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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
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A         misc/cataract/MIM-154050.tab
A         misc/cataract/MIM-600897.tab
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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
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A         obsoleted-entries/OMIM-312100.tab
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A         obsoleted-entries/OMIM-315000.tab
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At revision 5049
[workspace] $ /bin/sh -xe /tmp/jenkins5662970453290788057.sh
+ make -C misc
make: Entering directory '/var/lib/jenkins/jobs/hpo.annotations/workspace/misc'
mkdir -p data
# load orphanet data
wget -N -P data http://www.orphadata.org/data/xml/en_product4_HPO.xml
--2018-06-13 21:42:25--  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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  2200K .......... .......... .......... .......... ..........  8% 66.1M 5s
  2250K .......... .......... .......... .......... ..........  8%  110M 5s
  2300K .......... .......... .......... .......... ..........  8% 72.6M 5s
  2350K .......... .......... .......... .......... ..........  8% 98.5M 5s
  2400K .......... .......... .......... .......... ..........  9% 76.4M 5s
  2450K .......... .......... .......... .......... ..........  9% 1.79M 5s
  2500K .......... .......... .......... .......... ..........  9%  102M 5s
  2550K .......... .......... .......... .......... ..........  9% 68.4M 5s
  2600K .......... .......... .......... .......... ..........  9%  112M 5s
  2650K .......... .......... .......... .......... .......... 10% 71.1M 5s
  2700K .......... .......... .......... .......... .......... 10%  112M 5s
  2750K .......... .......... .......... .......... .......... 10% 89.6M 4s
  2800K .......... .......... .......... .......... .......... 10% 68.5M 4s
  2850K .......... .......... .......... .......... .......... 10% 73.0M 4s
  2900K .......... .......... .......... .......... .......... 10% 98.7M 4s
  2950K .......... .......... .......... .......... .......... 11%  121M 4s
  3000K .......... .......... .......... .......... .......... 11% 1.83M 4s
  3050K .......... .......... .......... .......... .......... 11% 77.4M 4s
  3100K .......... .......... .......... .......... .......... 11% 93.2M 4s
  3150K .......... .......... .......... .......... .......... 11% 84.7M 4s
  3200K .......... .......... .......... .......... .......... 12% 90.5M 4s
  3250K .......... .......... .......... .......... .......... 12%  115M 4s
  3300K .......... .......... .......... .......... .......... 12% 79.8M 4s
  3350K .......... .......... .......... .......... .......... 12% 97.2M 4s
  3400K .......... .......... .......... .......... .......... 12% 86.9M 4s
  3450K .......... .......... .......... .......... .......... 13% 97.7M 4s
  3500K .......... .......... .......... .......... .......... 13%  112M 4s
  3550K .......... .......... .......... .......... .......... 13% 71.2M 4s
  3600K .......... .......... .......... .......... .......... 13%  112M 4s
  3650K .......... .......... .......... .......... .......... 13% 86.1M 4s
  3700K .......... .......... .......... .......... .......... 13% 1.90M 4s
  3750K .......... .......... .......... .......... .......... 14% 73.6M 4s
  3800K .......... .......... .......... .......... .......... 14% 86.9M 4s
  3850K .......... .......... .......... .......... .......... 14% 89.6M 3s
  3900K .......... .......... .......... .......... .......... 14%  119M 3s
  3950K .......... .......... .......... .......... .......... 14% 82.8M 3s
  4000K .......... .......... .......... .......... .......... 15% 76.1M 3s
  4050K .......... .......... .......... .......... .......... 15%  100M 3s
  4100K .......... .......... .......... .......... .......... 15% 88.2M 3s
  4150K .......... .......... .......... .......... .......... 15%  101M 3s
  4200K .......... .......... .......... .......... .......... 15% 85.0M 3s
  4250K .......... .......... .......... .......... .......... 15% 87.5M 3s
  4300K .......... .......... .......... .......... .......... 16%  110M 3s
  4350K .......... .......... .......... .......... .......... 16% 84.1M 3s
