1s
 16150K .......... .......... .......... .......... .......... 61%  102M 1s
 16200K .......... .......... .......... .......... .......... 61% 24.0M 1s
 16250K .......... .......... .......... .......... .......... 61%  106M 1s
 16300K .......... .......... .......... .......... .......... 61%  115M 1s
 16350K .......... .......... .......... .......... .......... 61%  104M 1s
 16400K .......... .......... .......... .......... .......... 62% 59.1M 1s
 16450K .......... .......... .......... .......... .......... 62% 98.1M 1s
 16500K .......... .......... .......... .......... .......... 62% 76.0M 1s
 16550K .......... .......... .......... .......... .......... 62%  102M 1s
 16600K .......... .......... .......... .......... .......... 62%  117M 1s
 16650K .......... .......... .......... .......... .......... 62%  104M 1s
 16700K .......... .......... .......... .......... .......... 63%  119M 1s
 16750K .......... .......... .......... .......... .......... 63% 5.19M 1s
 16800K .......... .......... .......... .......... .......... 63% 69.8M 1s
 16850K .......... .......... .......... .......... .......... 63%  121M 1s
 16900K .......... .......... .......... .......... .......... 63% 99.9M 0s
 16950K .......... .......... .......... .......... .......... 64% 88.4M 0s
 17000K .......... .......... .......... .......... .......... 64% 53.4M 0s
 17050K .......... .......... .......... .......... .......... 64%  116M 0s
 17100K .......... .......... .......... .......... .......... 64% 71.0M 0s
 17150K .......... .......... .......... .......... .......... 64%  106M 0s
 17200K .......... .......... .......... .......... .......... 65%  106M 0s
 17250K .......... .......... .......... .......... .......... 65%  120M 0s
 17300K .......... .......... .......... .......... .......... 65%  100M 0s
 17350K .......... .......... .......... .......... .......... 65%  119M 0s
 17400K .......... .......... .......... .......... .......... 65% 88.2M 0s
 17450K .......... .......... .......... .......... .......... 65%  100M 0s
 17500K .......... .......... .......... .......... .......... 66% 96.4M 0s
 17550K .......... .......... .......... .......... .......... 66% 87.7M 0s
 17600K .......... .......... .......... .......... .......... 66%  116M 0s
 17650K .......... .......... .......... .......... .......... 66%  108M 0s
 17700K .......... .......... .......... .......... .......... 66%  113M 0s
 17750K .......... .......... .......... .......... .......... 67% 97.6M 0s
 17800K .......... .......... .......... .......... .......... 67%  120M 0s
 17850K .......... .......... .......... .......... .......... 67%  104M 0s
 17900K .......... .......... .......... .......... .......... 67%  120M 0s
 17950K .......... .......... .......... .......... .......... 67%  100M 0s
 18000K .......... .......... .......... .......... .......... 68%  101M 0s
 18050K .......... .......... .......... .......... .......... 68%  116M 0s
 18100K .......... .......... .......... .......... .......... 68% 97.9M 0s
 18150K .......... .......... .......... .......... .......... 68% 29.3M 0s
 18200K .......... .......... .......... .......... .......... 68% 74.6M 0s
 18250K .......... .......... .......... .......... .......... 69% 99.3M 0s
 18300K .......... .......... .......... .......... .......... 69%  121M 0s
 18350K .......... .......... .......... .......... .......... 69%  105M 0s
 18400K .......... .......... .......... .......... .......... 69%  114M 0s
 18450K .......... .......... .......... .......... .......... 69%  106M 0s
 18500K .......... .......... .......... .......... .......... 69%  119M 0s
 18550K .......... .......... .......... .......... .......... 70% 97.2M 0s
 18600K .......... .......... .......... .......... .......... 70% 98.4M 0s
 18650K .......... .......... .......... .......... .......... 70%  110M 0s
 18700K .......... .......... .......... .......... .......... 70% 94.0M 0s
 18750K .......... .......... .......... .......... .......... 70%  105M 0s
 18800K .......... .......... .......... .......... .......... 71%  113M 0s
 18850K .......... .......... .......... .......... .......... 71%  107M 0s
 18900K .......... .......... .......... .......... .......... 71% 94.5M 0s
 18950K .......... .......... .......... .......... .......... 71%  107M 0s
 19000K .......... .......... .......... .......... .......... 71% 74.6M 0s
 19050K .......... .......... .......... .......... .......... 72% 5.19M 0s
 19100K .......... .......... .......... .......... .......... 72% 74.2M 0s
 19150K .......... .......... .......... .......... .......... 72% 54.1M 0s
 19200K .......... .......... .......... .......... .......... 72%  109M 0s
 19250K .......... .......... .......... .......... .......... 72% 89.4M 0s
 19300K .......... .......... .......... .......... .......... 72% 82.8M 0s
 19350K .......... .......... .......... .......... .......... 73% 90.9M 0s
 19400K .......... .......... .......... .......... .......... 73% 96.1M 0s
 19450K .......... .......... .......... .......... .......... 73%  109M 0s
 19500K .......... .......... .......... .......... .......... 73%  101M 0s
 19550K .......... .......... .......... .......... .......... 73%  117M 0s
 19600K .......... .......... .......... .......... .......... 74%  104M 0s
 19650K .......... .......... .......... .......... .......... 74%  120M 0s
 19700K .......... .......... .......... .......... .......... 74% 93.9M 0s
 19750K .......... .......... .......... .......... .......... 74%  110M 0s
 19800K .......... .......... .......... .......... .......... 74%  103M 0s
 19850K .......... .......... .......... .......... .......... 75%  104M 0s
 19900K .......... .......... .......... .......... .......... 75%  103M 0s
 19950K .......... .......... .......... .......... .......... 75% 98.9M 0s
 20000K .......... .......... .......... .......... .......... 75%  106M 0s
 20050K .......... .......... .......... .......... .......... 75%  116M 0s
