SuccessConsole Output

Skipping 310 KB.. Full Log
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 27850K .......... .......... ...                             100%  141M=1.7s

2018-10-09 10:00:18 (16.1 MB/s) - ‘data/en_product4_HPO.xml’ saved [28542549/28542549]

# loads the HPO
wget -N -P data http://purl.obolibrary.org/obo/hp.obo
--2018-10-09 10:00:18--  http://purl.obolibrary.org/obo/hp.obo
Resolving proxy.charite.de (proxy.charite.de)... 141.42.1.215
Connecting to proxy.charite.de (proxy.charite.de)|141.42.1.215|:8080... connected.
Proxy request sent, awaiting response... 302 Found
Location: https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo [following]
--2018-10-09 10:00:18--  https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo
Connecting to proxy.charite.de (proxy.charite.de)|141.42.1.215|:8080... connected.
Proxy request sent, awaiting response... 200 OK
Length: 6192170 (5.9M) [text/plain]
Saving to: ‘data/hp.obo’

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Last-modified header missing -- time-stamps turned off.
2018-10-09 10:00:18 (16.7 MB/s) - ‘data/hp.obo’ saved [6192170/6192170]

mkdir -p jar
wget -N -P jar https://github.com/monarch-initiative/hpoannotqc/releases/download/v1.2.2/HpoAnnotQc.jar
--2018-10-09 10:00:18--  https://github.com/monarch-initiative/hpoannotqc/releases/download/v1.2.2/HpoAnnotQc.jar
Resolving proxy.charite.de (proxy.charite.de)... 141.42.1.215
Connecting to proxy.charite.de (proxy.charite.de)|141.42.1.215|:8080... connected.
Proxy request sent, awaiting response... 302 Found
Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/120038140/fb1f44d6-8f3c-11e8-9f06-df962ed60c03?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20181009%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20181009T080051Z&X-Amz-Expires=300&X-Amz-Signature=8e8053896cc9025e279845331f8abf1ed9aceec7153d3eb9d6bea2f11e2dd15d&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DHpoAnnotQc.jar&response-content-type=application%2Foctet-stream [following]
--2018-10-09 10:00:19--  https://github-production-release-asset-2e65be.s3.amazonaws.com/120038140/fb1f44d6-8f3c-11e8-9f06-df962ed60c03?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20181009%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20181009T080051Z&X-Amz-Expires=300&X-Amz-Signature=8e8053896cc9025e279845331f8abf1ed9aceec7153d3eb9d6bea2f11e2dd15d&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DHpoAnnotQc.jar&response-content-type=application%2Foctet-stream
Connecting to proxy.charite.de (proxy.charite.de)|141.42.1.215|:8080... connected.
Proxy request sent, awaiting response... 200 OK
Length: 17653504 (17M) [application/octet-stream]
Saving to: ‘jar/HpoAnnotQc.jar’

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  5850K .......... .......... .......... .......... .......... 34% 16.2M 5s
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  5950K .......... .......... .......... .......... .......... 34% 1.10M 5s
  6000K .......... .......... .......... .......... .......... 35% 1.09M 5s
  6050K .......... .......... .......... .......... .......... 35% 4.25M 5s
  6100K .......... .......... .......... .......... .......... 35% 13.3M 5s
  6150K .......... .......... .......... .......... .......... 35% 11.7M 5s
  6200K .......... .......... .......... .......... .......... 36% 1.09M 5s
  6250K .......... .......... .......... .......... .......... 36% 1.05M 5s
  6300K .......... .......... .......... .......... .......... 36% 25.1M 5s
  6350K .......... .......... .......... .......... .......... 37% 6.42M 5s
  6400K .......... .......... .......... .......... .......... 37% 7.97M 5s
  6450K .......... .......... .......... .......... .......... 37% 13.4M 5s
  6500K .......... .......... .......... .......... .......... 37% 1.10M 5s
  6550K .......... .......... .......... .......... .......... 38% 28.7M 5s
  6600K .......... .......... .......... .......... .......... 38% 1.05M 5s
  6650K .......... .......... .......... .......... .......... 38% 28.7M 5s
  6700K .......... .......... .......... .......... .......... 39% 7.18M 5s
  6750K .......... .......... .......... .......... .......... 39% 8.06M 5s
  6800K .......... .......... .......... .......... .......... 39% 36.6M 5s
  6850K .......... .......... .......... .......... .......... 40% 14.0M 5s
  6900K .......... .......... .......... .......... .......... 40% 1.09M 5s
  6950K .......... .......... .......... .......... .......... 40% 27.7M 5s
  7000K .......... .......... .......... .......... .......... 40% 1.07M 5s
  7050K .......... .......... .......... .......... .......... 41% 43.3M 5s
  7100K .......... .......... .......... .......... .......... 41% 13.1M 5s
  7150K .......... .......... .......... .......... .......... 41% 7.81M 5s
  7200K .......... .......... .......... .......... .......... 42% 8.19M 5s
  7250K .......... .......... .......... .......... .......... 42% 63.9M 4s
  7300K .......... .......... .......... .......... .......... 42% 17.1M 4s
  7350K .......... .......... .......... .......... .......... 42% 1.10M 4s
  7400K .......... .......... .......... .......... .......... 43% 38.5M 4s
  7450K .......... .......... .......... .......... .......... 43% 1.08M 4s
  7500K .......... .......... .......... .......... .......... 43% 36.3M 4s
  7550K .......... .......... .......... .......... .......... 44% 12.5M 4s
  7600K .......... .......... .......... .......... .......... 44% 8.42M 4s
  7650K .......... .......... .......... .......... .......... 44% 7.83M 4s
  7700K .......... .......... .......... .......... .......... 44% 90.3M 4s
  7750K .......... .......... .......... .......... .......... 45% 14.6M 4s
  7800K .......... .......... .......... .......... .......... 45% 1.14M 4s
  7850K .......... .......... .......... .......... .......... 45% 14.6M 4s
  7900K .......... .......... .......... .......... .......... 46% 1.10M 4s
  7950K .......... .......... .......... .......... .......... 46% 47.4M 4s
  8000K .......... .......... .......... .......... .......... 46% 28.4M 4s
  8050K .......... .......... .......... .......... .......... 46% 4.79M 4s
  8100K .......... .......... .......... .......... .......... 47% 26.6M 4s
  8150K .......... .......... .......... .......... .......... 47% 14.8M 4s
  8200K .......... .......... .......... .......... .......... 47% 30.9M 4s
  8250K .......... .......... .......... .......... .......... 48% 13.5M 4s
  8300K .......... .......... .......... .......... .......... 48% 1.13M 4s
  8350K .......... .......... .......... .......... .......... 48% 1.79M 4s
  8400K .......... .......... .......... .......... .......... 49% 2.66M 4s
  8450K .......... .......... .......... .......... .......... 49% 16.9M 4s
  8500K .......... .......... .......... .......... .......... 49% 8.95M 4s
  8550K .......... .......... .......... .......... .......... 49% 8.67M 4s