  4400K .......... .......... .......... .......... .......... 16% 75.9M 3s
  4450K .......... .......... .......... .......... .......... 16% 69.6M 3s
  4500K .......... .......... .......... .......... .......... 16%  100M 3s
  4550K .......... .......... .......... .......... .......... 17% 87.3M 3s
  4600K .......... .......... .......... .......... .......... 17% 2.06M 3s
  4650K .......... .......... .......... .......... .......... 17% 82.0M 3s
  4700K .......... .......... .......... .......... .......... 17% 82.1M 3s
  4750K .......... .......... .......... .......... .......... 17% 74.2M 3s
  4800K .......... .......... .......... .......... .......... 18% 88.5M 3s
  4850K .......... .......... .......... .......... .......... 18% 68.8M 3s
  4900K .......... .......... .......... .......... .......... 18%  101M 3s
  4950K .......... .......... .......... .......... .......... 18% 84.8M 3s
  5000K .......... .......... .......... .......... .......... 18% 96.3M 3s
  5050K .......... .......... .......... .......... .......... 18% 65.8M 3s
  5100K .......... .......... .......... .......... .......... 19% 75.3M 3s
  5150K .......... .......... .......... .......... .......... 19% 67.5M 3s
  5200K .......... .......... .......... .......... .......... 19%  115M 3s
  5250K .......... .......... .......... .......... .......... 19% 98.9M 3s
  5300K .......... .......... .......... .......... .......... 19% 76.0M 3s
  5350K .......... .......... .......... .......... .......... 20%  112M 2s
  5400K .......... .......... .......... .......... .......... 20%  111M 2s
  5450K .......... .......... .......... .......... .......... 20% 78.7M 2s
  5500K .......... .......... .......... .......... .......... 20% 92.4M 2s
  5550K .......... .......... .......... .......... .......... 20%  104M 2s
  5600K .......... .......... .......... .......... .......... 20% 2.30M 2s
  5650K .......... .......... .......... .......... .......... 21% 82.4M 2s
  5700K .......... .......... .......... .......... .......... 21% 81.0M 2s
  5750K .......... .......... .......... .......... .......... 21%  112M 2s
  5800K .......... .......... .......... .......... .......... 21% 69.6M 2s
  5850K .......... .......... .......... .......... .......... 21% 81.3M 2s
  5900K .......... .......... .......... .......... .......... 22%  117M 2s
  5950K .......... .......... .......... .......... .......... 22% 75.3M 2s
  6000K .......... .......... .......... .......... .......... 22%  101M 2s
  6050K .......... .......... .......... .......... .......... 22% 68.4M 2s
  6100K .......... .......... .......... .......... .......... 22%  117M 2s
  6150K .......... .......... .......... .......... .......... 23% 94.7M 2s
  6200K .......... .......... .......... .......... .......... 23% 83.2M 2s
  6250K .......... .......... .......... .......... .......... 23%  100M 2s
  6300K .......... .......... .......... .......... .......... 23% 91.5M 2s
  6350K .......... .......... .......... .......... .......... 23%  103M 2s
  6400K .......... .......... .......... .......... .......... 23% 99.8M 2s
  6450K .......... .......... .......... .......... .......... 24% 99.3M 2s
  6500K .......... .......... .......... .......... .......... 24% 97.1M 2s
  6550K .......... .......... .......... .......... .......... 24%  111M 2s
  6600K .......... .......... .......... .......... .......... 24% 99.0M 2s
  6650K .......... .......... .......... .......... .......... 24% 87.5M 2s
  6700K .......... .......... .......... .......... .......... 25%  116M 2s
  6750K .......... .......... .......... .......... .......... 25%  113M 2s
  6800K .......... .......... .......... .......... .......... 25% 92.8M 2s
  6850K .......... .......... .......... .......... .......... 25%  113M 2s
  6900K .......... .......... .......... .......... .......... 25% 2.47M 2s
  6950K .......... .......... .......... .......... .......... 26% 86.5M 2s
  7000K .......... .......... .......... .......... .......... 26%  100M 2s
  7050K .......... .......... .......... .......... .......... 26% 98.1M 2s
  7100K .......... .......... .......... .......... .......... 26% 91.8M 2s
  7150K .......... .......... .......... .......... .......... 26%  116M 2s
  7200K .......... .......... .......... .......... .......... 26%  101M 2s
  7250K .......... .......... .......... .......... .......... 27% 91.7M 2s