 20100K .......... .......... .......... .......... .......... 75% 96.8M 0s
 20150K .......... .......... .......... .......... .......... 76%  126M 0s
 20200K .......... .......... .......... .......... .......... 76% 98.5M 0s
 20250K .......... .......... .......... .......... .......... 76% 70.4M 0s
 20300K .......... .......... .......... .......... .......... 76%  104M 0s
 20350K .......... .......... .......... .......... .......... 76% 62.6M 0s
 20400K .......... .......... .......... .......... .......... 77% 88.0M 0s
 20450K .......... .......... .......... .......... .......... 77% 96.8M 0s
 20500K .......... .......... .......... .......... .......... 77%  117M 0s
 20550K .......... .......... .......... .......... .......... 77% 98.1M 0s
 20600K .......... .......... .......... .......... .......... 77%  118M 0s
 20650K .......... .......... .......... .......... .......... 78%  103M 0s
 20700K .......... .......... .......... .......... .......... 78%  123M 0s
 20750K .......... .......... .......... .......... .......... 78%  108M 0s
 20800K .......... .......... .......... .......... .......... 78%  106M 0s
 20850K .......... .......... .......... .......... .......... 78%  124M 0s
 20900K .......... .......... .......... .......... .......... 79% 89.0M 0s
 20950K .......... .......... .......... .......... .......... 79% 64.6M 0s
 21000K .......... .......... .......... .......... .......... 79%  115M 0s
 21050K .......... .......... .......... .......... .......... 79%  106M 0s
 21100K .......... .......... .......... .......... .......... 79%  105M 0s
 21150K .......... .......... .......... .......... .......... 79%  123M 0s
 21200K .......... .......... .......... .......... .......... 80%  104M 0s
 21250K .......... .......... .......... .......... .......... 80%  123M 0s
 21300K .......... .......... .......... .......... .......... 80%  104M 0s
 21350K .......... .......... .......... .......... .......... 80%  117M 0s
 21400K .......... .......... .......... .......... .......... 80% 5.11M 0s
 21450K .......... .......... .......... .......... .......... 81% 57.5M 0s
 21500K .......... .......... .......... .......... .......... 81% 94.1M 0s
 21550K .......... .......... .......... .......... .......... 81%  105M 0s
 21600K .......... .......... .......... .......... .......... 81%  121M 0s
 21650K .......... .......... .......... .......... .......... 81% 90.0M 0s
 21700K .......... .......... .......... .......... .......... 82% 91.9M 0s
 21750K .......... .......... .......... .......... .......... 82%  108M 0s
 21800K .......... .......... .......... .......... .......... 82% 41.5M 0s
 21850K .......... .......... .......... .......... .......... 82%  103M 0s
 21900K .......... .......... .......... .......... .......... 82%  119M 0s
 21950K .......... .......... .......... .......... .......... 82%  115M 0s
 22000K .......... .......... .......... .......... .......... 83%  103M 0s
 22050K .......... .......... .......... .......... .......... 83%  110M 0s
 22100K .......... .......... .......... .......... .......... 83%  102M 0s
 22150K .......... .......... .......... .......... .......... 83%  117M 0s
 22200K .......... .......... .......... .......... .......... 83%  105M 0s
 22250K .......... .......... .......... .......... .......... 84%  119M 0s
 22300K .......... .......... .......... .......... .......... 84%  105M 0s
 22350K .......... .......... .......... .......... .......... 84%  108M 0s
 22400K .......... .......... .......... .......... .......... 84%  119M 0s
 22450K .......... .......... .......... .......... .......... 84% 96.6M 0s
 22500K .......... .......... .......... .......... .......... 85%  119M 0s
 22550K .......... .......... .......... .......... .......... 85%  109M 0s
 22600K .......... .......... .......... .......... .......... 85%  106M 0s
 22650K .......... .......... .......... .......... .......... 85%  121M 0s
 22700K .......... .......... .......... .......... .......... 85%  106M 0s
 22750K .......... .......... .......... .......... .......... 85%  115M 0s
 22800K .......... .......... .......... .......... .......... 86% 95.7M 0s
 22850K .......... .......... .......... .......... .......... 86%  116M 0s
 22900K .......... .......... .......... .......... .......... 86%  102M 0s
 22950K .......... .......... .......... .......... .......... 86%  123M 0s
 23000K .......... .......... .......... .......... .......... 86%  109M 0s
 23050K .......... .......... .......... .......... .......... 87% 99.7M 0s
 23100K .......... .......... .......... .......... .......... 87% 99.7M 0s
 23150K .......... .......... .......... .......... .......... 87% 89.9M 0s
 23200K .......... .......... .......... .......... .......... 87%  109M 0s
 23250K .......... .......... .......... .......... .......... 87% 98.9M 0s
 23300K .......... .......... .......... .......... .......... 88%  105M 0s
 23350K .......... .......... .......... .......... .......... 88%  123M 0s
 23400K .......... .......... .......... .......... .......... 88%  107M 0s
 23450K .......... .......... .......... .......... .......... 88%  106M 0s
 23500K .......... .......... .......... .......... .......... 88%  113M 0s
 23550K .......... .......... .......... .......... .......... 88%  116M 0s
 23600K .......... .......... .......... .......... .......... 89% 93.5M 0s
 23650K .......... .......... .......... .......... .......... 89%  109M 0s
 23700K .......... .......... .......... .......... .......... 89%  112M 0s
 23750K .......... .......... .......... .......... .......... 89% 96.7M 0s
 23800K .......... .......... .......... .......... .......... 89%  105M 0s
 23850K .......... .......... .......... .......... .......... 90% 90.5M 0s
 23900K .......... .......... .......... .......... .......... 90% 5.18M 0s
 23950K .......... .......... .......... .......... .......... 90% 95.8M 0s
 24000K .......... .......... .......... .......... .......... 90%  107M 0s