  8600K .......... .......... .......... .......... .......... 50% 15.2M 4s
  8650K .......... .......... .......... .......... .......... 50% 98.3M 4s
  8700K .......... .......... .......... .......... .......... 50% 10.4M 4s
  8750K .......... .......... .......... .......... .......... 51% 1.16M 4s
  8800K .......... .......... .......... .......... .......... 51% 21.0M 3s
  8850K .......... .......... .......... .......... .......... 51% 1.10M 3s
  8900K .......... .......... .......... .......... .......... 51% 26.2M 3s
  8950K .......... .......... .......... .......... .......... 52% 17.5M 3s
  9000K .......... .......... .......... .......... .......... 52% 7.92M 3s
  9050K .......... .......... .......... .......... .......... 52% 12.8M 3s
  9100K .......... .......... .......... .......... .......... 53% 10.5M 3s
  9150K .......... .......... .......... .......... .......... 53% 97.5M 3s
  9200K .......... .......... .......... .......... .......... 53% 15.1M 3s
  9250K .......... .......... .......... .......... .......... 53% 1.03M 3s
  9300K .......... .......... .......... .......... .......... 54% 2.02M 3s
  9350K .......... .......... .......... .......... .......... 54% 2.34M 3s
  9400K .......... .......... .......... .......... .......... 54% 28.0M 3s
  9450K .......... .......... .......... .......... .......... 55% 36.1M 3s
  9500K .......... .......... .......... .......... .......... 55% 6.09M 3s
  9550K .......... .......... .......... .......... .......... 55% 35.4M 3s
  9600K .......... .......... .......... .......... .......... 55% 15.6M 3s
  9650K .......... .......... .......... .......... .......... 56% 40.3M 3s
  9700K .......... .......... .......... .......... .......... 56% 9.27M 3s
  9750K .......... .......... .......... .......... .......... 56% 1.13M 3s
  9800K .......... .......... .......... .......... .......... 57% 1.44M 3s
  9850K .......... .......... .......... .......... .......... 57% 4.62M 3s
  9900K .......... .......... .......... .......... .......... 57% 12.0M 3s
  9950K .......... .......... .......... .......... .......... 58% 23.2M 3s
 10000K .......... .......... .......... .......... .......... 58% 3.61M 3s
 10050K .......... .......... .......... .......... .......... 58% 35.5M 3s
 10100K .......... .......... .......... .......... .......... 58% 92.3M 3s
 10150K .......... .......... .......... .......... .......... 59% 97.4M 3s
 10200K .......... .......... .......... .......... .......... 59% 26.7M 3s
 10250K .......... .......... .......... .......... .......... 59% 1.13M 3s
 10300K .......... .......... .......... .......... .......... 60% 1.92M 3s
 10350K .......... .......... .......... .......... .......... 60% 2.54M 3s
 10400K .......... .......... .......... .......... .......... 60% 12.6M 3s
 10450K .......... .......... .......... .......... .......... 60% 19.2M 3s
 10500K .......... .......... .......... .......... .......... 61% 3.66M 3s
 10550K .......... .......... .......... .......... .......... 61% 38.6M 3s
 10600K .......... .......... .......... .......... .......... 61% 93.1M 3s
 10650K .......... .......... .......... .......... .......... 62% 73.4M 2s
 10700K .......... .......... .......... .......... .......... 62% 49.4M 2s
 10750K .......... .......... .......... .......... .......... 62% 1.12M 2s
 10800K .......... .......... .......... .......... .......... 62% 1.91M 2s
 10850K .......... .......... .......... .......... .......... 63% 2.39M 2s
 10900K .......... .......... .......... .......... .......... 63% 6.54M 2s
 10950K .......... .......... .......... .......... .......... 63% 35.9M 2s
 11000K .......... .......... .......... .......... .......... 64% 3.98M 2s
 11050K .......... .......... .......... .......... .......... 64% 41.8M 2s
 11100K .......... .......... .......... .......... .......... 64% 47.5M 2s
 11150K .......... .......... .......... .......... .......... 64% 31.1M 2s
 11200K .......... .......... .......... .......... .......... 65%  104M 2s
 11250K .......... .......... .......... .......... .......... 65% 1.20M 2s
 11300K .......... .......... .......... .......... .......... 65% 1.92M 2s
 11350K .......... .......... .......... .......... .......... 66% 2.43M 2s
 11400K .......... .......... .......... .......... .......... 66% 6.67M 2s
 11450K .......... .......... .......... .......... .......... 66% 25.8M 2s
 11500K .......... .......... .......... .......... .......... 66% 18.1M 2s
 11550K .......... .......... .......... .......... .......... 67% 5.55M 2s
 11600K .......... .......... .......... .......... .......... 67% 80.2M 2s
 11650K .......... .......... .......... .......... .......... 67% 58.0M 2s
 11700K .......... .......... .......... .......... .......... 68% 92.4M 2s
 11750K .......... .......... .......... .......... .......... 68% 1.13M 2s
 11800K .......... .......... .......... .......... .......... 68% 75.7M 2s
 11850K .......... .......... .......... .......... .......... 69% 1.14M 2s
 11900K .......... .......... .......... .......... .......... 69% 5.05M 2s
 11950K .......... .......... .......... .......... .......... 69% 91.6M 2s
 12000K .......... .......... .......... .......... .......... 69% 27.4M 2s
 12050K .......... .......... .......... .......... .......... 70% 4.52M 2s
 12100K .......... .......... .......... .......... .......... 70% 80.3M 2s
 12150K .......... .......... .......... .......... .......... 70% 81.0M 2s
 12200K .......... .......... .......... .......... .......... 71% 52.4M 2s
 12250K .......... .......... .......... .......... .......... 71% 1.14M 2s
 12300K .......... .......... .......... .......... .......... 71% 57.5M 2s
 12350K .......... .......... .......... .......... .......... 71% 1.47M 2s
 12400K .......... .......... .......... .......... .......... 72% 3.90M 2s
 12450K .......... .......... .......... .......... .......... 72% 6.04M 2s
 12500K .......... .......... .......... .......... .......... 72% 29.7M 2s
 12550K .......... .......... .......... .......... .......... 73% 4.85M 2s
 12600K .......... .......... .......... .......... .......... 73% 48.7M 2s
 12650K .......... .......... .......... .......... .......... 73% 87.0M 2s
 12700K .......... .......... .......... .......... .......... 73% 85.1M 2s
 12750K .......... .......... .......... .......... .......... 74% 75.4M 2s
 12800K .......... .......... .......... .......... .......... 74% 1.11M 2s
 12850K .......... .......... .......... .......... .......... 74% 74.4M 2s
 12900K .......... .......... .......... .......... .......... 75% 1.11M 2s
 12950K .......... .......... .......... .......... .......... 75% 6.52M 2s
 13000K .......... .......... .......... .......... .......... 75% 16.5M 1s
 13050K .......... .......... .......... .......... .......... 75% 48.9M 1s
 13100K .......... .......... .......... .......... .......... 76% 5.54M 1s