  7300K .......... .......... .......... .......... .......... 27% 75.0M 2s
  7350K .......... .......... .......... .......... .......... 27% 94.0M 2s
  7400K .......... .......... .......... .......... .......... 27%  111M 2s
  7450K .......... .......... .......... .......... .......... 27% 75.6M 2s
  7500K .......... .......... .......... .......... .......... 28%  106M 2s
  7550K .......... .......... .......... .......... .......... 28% 79.8M 2s
  7600K .......... .......... .......... .......... .......... 28%  114M 2s
  7650K .......... .......... .......... .......... .......... 28% 85.5M 2s
  7700K .......... .......... .......... .......... .......... 28%  103M 2s
  7750K .......... .......... .......... .......... .......... 28% 80.5M 2s
  7800K .......... .......... .......... .......... .......... 29%  113M 2s
  7850K .......... .......... .......... .......... .......... 29%  105M 2s
  7900K .......... .......... .......... .......... .......... 29% 85.1M 2s
  7950K .......... .......... .......... .......... .......... 29%  113M 2s
  8000K .......... .......... .......... .......... .......... 29% 95.9M 2s
  8050K .......... .......... .......... .......... .......... 30%  117M 2s
  8100K .......... .......... .......... .......... .......... 30% 96.8M 2s
  8150K .......... .......... .......... .......... .......... 30% 85.3M 2s
  8200K .......... .......... .......... .......... .......... 30% 97.1M 2s
  8250K .......... .......... .......... .......... .......... 30% 96.0M 2s
  8300K .......... .......... .......... .......... .......... 31% 93.6M 2s
  8350K .......... .......... .......... .......... .......... 31%  103M 2s
  8400K .......... .......... .......... .......... .......... 31%  112M 2s
  8450K .......... .......... .......... .......... .......... 31% 96.7M 2s
  8500K .......... .......... .......... .......... .......... 31% 2.83M 2s
  8550K .......... .......... .......... .......... .......... 31%  112M 2s
  8600K .......... .......... .......... .......... .......... 32% 87.1M 2s
  8650K .......... .......... .......... .......... .......... 32% 81.6M 1s
  8700K .......... .......... .......... .......... .......... 32% 98.7M 1s
  8750K .......... .......... .......... .......... .......... 32% 93.7M 1s
  8800K .......... .......... .......... .......... .......... 32%  105M 1s
  8850K .......... .......... .......... .......... .......... 33% 85.4M 1s
  8900K .......... .......... .......... .......... .......... 33% 86.4M 1s
  8950K .......... .......... .......... .......... .......... 33%  119M 1s
  9000K .......... .......... .......... .......... .......... 33%  108M 1s
  9050K .......... .......... .......... .......... .......... 33% 77.3M 1s
  9100K .......... .......... .......... .......... .......... 34%  106M 1s
  9150K .......... .......... .......... .......... .......... 34% 90.8M 1s
  9200K .......... .......... .......... .......... .......... 34%  111M 1s
  9250K .......... .......... .......... .......... .......... 34% 85.9M 1s
  9300K .......... .......... .......... .......... .......... 34%  105M 1s
  9350K .......... .......... .......... .......... .......... 34%  120M 1s
  9400K .......... .......... .......... .......... .......... 35% 86.8M 1s
  9450K .......... .......... .......... .......... .......... 35%  111M 1s
  9500K .......... .......... .......... .......... .......... 35% 92.8M 1s
  9550K .......... .......... .......... .......... .......... 35%  113M 1s
  9600K .......... .......... .......... .......... .......... 35% 82.5M 1s
  9650K .......... .......... .......... .......... .......... 36%  116M 1s
  9700K .......... .......... .......... .......... .......... 36% 94.6M 1s
  9750K .......... .......... .......... .......... .......... 36%  101M 1s
  9800K .......... .......... .......... .......... .......... 36% 94.2M 1s
  9850K .......... .......... .......... .......... .......... 36% 81.2M 1s
  9900K .......... .......... .......... .......... .......... 36%  120M 1s
  9950K .......... .......... .......... .......... .......... 37% 81.6M 1s
 10000K .......... .......... .......... .......... .......... 37%  100M 1s
 10050K .......... .......... .......... .......... .......... 37% 1.35M 1s
 10100K .......... .......... .......... .......... .......... 37%  109M 1s