 24050K .......... .......... .......... .......... .......... 90%  112M 0s
 24100K .......... .......... .......... .......... .......... 91%  113M 0s
 24150K .......... .......... .......... .......... .......... 91% 87.2M 0s
 24200K .......... .......... .......... .......... .......... 91% 93.4M 0s
 24250K .......... .......... .......... .......... .......... 91% 99.1M 0s
 24300K .......... .......... .......... .......... .......... 91%  105M 0s
 24350K .......... .......... .......... .......... .......... 92%  120M 0s
 24400K .......... .......... .......... .......... .......... 92% 93.4M 0s
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 24850K .......... .......... .......... .......... .......... 93%  116M 0s
 24900K .......... .......... .......... .......... .......... 94%  102M 0s
 24950K .......... .......... .......... .......... .......... 94%  121M 0s
 25000K .......... .......... .......... .......... .......... 94%  107M 0s
 25050K .......... .......... .......... .......... .......... 94%  119M 0s
 25100K .......... .......... .......... .......... .......... 94%  114M 0s
 25150K .......... .......... .......... .......... .......... 95%  102M 0s
 25200K .......... .......... .......... .......... .......... 95%  118M 0s
 25250K .......... .......... .......... .......... .......... 95%  105M 0s
 25300K .......... .......... .......... .......... .......... 95%  117M 0s
 25350K .......... .......... .......... .......... .......... 95%  107M 0s
 25400K .......... .......... .......... .......... .......... 95%  118M 0s
 25450K .......... .......... .......... .......... .......... 96%  106M 0s
 25500K .......... .......... .......... .......... .......... 96%  114M 0s
 25550K .......... .......... .......... .......... .......... 96%  109M 0s
 25600K .......... .......... .......... .......... .......... 96%  117M 0s
 25650K .......... .......... .......... .......... .......... 96%  106M 0s
 25700K .......... .......... .......... .......... .......... 97%  109M 0s
 25750K .......... .......... .......... .......... .......... 97% 85.6M 0s
 25800K .......... .......... .......... .......... .......... 97%  104M 0s
 25850K .......... .......... .......... .......... .......... 97%  118M 0s
 25900K .......... .......... .......... .......... .......... 97%  103M 0s
 25950K .......... .......... .......... .......... .......... 98%  118M 0s
 26000K .......... .......... .......... .......... .......... 98%  105M 0s
 26050K .......... .......... .......... .......... .......... 98%  119M 0s
 26100K .......... .......... .......... .......... .......... 98%  109M 0s
 26150K .......... .......... .......... .......... .......... 98%  106M 0s
 26200K .......... .......... .......... .......... .......... 98%  114M 0s
 26250K .......... .......... .......... .......... .......... 99% 97.9M 0s
 26300K .......... .......... .......... .......... .......... 99%  115M 0s
 26350K .......... .......... .......... .......... .......... 99%  105M 0s
 26400K .......... .......... .......... .......... .......... 99%  117M 0s
 26450K .......... .......... .......... .......... .......... 99%  106M 0s
 26500K .......... ........                                   100% 2.27M=1.0s

2018-05-14 07:50:27 (25.7 MB/s) - ‘data/en_product4_HPO.xml’ saved [27154644/27154644]

# loads the HPO
wget -N -P data http://purl.obolibrary.org/obo/hp.obo
--2018-05-14 07:50:27--  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]
--2018-05-14 07:50:28--  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: 5909799 (5.6M) [text/plain]
Saving to: ‘data/hp.obo’

     0K .......... .......... .......... .......... ..........  0% 1.48M 4s
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  1950K .......... .......... .......... .......... .......... 34% 15.5M 0s
  2000K .......... .......... .......... .......... .......... 35% 11.5M 0s
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  4250K .......... .......... .......... .......... .......... 74% 11.1M 0s
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  4550K .......... .......... .......... .......... .......... 79% 13.1M 0s
  4600K .......... .......... .......... .......... .......... 80% 11.1M 0s
  4650K .......... .......... .......... .......... .......... 81% 15.7M 0s
  4700K .......... .......... .......... .......... .......... 82% 23.7M 0s
  4750K .......... .......... .......... .......... .......... 83% 23.8M 0s
  4800K .......... .......... .......... .......... .......... 84% 14.6M 0s
  4850K .......... .......... .......... .......... .......... 84% 32.6M 0s
  4900K .......... .......... .......... .......... .......... 85% 69.3M 0s
  4950K .......... .......... .......... .......... .......... 86% 28.2M 0s
  5000K .......... .......... .......... .......... .......... 87% 29.5M 0s
  5050K .......... .......... .......... .......... .......... 88% 19.7M 0s
  5100K .......... .......... .......... .......... .......... 89% 26.3M 0s
  5150K .......... .......... .......... .......... .......... 90% 30.0M 0s
  5200K .......... .......... .......... .......... .......... 90% 18.7M 0s
  5250K .......... .......... .......... .......... .......... 91% 18.8M 0s
  5300K .......... .......... .......... .......... .......... 92% 18.7M 0s
  5350K .......... .......... .......... .......... .......... 93% 32.4M 0s
  5400K .......... .......... .......... .......... .......... 94% 24.1M 0s
  5450K .......... .......... .......... .......... .......... 95% 23.2M 0s
  5500K .......... .......... .......... .......... .......... 96% 27.8M 0s
  5550K .......... .......... .......... .......... .......... 97% 27.0M 0s
  5600K .......... .......... .......... .......... .......... 97% 15.5M 0s
  5650K .......... .......... .......... .......... .......... 98% 29.2M 0s
  5700K .......... .......... .......... .......... .......... 99% 31.1M 0s
  5750K .......... .......... .                               100% 19.5M=0.6s

Last-modified header missing -- time-stamps turned off.