 13150K .......... .......... .......... .......... .......... 76% 27.8M 1s
 13200K .......... .......... .......... .......... .......... 76%  102M 1s
 13250K .......... .......... .......... .......... .......... 77% 74.6M 1s
 13300K .......... .......... .......... .......... .......... 77% 1.07M 1s
 13350K .......... .......... .......... .......... .......... 77% 88.2M 1s
 13400K .......... .......... .......... .......... .......... 78% 1.59M 1s
 13450K .......... .......... .......... .......... .......... 78% 4.10M 1s
 13500K .......... .......... .......... .......... .......... 78% 6.51M 1s
 13550K .......... .......... .......... .......... .......... 78% 17.5M 1s
 13600K .......... .......... .......... .......... .......... 79% 32.1M 1s
 13650K .......... .......... .......... .......... .......... 79% 5.21M 1s
 13700K .......... .......... .......... .......... .......... 79% 36.3M 1s
 13750K .......... .......... .......... .......... .......... 80% 96.8M 1s
 13800K .......... .......... .......... .......... .......... 80% 40.2M 1s
 13850K .......... .......... .......... .......... .......... 80% 1.01M 1s
 13900K .......... .......... .......... .......... .......... 80% 36.5M 1s
 13950K .......... .......... .......... .......... .......... 81% 1.36M 1s
 14000K .......... .......... .......... .......... .......... 81% 17.4M 1s
 14050K .......... .......... .......... .......... .......... 81% 6.46M 1s
 14100K .......... .......... .......... .......... .......... 82% 16.6M 1s
 14150K .......... .......... .......... .......... .......... 82% 5.22M 1s
 14200K .......... .......... .......... .......... .......... 82% 46.4M 1s
 14250K .......... .......... .......... .......... .......... 82% 73.3M 1s
 14300K .......... .......... .......... .......... .......... 83%  113M 1s
 14350K .......... .......... .......... .......... .......... 83% 40.7M 1s
 14400K .......... .......... .......... .......... .......... 83% 1.00M 1s
 14450K .......... .......... .......... .......... .......... 84% 35.1M 1s
 14500K .......... .......... .......... .......... .......... 84% 1.28M 1s
 14550K .......... .......... .......... .......... .......... 84% 5.44M 1s
 14600K .......... .......... .......... .......... .......... 84% 21.3M 1s
 14650K .......... .......... .......... .......... .......... 85% 38.0M 1s
 14700K .......... .......... .......... .......... .......... 85% 6.44M 1s
 14750K .......... .......... .......... .......... .......... 85% 45.2M 1s
 14800K .......... .......... .......... .......... .......... 86% 55.2M 1s
 14850K .......... .......... .......... .......... .......... 86% 26.4M 1s
 14900K .......... .......... .......... .......... .......... 86% 93.1M 1s
 14950K .......... .......... .......... .......... .......... 87% 1.01M 1s
 15000K .......... .......... .......... .......... .......... 87% 34.3M 1s
 15050K .......... .......... .......... .......... .......... 87% 1.32M 1s
 15100K .......... .......... .......... .......... .......... 87% 5.79M 1s
 15150K .......... .......... .......... .......... .......... 88% 17.3M 1s
 15200K .......... .......... .......... .......... .......... 88% 39.7M 1s
 15250K .......... .......... .......... .......... .......... 88% 4.82M 1s
 15300K .......... .......... .......... .......... .......... 89% 63.7M 1s
 15350K .......... .......... .......... .......... .......... 89%  112M 1s
 15400K .......... .......... .......... .......... .......... 89% 94.1M 1s
 15450K .......... .......... .......... .......... .......... 89%  106M 1s
 15500K .......... .......... .......... .......... .......... 90% 1.01M 1s
 15550K .......... .......... .......... .......... .......... 90% 29.0M 1s
 15600K .......... .......... .......... .......... .......... 90% 1.34M 1s
 15650K .......... .......... .......... .......... .......... 91% 5.59M 1s
 15700K .......... .......... .......... .......... .......... 91% 12.1M 0s
 15750K .......... .......... .......... .......... .......... 91% 37.5M 0s
 15800K .......... .......... .......... .......... .......... 91% 6.33M 0s
 15850K .......... .......... .......... .......... .......... 92% 42.1M 0s
 15900K .......... .......... .......... .......... .......... 92% 55.9M 0s
 15950K .......... .......... .......... .......... .......... 92%  106M 0s
 16000K .......... .......... .......... .......... .......... 93%  106M 0s
 16050K .......... .......... .......... .......... .......... 93% 1011K 0s
 16100K .......... .......... .......... .......... .......... 93% 2.84M 0s
 16150K .......... .......... .......... .......... .......... 93% 2.41M 0s
 16200K .......... .......... .......... .......... .......... 94% 5.16M 0s
 16250K .......... .......... .......... .......... .......... 94% 15.2M 0s
 16300K .......... .......... .......... .......... .......... 94% 46.4M 0s
 16350K .......... .......... .......... .......... .......... 95% 6.07M 0s
 16400K .......... .......... .......... .......... .......... 95% 41.2M 0s
 16450K .......... .......... .......... .......... .......... 95% 60.9M 0s
 16500K .......... .......... .......... .......... .......... 95% 68.8M 0s
 16550K .......... .......... .......... .......... .......... 96% 42.0M 0s
 16600K .......... .......... .......... .......... .......... 96% 1.03M 0s
 16650K .......... .......... .......... .......... .......... 96% 23.7M 0s
 16700K .......... .......... .......... .......... .......... 97% 1.34M 0s
 16750K .......... .......... .......... .......... .......... 97% 5.90M 0s
 16800K .......... .......... .......... .......... .......... 97% 11.9M 0s
 16850K .......... .......... .......... .......... .......... 98% 34.6M 0s
 16900K .......... .......... .......... .......... .......... 98% 6.18M 0s
 16950K .......... .......... .......... .......... .......... 98% 20.2M 0s
 17000K .......... .......... .......... .......... .......... 98% 37.9M 0s
 17050K .......... .......... .......... .......... .......... 99%  101M 0s
 17100K .......... .......... .......... .......... .......... 99%  104M 0s
 17150K .......... .......... .......... .......... .......... 99% 1.05M 0s
 17200K .......... .......... .......... .........            100% 20.7M=5.5s

2018-10-09 10:00:25 (3.09 MB/s) - ‘jar/HpoAnnotQc.jar’ saved [17653504/17653504]

java -Xmx1G -jar jar/HpoAnnotQc.jar big-file --orphadata "data/en_product4_HPO.xml"  --hpo "data/hp.obo" --small-files "../annotated/" --out "phenotype.hpoa"
log4j:WARN No appenders could be found for logger (org.openrdf.rio.RDFParserRegistry).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
2018-10-09 10:00:30.070 ERROR main [main] (V2SmallFileIngestor.java:69) - Finished with input of 7421 files with 98546 annotations
2018-10-09 10:00:30.072 ERROR main [main] (V2SmallFileIngestor.java:70) - A total of 98 entries found in the small file directory were omitted.