 10150K .......... .......... .......... .......... .......... 37% 99.6M 1s
 10200K .......... .......... .......... .......... .......... 38%  110M 1s
 10250K .......... .......... .......... .......... .......... 38%  111M 1s
 10300K .......... .......... .......... .......... .......... 38%  113M 1s
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 10400K .......... .......... .......... .......... .......... 38% 4.31M 1s
 10450K .......... .......... .......... .......... .......... 39%  105M 1s
 10500K .......... .......... .......... .......... .......... 39%  102M 1s
 10550K .......... .......... .......... .......... .......... 39%  119M 1s
 10600K .......... .......... .......... .......... .......... 39% 99.2M 1s
 10650K .......... .......... .......... .......... .......... 39%  114M 1s
 10700K .......... .......... .......... .......... .......... 39%  107M 1s
 10750K .......... .......... .......... .......... .......... 40%  113M 1s
 10800K .......... .......... .......... .......... .......... 40%  114M 1s
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 11150K .......... .......... .......... .......... .......... 41%  113M 1s
 11200K .......... .......... .......... .......... .......... 41%  113M 1s
 11250K .......... .......... .......... .......... .......... 41% 97.9M 1s
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 11350K .......... .......... .......... .......... .......... 42%  113M 1s
 11400K .......... .......... .......... .......... .......... 42%  114M 1s
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 11500K .......... .......... .......... .......... .......... 42%  112M 1s
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 11700K .......... .......... .......... .......... .......... 43%  108M 1s
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 11800K .......... .......... .......... .......... .......... 44%  104M 1s
 11850K .......... .......... .......... .......... .......... 44%  113M 1s
 11900K .......... .......... .......... .......... .......... 44%  113M 1s
 11950K .......... .......... .......... .......... .......... 44% 95.9M 1s
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 12100K .......... .......... .......... .......... .......... 45%  112M 1s
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 13100K .......... .......... .......... .......... .......... 48% 5.79M 1s
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 13250K .......... .......... .......... .......... .......... 49%  108M 1s
 13300K .......... .......... .......... .......... .......... 49%  106M 1s
 13350K .......... .......... .......... .......... .......... 49% 74.3M 1s
 13400K .......... .......... .......... .......... .......... 49% 96.9M 1s
 13450K .......... .......... .......... .......... .......... 50%  120M 1s
 13500K .......... .......... .......... .......... .......... 50%  105M 1s
 13550K .......... .......... .......... .......... .......... 50%  103M 1s
 13600K .......... .......... .......... .......... .......... 50%  107M 1s
 13650K .......... .......... .......... .......... .......... 50%  106M 1s
 13700K .......... .......... .......... .......... .......... 51% 93.8M 1s
 13750K .......... .......... .......... .......... .......... 51% 98.9M 1s
 13800K .......... .......... .......... .......... .......... 51% 88.9M 1s
 13850K .......... .......... .......... .......... .......... 51% 97.6M 1s
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 13950K .......... .......... .......... .......... .......... 52% 97.5M 1s
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 14200K .......... .......... .......... .......... .......... 52% 98.4M 1s
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 14650K .......... .......... .......... .......... .......... 54% 87.5M 1s
 14700K .......... .......... .......... .......... .......... 54% 2.82M 1s
 14750K .......... .......... .......... .......... .......... 55% 82.4M 1s
 14800K .......... .......... .......... .......... .......... 55% 70.5M 1s
 14850K .......... .......... .......... .......... .......... 55% 89.8M 1s
 14900K .......... .......... .......... .......... .......... 55%  105M 1s
 14950K .......... .......... .......... .......... .......... 55% 70.3M 1s
 15000K .......... .......... .......... .......... .......... 55% 88.2M 1s