2018-05-14 07:50:28 (10.2 MB/s) - ‘data/hp.obo’ saved [5909799/5909799]

mkdir -p jar
wget -N -P jar https://github.com/monarch-initiative/hpoannotqc/releases/download/v0.2.3/HpoAnnotQc.jar
--2018-05-14 07:50:28--  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%2F20180514%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180514T055054Z&X-Amz-Expires=300&X-Amz-Signature=6908dca3fbeaab8a4442a1e30efd836b8b7d1602696b0cd0b043823129d8af26&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DHpoAnnotQc.jar&response-content-type=application%2Foctet-stream [following]
--2018-05-14 07:50:29--  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%2F20180514%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180514T055054Z&X-Amz-Expires=300&X-Amz-Signature=6908dca3fbeaab8a4442a1e30efd836b8b7d1602696b0cd0b043823129d8af26&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’

     0K .......... .......... .......... .......... ..........  0%  165K 1m44s
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   150K .......... .......... .......... .......... ..........  1%  494K 60s
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  3900K .......... .......... .......... .......... .......... 22% 84.5M 6s
  3950K .......... .......... .......... .......... .......... 23%  104M 6s
  4000K .......... .......... .......... .......... .......... 23%  103M 6s
  4050K .......... .......... .......... .......... .......... 23% 72.6M 6s
  4100K .......... .......... .......... .......... .......... 24% 97.3M 6s
  4150K .......... .......... .......... .......... .......... 24%  103M 6s
  4200K .......... .......... .......... .......... .......... 24%  105M 6s
  4250K .......... .......... .......... .......... .......... 24% 92.3M 6s
  4300K .......... .......... .......... .......... .......... 25%  107M 6s
  4350K .......... .......... .......... .......... .......... 25% 98.9M 6s
  4400K .......... .......... .......... .......... .......... 25%  106M 6s
  4450K .......... .......... .......... .......... .......... 26% 72.1M 5s
  4500K .......... .......... .......... .......... .......... 26%  101M 5s
  4550K .......... .......... .......... .......... .......... 26%  105M 5s
  4600K .......... .......... .......... .......... .......... 26% 97.2M 5s
  4650K .......... .......... .......... .......... .......... 27% 94.5M 5s
  4700K .......... .......... .......... .......... .......... 27%  110M 5s
  4750K .......... .......... .......... .......... .......... 27% 1.37M 5s
  4800K .......... .......... .......... .......... .......... 28%  869K 5s
  4850K .......... .......... .......... .......... .......... 28% 71.7M 5s
  4900K .......... .......... .......... .......... .......... 28% 93.5M 5s
  4950K .......... .......... .......... .......... .......... 29% 92.4M 5s
  5000K .......... .......... .......... .......... .......... 29% 92.1M 5s
  5050K .......... .......... .......... .......... .......... 29% 88.0M 5s
  5100K .......... .......... .......... .......... .......... 29% 95.3M 5s
  5150K .......... .......... .......... .......... .......... 30%  101M 5s
  5200K .......... .......... .......... .......... .......... 30% 80.2M 5s
  5250K .......... .......... .......... .......... .......... 30% 47.6M 5s
  5300K .......... .......... .......... .......... .......... 31% 90.9M 5s
  5350K .......... .......... .......... .......... .......... 31% 94.1M 4s
  5400K .......... .......... .......... .......... .......... 31% 90.3M 4s
  5450K .......... .......... .......... .......... .......... 31% 90.3M 4s
  5500K .......... .......... .......... .......... .......... 32% 95.3M 4s
  5550K .......... .......... .......... .......... .......... 32% 98.0M 4s
  5600K .......... .......... .......... .......... .......... 32% 95.8M 4s
  5650K .......... .......... .......... .......... .......... 33% 73.5M 4s
  5700K .......... .......... .......... .......... .......... 33% 90.9M 4s
  5750K .......... .......... .......... .......... .......... 33%  116M 4s
  5800K .......... .......... .......... .......... .......... 33% 1.51M 4s
  5850K .......... .......... .......... .......... .......... 34%  878K 4s
  5900K .......... .......... .......... .......... .......... 34% 50.6M 4s
  5950K .......... .......... .......... .......... .......... 34% 50.4M 4s
  6000K .......... .......... .......... .......... .......... 35% 97.1M 4s
  6050K .......... .......... .......... .......... .......... 35% 80.6M 4s
  6100K .......... .......... .......... .......... .......... 35%  103M 4s
  6150K .......... .......... .......... .......... .......... 35% 98.9M 4s
  6200K .......... .......... .......... .......... .......... 36%  104M 4s
  6250K .......... .......... .......... .......... .......... 36%  106M 4s
  6300K .......... .......... .......... .......... .......... 36%  102M 4s
  6350K .......... .......... .......... .......... .......... 37%  102M 4s
  6400K .......... .......... .......... .......... .......... 37% 98.1M 4s
  6450K .......... .......... .......... .......... .......... 37% 82.0M 4s
  6500K .......... .......... .......... .......... .......... 38%  104M 3s
  6550K .......... .......... .......... .......... .......... 38%  102M 3s
  6600K .......... .......... .......... .......... .......... 38%  103M 3s
  6650K .......... .......... .......... .......... .......... 38% 92.2M 3s