2018-10-09 10:00:30.357 ERROR main [main] (OrphanetXML2HpoDiseaseModelParser.java:89) - [ERROR] Could not find TermId for Orphanet HPO ID "HP:0500014"
2018-10-09 10:00:30.657 ERROR main [main] (OrphanetXML2HpoDiseaseModelParser.java:89) - [ERROR] Could not find TermId for Orphanet HPO ID "HP:0500014"
2018-10-09 10:00:30.885 ERROR main [main] (OrphanetXML2HpoDiseaseModelParser.java:89) - [ERROR] Could not find TermId for Orphanet HPO ID "HP:0500014"
2018-10-09 10:00:30.885 ERROR main [main] (OrphanetXML2HpoDiseaseModelParser.java:89) - [ERROR] Could not find TermId for Orphanet HPO ID "HP:0500014"
2018-10-09 10:00:30.944 ERROR main [main] (OrphanetXML2HpoDiseaseModelParser.java:89) - [ERROR] Could not find TermId for Orphanet HPO ID "HP:0500014"
We extracted 3246 orphanet disorders with 68651 annotations 
org.monarchinitiative.hpoannotqc.exception.HPOException: Could not determine aspect of TermId HP:0040284
	at org.monarchinitiative.hpoannotqc.bigfile.V2BigFile.getAspectV2(V2BigFile.java:116)
	at org.monarchinitiative.hpoannotqc.bigfile.V2BigFile.transformEntry2BigFileLineV2(V2BigFile.java:88)
	at org.monarchinitiative.hpoannotqc.bigfile.V2BigFile.outputBigFileV2(V2BigFile.java:63)
	at org.monarchinitiative.hpoannotqc.bigfile.BigFileWriter.outputBigFileV2(BigFileWriter.java:100)
	at org.monarchinitiative.hpoannotqc.cmd.BigFileCommand.execute(BigFileCommand.java:78)
	at org.monarchinitiative.hpoannotqc.Main.main(Main.java:24)
org.monarchinitiative.hpoannotqc.exception.HPOException: Could not determine aspect of TermId HP:0040284
	at org.monarchinitiative.hpoannotqc.bigfile.V2BigFile.getAspectV2(V2BigFile.java:116)
	at org.monarchinitiative.hpoannotqc.bigfile.V2BigFile.transformEntry2BigFileLineV2(V2BigFile.java:88)
	at org.monarchinitiative.hpoannotqc.bigfile.V2BigFile.outputBigFileV2(V2BigFile.java:63)
	at org.monarchinitiative.hpoannotqc.bigfile.BigFileWriter.outputBigFileV2(BigFileWriter.java:100)
	at org.monarchinitiative.hpoannotqc.cmd.BigFileCommand.execute(BigFileCommand.java:78)
	at org.monarchinitiative.hpoannotqc.Main.main(Main.java:24)
org.monarchinitiative.hpoannotqc.exception.HPOException: Could not determine aspect of TermId HP:0040284
	at org.monarchinitiative.hpoannotqc.bigfile.V2BigFile.getAspectV2(V2BigFile.java:116)
	at org.monarchinitiative.hpoannotqc.bigfile.V2BigFile.transformEntry2BigFileLineV2(V2BigFile.java:88)
	at org.monarchinitiative.hpoannotqc.bigfile.V2BigFile.outputBigFileV2(V2BigFile.java:63)
	at org.monarchinitiative.hpoannotqc.bigfile.BigFileWriter.outputBigFileV2(BigFileWriter.java:100)
	at org.monarchinitiative.hpoannotqc.cmd.BigFileCommand.execute(BigFileCommand.java:78)
	at org.monarchinitiative.hpoannotqc.Main.main(Main.java:24)
We output a total of 98546 big file lines
2018-10-09 10:00:31.802 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Severe visual impairment instead of Severe vision loss for Severe vision loss: see following line
2018-10-09 10:00:31.803 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:309555	MENTAL RETARDATION WITH OPTIC ATROPHY, DEAFNESS, AND SEIZURES	HP:0001141	Severe visual impairment								OMIM:309555	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.803 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.803 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:598500	WOLFRAM SYNDROME, MITOCHONDRIAL FORM	HP:0002459	Abnormal autonomic nervous system physiology								OMIM:598500	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.803 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.803 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:300894	#300894 NEURODEGENERATION WITH BRAIN IRON ACCUMULATION 5; NBIA5;;BETA-PROPELLER PROTEIN-ASSOCIATED NEURODEGENERATION; BPAN;;STATIC ENCEPHALOPATHY OF CHILDHOOD WITH NEURODEGENERATION IN ADULTHOOD;SENDA	HP:0002459	Abnormal autonomic nervous system physiology							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DYSAUTONOMIA	OMIM:300894	TAS	HPO:skoehler[2013-04-18]
2018-10-09 10:00:31.803 ERROR main [main] (V2LineQualityController.java:428) - Invalid frequency term (see next line): rare
2018-10-09 10:00:31.804 ERROR main [main] (V2LineQualityController.java:428) - Bad frequency [rare]: OMIM:603075	MACULAR DEGENERATION, AGE-RELATED, 1; ARMD1	HP:0025574	Macular hemorrhage			rare				OMIM-CS:headAndNeckEyes > MACULAR HEMORRHAGE (IN SOME PATIENTS)	OMIM:603075	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.804 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Abnormality of the eyelashes instead of Abnormal eyelash morphology for Abnormal eyelash morphology: see following line
2018-10-09 10:00:31.804 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:614237	HYPOTRICHOSIS 9; HYPT9	HP:0000499	Abnormality of the eyelashes					NOT		OMIM-CS:skinNailsHairHair > NORMAL EYELASHES	OMIM:614237	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.804 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.804 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:109150	MACHADO-JOSEPH DISEASE	HP:0002459	Abnormal autonomic nervous system physiology			HP:0040283					OMIM:109150	TAS	HPO:iea[2009-02-17]
2018-10-09 10:00:31.804 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.804 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:609241	SCHINDLER DISEASE, TYPE I	HP:0100704	Cortical visual impairment								OMIM:609241	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.805 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.805 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:256800	INSENSITIVITY TO PAIN, CONGENITAL, WITH ANHIDROSIS	HP:0002459	Abnormal autonomic nervous system physiology								OMIM:256800	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.805 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.805 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:617166	EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 47	HP:0100704	Cortical visual impairment			HP:0040283				OMIM-CS:headandneckeyes > CORTICAL VISUAL IMPAIRMENT (IN SOME PATIENTS)	OMIM:617166	TAS	HPO:skoehler[2017-07-13]
2018-10-09 10:00:31.805 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.805 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:218010	CORTICAL BLINDNESS, RETARDATION, AND POSTAXIAL POLYDACTYLY	HP:0100704	Cortical visual impairment								OMIM:218010	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.805 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures without impairment of consciousness or awareness instead of Focal aware seizure for Focal aware seizure: see following line
2018-10-09 10:00:31.805 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:608096	EPILEPSY, FAMILIAL TEMPORAL LOBE	HP:0002349	Focal seizures without impairment of consciousness or awareness								OMIM:608096	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.806 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures with impairment of consciousness or awareness instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.806 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:608096	EPILEPSY, FAMILIAL TEMPORAL LOBE	HP:0002384	Focal seizures with impairment of consciousness or awareness								OMIM:608096	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.806 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Severe visual impairment instead of Severe vision loss for Severe vision loss: see following line