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 15250K .......... .......... .......... .......... .......... 56% 87.1M 1s
 15300K .......... .......... .......... .......... .......... 57% 83.1M 1s
 15350K .......... .......... .......... .......... .......... 57% 81.5M 1s
 15400K .......... .......... .......... .......... .......... 57% 93.2M 1s
 15450K .......... .......... .......... .......... .......... 57% 97.0M 1s
 15500K .......... .......... .......... .......... .......... 57%  106M 1s
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 15600K .......... .......... .......... .......... .......... 58%  106M 1s
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 15700K .......... .......... .......... .......... .......... 58% 93.3M 1s
 15750K .......... .......... .......... .......... .......... 58% 94.6M 1s
 15800K .......... .......... .......... .......... .......... 58%  106M 1s
 15850K .......... .......... .......... .......... .......... 59% 95.1M 1s
 15900K .......... .......... .......... .......... .......... 59% 85.9M 1s
 15950K .......... .......... .......... .......... .......... 59%  108M 1s
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 16050K .......... .......... .......... .......... .......... 59% 81.3M 1s
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 16200K .......... .......... .......... .......... .......... 60% 92.0M 1s
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 16300K .......... .......... .......... .......... .......... 60% 94.0M 1s
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 26900K ......                                                100% 97.4M=1.1s

2018-06-13 21:42:27 (24.2 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 21:42:27--  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]
--2018-06-13 21:42:27--  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’

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  5750K .......... .......... .                               100%  153M=0.6s

Last-modified header missing -- time-stamps turned off.
2018-06-13 21:42:28 (9.29 MB/s) - ‘data/hp.obo’ saved [5909799/5909799]

mkdir -p jar
wget -N -P jar https://github.com/Phenomics/hpo-build-jars/raw/master/generateAnnotationFile.jar
--2018-06-13 21:42:28--  https://github.com/Phenomics/hpo-build-jars/raw/master/generateAnnotationFile.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://raw.githubusercontent.com/Phenomics/hpo-build-jars/master/generateAnnotationFile.jar [following]
--2018-06-13 21:42:29--  https://raw.githubusercontent.com/Phenomics/hpo-build-jars/master/generateAnnotationFile.jar
Connecting to proxy.charite.de (proxy.charite.de)|141.42.1.215|:8080... connected.
Proxy request sent, awaiting response... 200 OK
Length: 11365618 (11M) [application/octet-stream]
Saving to: ‘jar/generateAnnotationFile.jar’

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Last-modified header missing -- time-stamps turned off.
2018-06-13 21:42:30 (14.2 MB/s) - ‘jar/generateAnnotationFile.jar’ saved [11365618/11365618]

java -Xmx1G -jar jar/generateAnnotationFile.jar --orphadata "data/en_product4_HPO.xml" --out-folder "." --hpo_ontology "data/hp.obo" --berkeley-annotated "../annotated/"
parse: data/hp.obo
Jun 13, 2018 9:42:30 PM ontologizer.go.OBOParser doParse
INFO: Got 13537 terms and 17162 relations in 273 ms
Details of parsed obo file:
  data-version:		releases/2018-03-08
  format:		1.2
  term definitions:	13537
Jun 13, 2018 9:42:30 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
Jun 13, 2018 9:42:31 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (Phenotypic abnormality (HP:0000118)
/var/lib/jenkins/jobs/hpo.annotations/workspace/misc/../annotated
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...........................OOOOOHHHHHHHHHHOMIM:253260	BIOTINIDASE DEFICIENCYMULTIPLE CARBOXYLASE DEFICIENCY, LATE-ONSET	HP:0410145	decreased biotinidase activity								PMID:3930842	PCS	HPO:nvasilevsky	2018-03-12
not found or only obsolete term found for: HP:0410145
makefile:40: recipe for target 'generate-annotation-file' failed
make: *** [generate-annotation-file] Error 1
make: Leaving directory '/var/lib/jenkins/jobs/hpo.annotations/workspace/misc'
Build step 'Execute shell' marked build as failure
Archiving artifacts
Sending e-mails to: sebastian.koehler@charite.de
Finished: FAILURE