  6700K .......... .......... .......... .......... .......... 39%  104M 3s
  6750K .......... .......... .......... .......... .......... 39%  101M 3s
  6800K .......... .......... .......... .......... .......... 39%  103M 3s
  6850K .......... .......... .......... .......... .......... 40% 83.4M 3s
  6900K .......... .......... .......... .......... .......... 40%  112M 3s
  6950K .......... .......... .......... .......... .......... 40%  123M 3s
  7000K .......... .......... .......... .......... .......... 40% 1.49M 3s
  7050K .......... .......... .......... .......... .......... 41%  880K 3s
  7100K .......... .......... .......... .......... .......... 41% 58.5M 3s
  7150K .......... .......... .......... .......... .......... 41% 56.8M 3s
  7200K .......... .......... .......... .......... .......... 42% 97.6M 3s
  7250K .......... .......... .......... .......... .......... 42% 82.2M 3s
  7300K .......... .......... .......... .......... .......... 42% 99.6M 3s
  7350K .......... .......... .......... .......... .......... 42% 99.9M 3s
  7400K .......... .......... .......... .......... .......... 43%  102M 3s
  7450K .......... .......... .......... .......... .......... 43% 89.9M 3s
  7500K .......... .......... .......... .......... .......... 43%  101M 3s
  7550K .......... .......... .......... .......... .......... 44%  102M 3s
  7600K .......... .......... .......... .......... .......... 44%  104M 3s
  7650K .......... .......... .......... .......... .......... 44% 82.6M 3s
  7700K .......... .......... .......... .......... .......... 44% 99.7M 3s
  7750K .......... .......... .......... .......... .......... 45%  104M 3s
  7800K .......... .......... .......... .......... .......... 45%  103M 3s
  7850K .......... .......... .......... .......... .......... 45% 93.6M 3s
  7900K .......... .......... .......... .......... .......... 46%  102M 3s
  7950K .......... .......... .......... .......... .......... 46% 99.5M 3s
  8000K .......... .......... .......... .......... .......... 46%  105M 3s
  8050K .......... .......... .......... .......... .......... 46% 83.0M 3s
  8100K .......... .......... .......... .......... .......... 47%  103M 2s
  8150K .......... .......... .......... .......... .......... 47%  101M 2s
  8200K .......... .......... .......... .......... .......... 47%  106M 2s
  8250K .......... .......... .......... .......... .......... 48%  114M 2s
  8300K .......... .......... .......... .......... .......... 48%  120M 2s
  8350K .......... .......... .......... .......... .......... 48% 1.58M 2s
  8400K .......... .......... .......... .......... .......... 49% 89.3M 2s
  8450K .......... .......... .......... .......... .......... 49%  879K 2s
  8500K .......... .......... .......... .......... .......... 49% 78.7M 2s
  8550K .......... .......... .......... .......... .......... 49% 48.9M 2s
  8600K .......... .......... .......... .......... .......... 50% 87.9M 2s
  8650K .......... .......... .......... .......... .......... 50% 94.1M 2s
  8700K .......... .......... .......... .......... .......... 50% 97.5M 2s
  8750K .......... .......... .......... .......... .......... 51% 98.3M 2s
  8800K .......... .......... .......... .......... .......... 51%  102M 2s
  8850K .......... .......... .......... .......... .......... 51% 81.4M 2s
  8900K .......... .......... .......... .......... .......... 51%  102M 2s
  8950K .......... .......... .......... .......... .......... 52% 98.1M 2s
  9000K .......... .......... .......... .......... .......... 52%  102M 2s
  9050K .......... .......... .......... .......... .......... 52% 96.5M 2s
  9100K .......... .......... .......... .......... .......... 53%  103M 2s
  9150K .......... .......... .......... .......... .......... 53% 98.6M 2s
  9200K .......... .......... .......... .......... .......... 53%  103M 2s
  9250K .......... .......... .......... .......... .......... 53% 82.5M 2s
  9300K .......... .......... .......... .......... .......... 54%  106M 2s
  9350K .......... .......... .......... .......... .......... 54%  103M 2s
  9400K .......... .......... .......... .......... .......... 54%  102M 2s
  9450K .......... .......... .......... .......... .......... 55% 96.0M 2s
  9500K .......... .......... .......... .......... .......... 55% 98.3M 2s
  9550K .......... .......... .......... .......... .......... 55%  105M 2s
  9600K .......... .......... .......... .......... .......... 55%  110M 2s
  9650K .......... .......... .......... .......... .......... 56% 88.6M 2s
  9700K .......... .......... .......... .......... .......... 56%  111M 2s
  9750K .......... .......... .......... .......... .......... 56%  107M 2s
  9800K .......... .......... .......... .......... .......... 57%  112M 2s
  9850K .......... .......... .......... .......... .......... 57%  111M 2s
  9900K .......... .......... .......... .......... .......... 57%  132M 2s
  9950K .......... .......... .......... .......... .......... 58%  130M 2s
 10000K .......... .......... .......... .......... .......... 58% 1.54M 2s
 10050K .......... .......... .......... .......... .......... 58%  927K 2s
 10100K .......... .......... .......... .......... .......... 58% 84.5M 2s
 10150K .......... .......... .......... .......... .......... 59% 95.6M 2s
 10200K .......... .......... .......... .......... .......... 59% 42.5M 2s