2018-10-09 10:00:31.806 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:606996	SENIOR-LOKEN SYNDROME 4	HP:0001141	Severe visual impairment								OMIM:606996	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.807 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures with impairment of consciousness or awareness instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.807 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:607341	FOCAL CORTICAL DYSPLASIA OF TAYLOR	HP:0002384	Focal seizures with impairment of consciousness or awareness								OMIM:607341	TAS	HPO:probinson[2009-02-17]
2018-10-09 10:00:31.807 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures with impairment of consciousness or awareness instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.807 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:614527	#614527 CHROMOSOME 17q12 DELETION SYNDROME	HP:0002384	Focal seizures with impairment of consciousness or awareness			HP:0040283				OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > COMPLEX PARTIAL SEIZURES (IN SOME PATIENTS)	OMIM:614527	TAS	HPO:skoehler[2012-11-18]
2018-10-09 10:00:31.807 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.807 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:611277	#611277 GENERALIZED EPILEPSY WITH FEBRILE SEIZURES PLUS, TYPE 3; GEFSP3;;GEFS+, TYPE 3; GEFS+3FEBRILE SEIZURES, FAMILIAL, 8, INCLUDED; FEB8, INCLUDED	HP:0007359	Focal seizures							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > PARTIAL SEIZURES	OMIM:611277	TAS	HPO:skoehler[2012-10-17]
2018-10-09 10:00:31.807 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.807 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:615809	#615809 PONTOCEREBELLAR HYPOPLASIA, TYPE 9; PCH9	HP:0100704	Cortical visual impairment							OMIM-CS:HEAD AND NECK_EYES > CORTICAL BLINDNESS	OMIM:615809	TAS	HPO:skoehler[2014-06-24]
2018-10-09 10:00:31.808 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.808 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616351	#616351 MENTAL RETARDATION, AUTOSOMAL DOMINANT 34; MRD34	HP:0100704	Cortical visual impairment							OMIM-TX: 'bruxism, drooling, cortical visual impairment, bilateral ptosis, '	OMIM:616351	IEA	HPO:skoehler[2015-09-16]
2018-10-09 10:00:31.808 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0200027] for TermId [prefix=TermPrefix [value=HP], id=0005830] (Flexion contracture of toe): see following line
2018-10-09 10:00:31.808 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:300373	OSTEOPATHIA STRIATA WITH CRANIAL SCLEROSIS	HP:0200027	Flexion contracture of toe								OMIM:300373	TAS	HPO:skoehler[2010-06-18]
2018-10-09 10:00:31.808 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0000156] for TermId [prefix=TermPrefix [value=HP], id=0000218] (High palate): see following line
2018-10-09 10:00:31.808 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:300373	OSTEOPATHIA STRIATA WITH CRANIAL SCLEROSIS	HP:0000156	High palate			15%					OMIM:300373	TAS	HPO:skoehler[2010-06-20]
2018-10-09 10:00:31.808 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.808 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:614563	#614563 MENTAL RETARDATION, AUTOSOMAL DOMINANT 13; MRD13;;MENTAL RETARDATION, AUTOSOMAL DOMINANT, 13, WITH NEURONAL MIGRATIONDEFECTS	HP:0007359	Focal seizures							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > FOCAL SEIZURES	OMIM:614563	TAS	HPO:skoehler[2013-10-06]
2018-10-09 10:00:31.808 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Auras instead of Focal sensory seizure for Focal sensory seizure: see following line
2018-10-09 10:00:31.809 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:615400	EPILEPSY, FAMILIAL ADULT MYOCLONIC, 5; FAME5	HP:0011157	Auras							OMIM-CS:neurologicCentralNervousSystem > AUDITORY, OLFACTORY, AND VISUAL AURAS	OMIM:615400	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.809 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.809 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:601559	STUVE-WIEDEMANN SYNDROME	HP:0002459	Abnormal autonomic nervous system physiology								OMIM:601559	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.809 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.809 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:300643	#300643 ROLANDIC EPILEPSY, MENTAL RETARDATION, AND SPEECH DYSPRAXIA, X-LINKED;RESDX	HP:0007359	Focal seizures								OMIM:300643	IEA	HPO:skoehler[2013-01-11]
2018-10-09 10:00:31.809 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures with impairment of consciousness or awareness instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.809 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616683	LEUKODYSTROPHY, HYPOMYELINATING, 12	HP:0002384	Focal seizures with impairment of consciousness or awareness								PMID:26307567	PCS	HPO:probinson[2017-06-17]
2018-10-09 10:00:31.809 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.810 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616683	LEUKODYSTROPHY, HYPOMYELINATING, 12	HP:0100704	Cortical visual impairment							OMIM-CS:headandneckeyes > CORTICAL VISUAL IMPAIRMENT	OMIM:616683	TAS	HPO:skoehler[2017-07-13]
2018-10-09 10:00:31.810 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.810 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:616683	LEUKODYSTROPHY, HYPOMYELINATING, 12	HP:0002459	Abnormal autonomic nervous system physiology							OMIM-CS:neurologiccentralnervoussystem > AUTONOMIC DYSFUNCTION	OMIM:616683	TAS	HPO:skoehler[2017-07-13]
2018-10-09 10:00:31.810 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Severe visual impairment instead of Severe vision loss for Severe vision loss: see following line
2018-10-09 10:00:31.810 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:613617	#613617 RETINITIS PIGMENTOSA 58; RP58	HP:0001141	Severe visual impairment								OMIM:613617	TAS	HPO:probinson[2013-06-02]
2018-10-09 10:00:31.810 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures with impairment of consciousness or awareness instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.811 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:107650	APNEA, OBSTRUCTIVE SLEEP	HP:0002384	Focal seizures with impairment of consciousness or awareness								OMIM:107650	TAS	HPO:probinson[2009-02-17]
2018-10-09 10:00:31.811 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.811 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:614067	SPASTIC PARAPLEGIA 52, AUTOSOMAL RECESSIVE	HP:0007359	Focal seizures			HP:0040283				OMIM-CS:neurologiccentralnervoussystem > FOCAL SEIZURES (IN SOME PATIENTS)	OMIM:614067	TAS	HPO:skoehler[2017-07-13]
2018-10-09 10:00:31.811 ERROR main [main] (V2LineQualityController.java:428) - Invalid frequency term (see next line): rare
2018-10-09 10:00:31.811 ERROR main [main] (V2LineQualityController.java:428) - Bad frequency [rare]: OMIM:604364	EPILEPSY, FAMILIAL FOCAL, WITH VARIABLE FOCI 1; FFEVF1	HP:0031951	Nocturnal seizures			rare				OMIM-CS:neurologicCentralNervousSystem > NOCTURNAL SEIZURES (IN SOME PATIENTS)	OMIM:604364	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.811 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.811 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:300088	EPILEPSY, FEMALE-RESTRICTED, WITH MENTAL RETARDATION	HP:0007359	Focal seizures								OMIM:300088	TAS	HPO:probinson[2009-02-17]
2018-10-09 10:00:31.811 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Generalized seizures instead of Generalized-onset seizure for Generalized-onset seizure: see following line