 10250K .......... .......... .......... .......... .......... 59% 78.7M 2s
 10300K .......... .......... .......... .......... .......... 60% 97.9M 2s
 10350K .......... .......... .......... .......... .......... 60% 99.4M 2s
 10400K .......... .......... .......... .......... .......... 60%  106M 2s
 10450K .......... .......... .......... .......... .......... 60% 81.7M 2s
 10500K .......... .......... .......... .......... .......... 61% 98.1M 2s
 10550K .......... .......... .......... .......... .......... 61%  105M 2s
 10600K .......... .......... .......... .......... .......... 61%  101M 2s
 10650K .......... .......... .......... .......... .......... 62% 91.3M 1s
 10700K .......... .......... .......... .......... .......... 62% 99.3M 1s
 10750K .......... .......... .......... .......... .......... 62% 98.3M 1s
 10800K .......... .......... .......... .......... .......... 62%  103M 1s
 10850K .......... .......... .......... .......... .......... 63% 83.4M 1s
 10900K .......... .......... .......... .......... .......... 63%  105M 1s
 10950K .......... .......... .......... .......... .......... 63%  101M 1s
 11000K .......... .......... .......... .......... .......... 64% 98.1M 1s
 11050K .......... .......... .......... .......... .......... 64% 93.6M 1s
 11100K .......... .......... .......... .......... .......... 64%  101M 1s
 11150K .......... .......... .......... .......... .......... 64%  103M 1s
 11200K .......... .......... .......... .......... .......... 65%  103M 1s
 11250K .......... .......... .......... .......... .......... 65% 78.7M 1s
 11300K .......... .......... .......... .......... .......... 65%  103M 1s
 11350K .......... .......... .......... .......... .......... 66%  102M 1s
 11400K .......... .......... .......... .......... .......... 66%  103M 1s
 11450K .......... .......... .......... .......... .......... 66% 92.3M 1s
 11500K .......... .......... .......... .......... .......... 67%  105M 1s
 11550K .......... .......... .......... .......... .......... 67%  109M 1s
 11600K .......... .......... .......... .......... .......... 67%  109M 1s
 11650K .......... .......... .......... .......... .......... 67% 90.0M 1s
 11700K .......... .......... .......... .......... .......... 68%  112M 1s
 11750K .......... .......... .......... .......... .......... 68%  114M 1s
 11800K .......... .......... .......... .......... .......... 68%  126M 1s
 11850K .......... .......... .......... .......... .......... 69%  123M 1s
 11900K .......... .......... .......... .......... .......... 69%  130M 1s
 11950K .......... .......... .......... .......... .......... 69% 1.74M 1s
 12000K .......... .......... .......... .......... .......... 69% 90.3M 1s
 12050K .......... .......... .......... .......... .......... 70%  925K 1s
 12100K .......... .......... .......... .......... .......... 70% 85.6M 1s
 12150K .......... .......... .......... .......... .......... 70% 82.3M 1s
 12200K .......... .......... .......... .......... .......... 71% 69.5M 1s
 12250K .......... .......... .......... .......... .......... 71% 93.1M 1s
 12300K .......... .......... .......... .......... .......... 71% 95.5M 1s
 12350K .......... .......... .......... .......... .......... 71%  102M 1s
 12400K .......... .......... .......... .......... .......... 72%  102M 1s
 12450K .......... .......... .......... .......... .......... 72% 83.1M 1s
 12500K .......... .......... .......... .......... .......... 72%  103M 1s
 12550K .......... .......... .......... .......... .......... 73% 99.5M 1s
 12600K .......... .......... .......... .......... .......... 73%  104M 1s
 12650K .......... .......... .......... .......... .......... 73% 96.8M 1s
 12700K .......... .......... .......... .......... .......... 73%  103M 1s
 12750K .......... .......... .......... .......... .......... 74%  103M 1s
 12800K .......... .......... .......... .......... .......... 74% 99.5M 1s
 12850K .......... .......... .......... .......... .......... 74% 83.3M 1s
 12900K .......... .......... .......... .......... .......... 75%  104M 1s
 12950K .......... .......... .......... .......... .......... 75%  101M 1s
 13000K .......... .......... .......... .......... .......... 75%  104M 1s
 13050K .......... .......... .......... .......... .......... 76% 92.6M 1s
 13100K .......... .......... .......... .......... .......... 76%  107M 1s
 13150K .......... .......... .......... .......... .......... 76%  108M 1s
 13200K .......... .......... .......... .......... .......... 76% 38.8M 1s
 13250K .......... .......... .......... .......... .......... 77% 80.4M 1s
 13300K .......... .......... .......... .......... .......... 77%  104M 1s
 13350K .......... .......... .......... .......... .......... 77%  112M 1s
 13400K .......... .......... .......... .......... .......... 78%  114M 1s
 13450K .......... .......... .......... .......... .......... 78%  103M 1s
 13500K .......... .......... .......... .......... .......... 78%  113M 1s
 13550K .......... .......... .......... .......... .......... 78%  110M 1s
 13600K .......... .......... .......... .......... .......... 79%  109M 1s
 13650K .......... .......... .......... .......... .......... 79% 89.5M 1s
 13700K .......... .......... .......... .......... .......... 79%  109M 1s
 13750K .......... .......... .......... .......... .......... 80%  110M 1s