2018-10-09 10:00:31.812 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:605751	CONVULSIONS, BENIGN FAMILIAL INFANTILE, 2	HP:0002197	Generalized seizures								OMIM:605751	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.812 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.812 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:605751	CONVULSIONS, BENIGN FAMILIAL INFANTILE, 2	HP:0007359	Focal seizures								OMIM:605751	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.812 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.812 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:615474	#615474 PRIMARY ALDOSTERONISM, SEIZURES, AND NEUROLOGIC ABNORMALITIES; PASNA	HP:0100704	Cortical visual impairment			HP:0040283				OMIM-CS:HEAD AND NECK_EYES > CORTICAL BLINDNESS (IN ONE PATIENT)	OMIM:615474	TAS	HPO:skoehler[2013-11-18]
2018-10-09 10:00:31.812 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.812 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:105250	AMYLOIDOSIS, PRIMARY CUTANEOUS	HP:0002459	Abnormal autonomic nervous system physiology					NOT			OMIM:105250	TAS	HPO:skoehler[2010-06-18]
2018-10-09 10:00:31.812 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.812 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:615574	#615574 ASPARAGINE SYNTHETASE DEFICIENCY; ASNSD;;ASNS DEFICIENCY	HP:0100704	Cortical visual impairment								OMIM:615574	TAS	HPO:skoehler[2014-01-28]
2018-10-09 10:00:31.813 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.813 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616577	#616577 EPILEPSY, HEARING LOSS, AND MENTAL RETARDATION SYNDROME; EHLMRS	HP:0100704	Cortical visual impairment			HP:0040283				OMIM-CS:HEAD AND NECK_EYES > CORTICAL VISUAL IMPAIRMENT (IN SOME PATIENTS)	OMIM:616577	TAS	HPO:skoehler[2015-11-15]
2018-10-09 10:00:31.813 ERROR main [main] (V2LineQualityController.java:428) - Bad data created: OMIM:615612	%615612 DEVELOPMENTAL DYSPLASIA OF THE HIP 2; DDH2	HP:0000006	Autosomal dominant inheritance							OMIM-CS:INHERITANCE > AUTOSOMAL DOMINANT	OMIM:615612	TAS	HPO:skoehler[2014-02-06
2018-10-09 10:00:31.813 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.813 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:617711	EPILEPTIC ENCEPHALOPATHY, INFANTILE OR EARLY CHILDHOOD, 1; IECEE1	HP:0100704	Cortical visual impairment			HP:0040284				OMIM-CS:headAndNeckEyes > CORTICAL VISUAL IMPAIRMENT (IN SOME PATIENTS)	OMIM:617711	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.813 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.813 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:272100	SUDANOPHILIC CEREBRAL SCLEROSIS	HP:0100704	Cortical visual impairment								OMIM:272100	TAS	HPO:probinson[2009-02-17]
2018-10-09 10:00:31.813 ERROR main [main] (V2LineQualityController.java:428) - Invalid frequency term (see next line): Frequent
2018-10-09 10:00:31.813 ERROR main [main] (V2LineQualityController.java:428) - Bad frequency [Frequent]: OMIM:131400	EOSINOPHILIA, FAMILIAL	HP:0002113	Pulmonary infiltrates			Frequent					PMID:6033105	PCS	HPO:lccarmody[2018-10-04]
2018-10-09 10:00:31.813 ERROR main [main] (V2LineQualityController.java:428) - Invalid frequency term (see next line): Occasional
2018-10-09 10:00:31.814 ERROR main [main] (V2LineQualityController.java:428) - Bad frequency [Occasional]: OMIM:131400	EOSINOPHILIA, FAMILIAL	HP:0001873	Thrombocytopenia			Occasional					PMID:6033105	PCS	HPO:lccarmody[2018-10-04]
2018-10-09 10:00:31.814 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.814 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:614498	#614498 RIGIDITY AND MULTIFOCAL SEIZURE SYNDROME, LETHAL NEONATAL; RMFSL	HP:0002459	Abnormal autonomic nervous system physiology							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DYSAUTONOMIA	OMIM:614498	TAS	HPO:skoehler[2012-10-17]
2018-10-09 10:00:31.814 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Severe visual impairment instead of Severe vision loss for Severe vision loss: see following line
2018-10-09 10:00:31.814 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:271310	SPINOCEREBELLAR DEGENERATION AND CORNEAL DYSTROPHY	HP:0001141	Severe visual impairment								OMIM:271310	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.814 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.814 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:617188	MENTAL RETARDATION, AUTOSOMAL RECESSIVE 57	HP:0007359	Focal seizures							OMIM-CS:neurologiccentralnervoussystem > FOCAL SEIZURES	OMIM:617188	TAS	HPO:skoehler[2017-07-13]
2018-10-09 10:00:31.814 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Generalized seizures instead of Generalized-onset seizure for Generalized-onset seizure: see following line
2018-10-09 10:00:31.814 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:617188	MENTAL RETARDATION, AUTOSOMAL RECESSIVE 57	HP:0002197	Generalized seizures							OMIM-CS:neurologiccentralnervoussystem > GENERALIZED SEIZURES	OMIM:617188	TAS	HPO:skoehler[2017-07-13]
2018-10-09 10:00:31.814 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.815 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616239	COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 24; COXPD24	HP:0100704	Cortical visual impairment								OMIM:616239	TAS	HPO:skoehler[2015-12-30]
2018-10-09 10:00:31.815 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.815 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:608799	CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ie	HP:0100704	Cortical visual impairment								OMIM:608799	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.815 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Severe visual impairment instead of Severe vision loss for Severe vision loss: see following line
2018-10-09 10:00:31.815 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:601110	CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Id	HP:0001141	Severe visual impairment								OMIM:601110	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.815 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Severe visual impairment instead of Severe vision loss for Severe vision loss: see following line
2018-10-09 10:00:31.815 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:302200	CATARACT, CONGENITAL TOTAL, WITH POSTERIOR SUTURAL OPACITIES IN HETEROZYGOTES	HP:0001141	Severe visual impairment				Male				OMIM:302200	TAS	HPO:probinson[2009-02-17]
2018-10-09 10:00:31.815 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0008024] for TermId [prefix=TermPrefix [value=HP], id=0100018] (Nuclear cataract): see following line
2018-10-09 10:00:31.815 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:302200	CATARACT, CONGENITAL TOTAL, WITH POSTERIOR SUTURAL OPACITIES IN HETEROZYGOTES	HP:0008024	Nuclear cataract	HP:0003577	Congenital onset		Male				OMIM:302200	TAS	HPO:probinson[2009-02-17]
2018-10-09 10:00:31.815 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.815 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:613060	#613060 EPILEPSY, IDIOPATHIC GENERALIZED, SUSCEPTIBILITY TO, 10; EIG10GENERALIZED EPILEPSY WITH FEBRILE SEIZURES PLUS, TYPE 5, SUSCEPTIBILITYTO, INCLUDED; GEFS5, INCLUDED;;GEFS+, TYPE 5, SUSCEPTIBILITY TO, INCLUDED;;GEFS+5, SUSCEPTIBILITY TO, INCLUDED;;GEFSP5, SUSCEPTIBILITY TO, INCLUDED;;EPILEPSY, JUVENILE MYOCLONIC, SUSCEPTIBILITY TO, 7, INCLUDED; EJM7,INCLUDED	HP:0007359	Focal seizures							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > PARTIAL SEIZURES	OMIM:613060	TAS	HPO:skoehler[2012-10-17]