 13800K .......... .......... .......... .......... .......... 80%  112M 1s
 13850K .......... .......... .......... .......... .......... 80%  103M 1s
 13900K .......... .......... .......... .......... .......... 80%  113M 1s
 13950K .......... .......... .......... .......... .......... 81%  114M 1s
 14000K .......... .......... .......... .......... .......... 81% 1.86M 1s
 14050K .......... .......... .......... .......... .......... 81% 48.2M 1s
 14100K .......... .......... .......... .......... .......... 82%  931K 1s
 14150K .......... .......... .......... .......... .......... 82% 77.6M 1s
 14200K .......... .......... .......... .......... .......... 82% 93.4M 1s
 14250K .......... .......... .......... .......... .......... 82% 95.7M 1s
 14300K .......... .......... .......... .......... .......... 83%  103M 1s
 14350K .......... .......... .......... .......... .......... 83% 73.0M 1s
 14400K .......... .......... .......... .......... .......... 83%  103M 1s
 14450K .......... .......... .......... .......... .......... 84% 80.5M 0s
 14500K .......... .......... .......... .......... .......... 84%  101M 0s
 14550K .......... .......... .......... .......... .......... 84% 98.4M 0s
 14600K .......... .......... .......... .......... .......... 84% 96.4M 0s
 14650K .......... .......... .......... .......... .......... 85% 95.4M 0s
 14700K .......... .......... .......... .......... .......... 85%  103M 0s
 14750K .......... .......... .......... .......... .......... 85%  101M 0s
 14800K .......... .......... .......... .......... .......... 86%  106M 0s
 14850K .......... .......... .......... .......... .......... 86% 80.6M 0s
 14900K .......... .......... .......... .......... .......... 86%  101M 0s
 14950K .......... .......... .......... .......... .......... 87%  101M 0s
 15000K .......... .......... .......... .......... .......... 87%  104M 0s
 15050K .......... .......... .......... .......... .......... 87% 97.1M 0s
 15100K .......... .......... .......... .......... .......... 87% 99.7M 0s
 15150K .......... .......... .......... .......... .......... 88%  113M 0s
 15200K .......... .......... .......... .......... .......... 88%  109M 0s
 15250K .......... .......... .......... .......... .......... 88% 88.5M 0s
 15300K .......... .......... .......... .......... .......... 89%  107M 0s
 15350K .......... .......... .......... .......... .......... 89% 96.2M 0s
 15400K .......... .......... .......... .......... .......... 89%  114M 0s
 15450K .......... .......... .......... .......... .......... 89%  105M 0s
 15500K .......... .......... .......... .......... .......... 90%  110M 0s
 15550K .......... .......... .......... .......... .......... 90%  109M 0s
 15600K .......... .......... .......... .......... .......... 90%  112M 0s
 15650K .......... .......... .......... .......... .......... 91% 87.3M 0s
 15700K .......... .......... .......... .......... .......... 91%  114M 0s
 15750K .......... .......... .......... .......... .......... 91%  113M 0s
 15800K .......... .......... .......... .......... .......... 91%  109M 0s
 15850K .......... .......... .......... .......... .......... 92%  106M 0s
 15900K .......... .......... .......... .......... .......... 92%  110M 0s
 15950K .......... .......... .......... .......... .......... 92%  108M 0s
 16000K .......... .......... .......... .......... .......... 93%  114M 0s
 16050K .......... .......... .......... .......... .......... 93% 89.9M 0s
 16100K .......... .......... .......... .......... .......... 93%  110M 0s
 16150K .......... .......... .......... .......... .......... 93%  109M 0s
 16200K .......... .......... .......... .......... .......... 94%  110M 0s
 16250K .......... .......... .......... .......... .......... 94%  103M 0s
 16300K .......... .......... .......... .......... .......... 94%  116M 0s
 16350K .......... .......... .......... .......... .......... 95%  110M 0s
 16400K .......... .......... .......... .......... .......... 95%  108M 0s
 16450K .......... .......... .......... .......... .......... 95% 2.03M 0s
 16500K .......... .......... .......... .......... .......... 96% 61.2M 0s
 16550K .......... .......... .......... .......... .......... 96% 84.0M 0s
 16600K .......... .......... .......... .......... .......... 96%  914K 0s
 16650K .......... .......... .......... .......... .......... 96% 61.1M 0s
 16700K .......... .......... .......... .......... .......... 97% 28.3M 0s
 16750K .......... .......... .......... .......... .......... 97% 54.0M 0s
 16800K .......... .......... .......... .......... .......... 97% 45.1M 0s
 16850K .......... .......... .......... .......... .......... 98% 75.0M 0s
 16900K .......... .......... .......... .......... .......... 98% 90.0M 0s
 16950K .......... .......... .......... .......... .......... 98% 92.1M 0s
 17000K .......... .......... .......... .......... .......... 98% 99.5M 0s
 17050K .......... .......... .......... .......... .......... 99% 96.3M 0s
 17100K .......... .......... .......... .......... .......... 99%  103M 0s
 17150K .......... .......... .......... .......... .......... 99%  108M 0s
 17200K .......... .......... .......... .....                100%  114M=2.7s

2018-05-14 07:50:32 (6.15 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"
2018-05-14 07:50:33,188 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.