2018-10-09 10:00:31.816 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Increased mean corpuscular hemoglobin instead of Increased mean corpuscular hemoglobin concentration for Increased mean corpuscular hemoglobin concentration: see following line
2018-10-09 10:00:31.816 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616689	DEHYDRATED HEREDITARY STOMATOCYTOSIS 2; DHS2	HP:0025548	Increased mean corpuscular hemoglobin							OMIM-CS:hematology > INCREASED MEAN CORPUSCULAR HEMOGLOBIN (MCH)	OMIM:616689	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.816 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Increased mean corpuscular hemoglobin instead of Increased mean corpuscular hemoglobin concentration for Increased mean corpuscular hemoglobin concentration: see following line
2018-10-09 10:00:31.816 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616689	DEHYDRATED HEREDITARY STOMATOCYTOSIS 2; DHS2	HP:0025548	Increased mean corpuscular hemoglobin							OMIM-CS:hematology > INCREASED MEAN CORPUSCULAR HEMOGLOBIN CONCENTRATION (MCHC)	OMIM:616689	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.816 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0000655] for TermId [prefix=TermPrefix [value=HP], id=0007773] (Vitreoretinopathy): see following line
2018-10-09 10:00:31.816 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:143200	WAGNER SYNDROME 1	HP:0000655	Vitreoretinal degeneration								OMIM:143200	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.816 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Vitreoretinal degeneration instead of Vitreoretinopathy for Vitreoretinopathy: see following line
2018-10-09 10:00:31.816 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:143200	WAGNER SYNDROME 1	HP:0000655	Vitreoretinal degeneration								OMIM:143200	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.816 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Auditory auras instead of Focal sensory auditory seizure for Focal sensory auditory seizure: see following line
2018-10-09 10:00:31.816 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616436	EPILEPSY, FAMILIAL TEMPORAL LOBE, 7; ETL7	HP:0011158	Auditory auras								OMIM:616436	TAS	HPO:skoehler[2015-12-30]
2018-10-09 10:00:31.817 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.817 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:203700	MITOCHONDRIAL DNA DEPLETION SYNDROME 4A (ALPERS TYPE)	HP:0100704	Cortical visual impairment								OMIM:203700	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.817 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.817 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:615802	MENTAL RETARDATION, AUTOSOMAL RECESSIVE 42	HP:0100704	Cortical visual impairment			HP:0040283				OMIM-CS:headandneckeyes > CORTICAL VISUAL IMPAIRMENT (IN SOME PATIENTS)	OMIM:615802	TAS	HPO:skoehler[2017-07-13]
2018-10-09 10:00:31.817 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.817 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:617153	EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 45	HP:0100704	Cortical visual impairment							OMIM-CS:headandneckeyes > CORTICAL VISUAL IMPAIRMENT (IN 1 OF 2 PATIENTS)	OMIM:617153	TAS	HPO:skoehler[2017-07-13]
2018-10-09 10:00:31.817 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.817 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:300491	#300491 EPILEPSY, X-LINKED, WITH VARIABLE LEARNING DISABILITIES AND BEHAVIORDISORDERS	HP:0007359	Focal seizures								OMIM:300491	TAS	HPO:probinson[2013-12-15]
2018-10-09 10:00:31.817 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0000655] for TermId [prefix=TermPrefix [value=HP], id=0007773] (Vitreoretinopathy): see following line
2018-10-09 10:00:31.817 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:154780	MARSHALL SYNDROME	HP:0000655	Vitreoretinal degeneration								OMIM:154780	TAS	HPO:probinson[2009-02-17]
2018-10-09 10:00:31.818 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Vitreoretinal degeneration instead of Vitreoretinopathy for Vitreoretinopathy: see following line
2018-10-09 10:00:31.818 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:154780	MARSHALL SYNDROME	HP:0000655	Vitreoretinal degeneration								OMIM:154780	TAS	HPO:probinson[2009-02-17]
2018-10-09 10:00:31.818 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0007808] for TermId [prefix=TermPrefix [value=HP], id=0000480] (Retinal coloboma): see following line
2018-10-09 10:00:31.818 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:107550	107550 AORTIC ARCH INTERRUPTION, FACIAL PALSY, AND RETINAL COLOBOMA	HP:0007808	Retinal coloboma							OMIM-CS:EYES > BILATERAL RETINAL COLOBOMA	OMIM:107550	TAS	HPO:skoehler[2015-07-26]
2018-10-09 10:00:31.818 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.818 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616875	CEREBELLAR ATROPHY, VISUAL IMPAIRMENT, AND PSYCHOMOTOR RETARDATION	HP:0100704	Cortical visual impairment								PMID:26942288	PCS	HPO:probinson[2017-06-20]
2018-10-09 10:00:31.818 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Abnormality of esophagus morphology instead of Abnormal esophagus morphology for Abnormal esophagus morphology: see following line
2018-10-09 10:00:31.818 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:226600	#226600 EPIDERMOLYSIS BULLOSA DYSTROPHICA, AUTOSOMAL RECESSIVE; RDEB;;DYSTROPHIC EPIDERMOLYSIS BULLOSA, AUTOSOMAL RECESSIVE;;EPIDERMOLYSIS BULLOSA DYSTROPHICA, HALLOPEAU-SIEMENS TYPE; EBR1EPIDERMOLYSIS BULLOSA DYSTROPHICA, AUTOSOMAL RECESSIVE, LOCALISATAVARIANT, INCLUDED;;EPIDERMOLYSIS BULLOSA DYSTROPHICA INVERSA, AUTOSOMAL RECESSIVE, INCLUDED	HP:0002031	Abnormality of esophagus morphology							OMIM-CS:ABDOMEN_GASTROINTESTINAL > ESOPHAGEAL BLISTERS	OMIM:226600	TAS	HPO:skoehler[2012-11-21]
2018-10-09 10:00:31.818 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.818 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:617235	MYOCLONUS, INTRACTABLE, NEONATAL	HP:0100704	Cortical visual impairment							OMIM-CS:headandneckeyes > CORTICAL VISUAL IMPAIRMENT	OMIM:617235	TAS	HPO:skoehler[2017-07-13]
2018-10-09 10:00:31.818 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures with impairment of consciousness or awareness instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.819 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:251950	#251950 MITOCHONDRIAL MYOPATHY WITH LACTIC ACIDOSIS; MMLA	HP:0002384	Focal seizures with impairment of consciousness or awareness							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > COMPLEX PARTIAL SEIZURES	OMIM:251950	TAS	HPO:skoehler[2015-06-22]
2018-10-09 10:00:31.819 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Generalized seizures instead of Generalized-onset seizure for Generalized-onset seizure: see following line
2018-10-09 10:00:31.819 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:602066	CONVULSIONS, FAMILIAL INFANTILE, WITH PAROXYSMAL CHOREOATHETOSIS	HP:0002197	Generalized seizures								OMIM:602066	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.819 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.819 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:602066	CONVULSIONS, FAMILIAL INFANTILE, WITH PAROXYSMAL CHOREOATHETOSIS	HP:0007359	Focal seizures								OMIM:602066	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.819 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures with impairment of consciousness or awareness instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.819 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616172	#616172 GENERALIZED EPILEPSY WITH FEBRILE SEIZURES PLUS, TYPE 9; GEFSP9;;GEFS+, TYPE 9; GEFS+9	HP:0002384	Focal seizures with impairment of consciousness or awareness							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > COMPLEX PARTIAL SEIZURES	OMIM:616172	TAS	HPO:skoehler[2015-02-22]