2018-05-14 07:50:35.777 ERROR main [main] (V2SmallFileParser.java:76) - WARNING skipping annotation because we could not find term for (version mismatch?)HP:0410145
We finished with the input of 7267 V2 small files with a total of 92241 annotation lines
2018-05-14 07:50:36.327 ERROR main [main] (OrphanetXML2HpoDiseaseModelParser.java:92) - [ERROR] Could not find TermId for Orphanet HPO ID "HP:0001676"
2018-05-14 07:50:36.375 ERROR main [main] (OrphanetXML2HpoDiseaseModelParser.java:92) - [ERROR] Could not find TermId for Orphanet HPO ID "HP:0011607"
2018-05-14 07:50:36.475 ERROR main [main] (OrphanetXML2HpoDiseaseModelParser.java:92) - [ERROR] Could not find TermId for Orphanet HPO ID "HP:0002755"
We extracted 3113 orphanet disorders with 65318 annotations 
2018-05-14 07:50:36.742 FATAL main [main] (BigFileCommand.java:66) - [ERROR] Could not output V2 big file
java.io.IOException: No space left on device
	at java.io.FileOutputStream.writeBytes(Native Method) ~[?:1.8.0_151]
	at java.io.FileOutputStream.write(FileOutputStream.java:326) ~[?:1.8.0_151]
	at sun.nio.cs.StreamEncoder.writeBytes(StreamEncoder.java:221) ~[?:1.8.0_151]
	at sun.nio.cs.StreamEncoder.implWrite(StreamEncoder.java:282) ~[?:1.8.0_151]
	at sun.nio.cs.StreamEncoder.write(StreamEncoder.java:125) ~[?:1.8.0_151]
	at java.io.OutputStreamWriter.write(OutputStreamWriter.java:207) ~[?:1.8.0_151]
	at java.io.BufferedWriter.flushBuffer(BufferedWriter.java:129) ~[?:1.8.0_151]
	at java.io.BufferedWriter.write(BufferedWriter.java:230) ~[?:1.8.0_151]
	at java.io.Writer.write(Writer.java:157) ~[?:1.8.0_151]
	at org.monarchinitiative.hpoannotqc.bigfile.V2BigFile.outputBigFileV2(V2BigFile.java:70) ~[HpoAnnotQc.jar:0.2.4]
	at org.monarchinitiative.hpoannotqc.bigfile.BigFileWriter.outputBigFileV2(BigFileWriter.java:60) ~[HpoAnnotQc.jar:0.2.4]
	at org.monarchinitiative.hpoannotqc.cmd.BigFileCommand.execute(BigFileCommand.java:62) [HpoAnnotQc.jar:0.2.4]
	at org.monarchinitiative.hpoannotqc.Main.main(Main.java:24) [HpoAnnotQc.jar:0.2.4]
#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
ERROR: Build step failed with exception
java.io.IOException: No space left on device
	at sun.nio.ch.FileDispatcherImpl.pwrite0(Native Method)
	at sun.nio.ch.FileDispatcherImpl.pwrite(FileDispatcherImpl.java:66)
	at sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:89)
	at sun.nio.ch.IOUtil.write(IOUtil.java:51)
	at sun.nio.ch.FileChannelImpl.writeInternal(FileChannelImpl.java:778)
	at sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:764)
	at sun.nio.ch.FileChannelImpl.transferFromFileChannel(FileChannelImpl.java:636)
	at sun.nio.ch.FileChannelImpl.transferFrom(FileChannelImpl.java:708)
	at org.apache.tools.ant.util.ResourceUtils.copyResource(ResourceUtils.java:532)
	at org.apache.tools.ant.util.FileUtils.copyFile(FileUtils.java:559)
	at org.apache.tools.ant.taskdefs.Copy.doFileOperations(Copy.java:899)
Caused: Failed to copy /var/lib/jenkins/jobs/hpo.annotations.2018/workspace/misc_2018/phenotype.hpoa to /var/lib/jenkins/jobs/hpo.annotations.2018/builds/5059/archive/misc_2018/phenotype.hpoa due to No space left on device
	at org.apache.tools.ant.taskdefs.Copy.doFileOperations(Copy.java:914)
	at org.apache.tools.ant.taskdefs.Copy.execute(Copy.java:567)
	at hudson.Util.copyFile(Util.java:1190)
	at hudson.FilePath$42$1.visit(FilePath.java:2151)
	at hudson.util.DirScanner.scanSingle(DirScanner.java:49)
	at hudson.FilePath$ExplicitlySpecifiedDirScanner.scan(FilePath.java:2833)
	at hudson.FilePath$42.invoke(FilePath.java:2145)
	at hudson.FilePath$42.invoke(FilePath.java:2138)
	at hudson.FilePath.act(FilePath.java:997)
	at hudson.FilePath.act(FilePath.java:975)
	at hudson.FilePath.copyRecursiveTo(FilePath.java:2138)
	at jenkins.model.StandardArtifactManager.archive(StandardArtifactManager.java:61)
	at hudson.tasks.ArtifactArchiver.perform(ArtifactArchiver.java:245)
	at hudson.tasks.BuildStepCompatibilityLayer.perform(BuildStepCompatibilityLayer.java:81)
	at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20)
	at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:744)
	at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:690)
	at hudson.model.Build$BuildExecution.post2(Build.java:186)
	at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:635)
	at hudson.model.Run.execute(Run.java:1749)
	at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
	at hudson.model.ResourceController.execute(ResourceController.java:97)
	at hudson.model.Executor.run(Executor.java:421)
Build step 'Archive the artifacts' marked build as failure
Sending e-mails to: sebastian.koehler@charite.de peter.robinson@jax.org
ERROR: 452 4.3.1 Insufficient system storage

com.sun.mail.smtp.SMTPSendFailedException: 452 4.3.1 Insufficient system storage

	at com.sun.mail.smtp.SMTPTransport.issueSendCommand(SMTPTransport.java:2057)
	at com.sun.mail.smtp.SMTPTransport.mailFrom(SMTPTransport.java:1580)
	at com.sun.mail.smtp.SMTPTransport.sendMessage(SMTPTransport.java:1097)
	at javax.mail.Transport.send0(Transport.java:195)
	at javax.mail.Transport.send(Transport.java:124)
	at hudson.tasks.MailSender.run(MailSender.java:128)
	at hudson.tasks.Mailer.perform(Mailer.java:145)
	at hudson.tasks.BuildStepCompatibilityLayer.perform(BuildStepCompatibilityLayer.java:81)
	at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20)
	at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:744)
	at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:690)
	at hudson.model.Build$BuildExecution.post2(Build.java:186)
	at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:635)
	at hudson.model.Run.execute(Run.java:1749)
	at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
	at hudson.model.ResourceController.execute(ResourceController.java:97)
	at hudson.model.Executor.run(Executor.java:421)
Finished: FAILURE