2018-10-09 10:00:31.819 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.819 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:615244	NEPHROTIC SYNDROME, TYPE 8; NPHS8	HP:0100704	Cortical visual impairment								OMIM:615244	TAS	HPO:skoehler[2015-12-30]
2018-10-09 10:00:31.819 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.819 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:605021	#605021 MYOCLONIC EPILEPSY, FAMILIAL INFANTILE; FIME;;EIM	HP:0007359	Focal seizures								OMIM:605021	TAS	HPO:skoehler[2012-10-17]
2018-10-09 10:00:31.820 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Abnormality of muscle morphology instead of Abnormal muscle morphology for Abnormal muscle morphology: see following line
2018-10-09 10:00:31.820 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:606072	RIPPLING MUSCLE DISEASE	HP:0011805	Abnormality of muscle morphology								OMIM:606072	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.820 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.820 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:615510	#615510 ALACRIMA, ACHALASIA, AND MENTAL RETARDATION SYNDROME; AAMR	HP:0002459	Abnormal autonomic nervous system physiology							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > AUTONOMIC DYSFUNCTION	OMIM:615510	TAS	HPO:skoehler[2014-01-28]
2018-10-09 10:00:31.820 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.820 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:613457	#613457 CHROMOSOME 14q11-q22 DELETION SYNDROME	HP:0100704	Cortical visual impairment							OMIM-CS:HEAD AND NECK_EYES > CORTICAL BLINDNESS	OMIM:613457	TAS	HPO:skoehler[2012-10-17]
2018-10-09 10:00:31.820 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Generalized seizures instead of Generalized-onset seizure for Generalized-onset seizure: see following line
2018-10-09 10:00:31.820 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:254900	ACTION MYOCLONUS-RENAL FAILURE SYNDROME	HP:0002197	Generalized seizures								OMIM:254900	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.820 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Severe visual impairment instead of Severe vision loss for Severe vision loss: see following line
2018-10-09 10:00:31.820 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:300600	ALAND ISLAND EYE DISEASE	HP:0001141	Severe visual impairment								OMIM:300600	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.820 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.821 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616632	#616632 SEIZURES, CORTICAL BLINDNESS, MICROCEPHALY SYNDROME; SCBMS	HP:0100704	Cortical visual impairment							OMIM-CS:HEAD AND NECK_EYES > CORTICAL BLINDNESS	OMIM:616632	TAS	HPO:skoehler[2015-11-15]
2018-10-09 10:00:31.821 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0011498] for TermId [prefix=TermPrefix [value=HP], id=0000526] (Aniridia): see following line
2018-10-09 10:00:31.821 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:206750	ANIRIDIA, PARTIAL, WITH UNILATERAL RENAL AGENESIS AND PSYCHOMOTORRETARDATION	HP:0011498	Aniridia								OMIM:206750	TAS	HPO:probinson[2012-07-21]
2018-10-09 10:00:31.821 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures without impairment of consciousness or awareness instead of Focal aware seizure for Focal aware seizure: see following line
2018-10-09 10:00:31.821 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:600512	EPILEPSY, LATERAL TEMPORAL LOBE, AUTOSOMAL DOMINANT	HP:0002349	Focal seizures without impairment of consciousness or awareness								OMIM:600512	TAS	HPO:probinson[2009-02-17]
2018-10-09 10:00:31.821 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures with impairment of consciousness or awareness instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.821 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:600512	EPILEPSY, LATERAL TEMPORAL LOBE, AUTOSOMAL DOMINANT	HP:0002384	Focal seizures with impairment of consciousness or awareness								OMIM:600512	TAS	HPO:probinson[2009-02-17]
2018-10-09 10:00:31.821 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Auditory auras instead of Focal sensory auditory seizure for Focal sensory auditory seizure: see following line
2018-10-09 10:00:31.821 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:600512	EPILEPSY, LATERAL TEMPORAL LOBE, AUTOSOMAL DOMINANT	HP:0011158	Auditory auras								OMIM:600512	TAS	HPO:probinson[2012-07-31]
2018-10-09 10:00:31.821 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.821 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:615182	#615182 COMBINED D-2- AND L-2-HYDROXYGLUTARIC ACIDURIA; D2L2AD	HP:0100704	Cortical visual impairment			HP:0040283				OMIM-CS:HEAD AND NECK_EYES > CORTICAL BLINDNESS (1 PATIENT)	OMIM:615182	TAS	HPO:skoehler[2013-05-03]
2018-10-09 10:00:31.822 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.822 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:600513	EPILEPSY, NOCTURNAL FRONTAL LOBE, TYPE 1	HP:0007359	Focal seizures								PMID:7895015	PCS	HPO:probinson[2009-02-17]
2018-10-09 10:00:31.822 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Abnormality of the eyelashes instead of Abnormal eyelash morphology for Abnormal eyelash morphology: see following line
2018-10-09 10:00:31.822 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:611426	611426 TENTED EYEBROWS	HP:0000499	Abnormality of the eyelashes					NOT		OMIM-CS:HEAD AND NECK_EYES > NORMAL EYELASHES	OMIM:611426	TAS	HPO:skoehler[2014-11-27]
2018-10-09 10:00:31.822 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Abnormality of the eyelashes instead of Abnormal eyelash morphology for Abnormal eyelash morphology: see following line
2018-10-09 10:00:31.822 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:611426	611426 TENTED EYEBROWS	HP:0000499	Abnormality of the eyelashes					NOT		OMIM-CS:SKIN, NAILS, HAIR_HAIR > NORMAL EYELASHES	OMIM:611426	TAS	HPO:skoehler[2014-11-27]
2018-10-09 10:00:31.822 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.822 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616809	HYPERPHOSPHATASIA WITH MENTAL RETARDATION SYNDROME 6; HPMRS6	HP:0100704	Cortical visual impairment							OMIM-CS:headAndNeckEyes > CEREBRAL VISUAL IMPAIRMENT (FAMILY A)	OMIM:616809	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.822 ERROR main [main] (V2LineQualityController.java:428) - Invalid frequency term (see next line): Chronic
2018-10-09 10:00:31.822 ERROR main [main] (V2LineQualityController.java:428) - Bad frequency [Chronic]: OMIM:615224	#615224 ADVANCED SLEEP PHASE SYNDROME, FAMILIAL, 2; FASPS2	HP:0002076	Migraine			Chronic					PMID:23636092	PCS	HPO:lccarmody[2018-09-19];HPO:lccarmody[2018-09-19]
2018-10-09 10:00:31.822 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.822 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:610131	#610131 PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA WITH MITOCHONDRIAL DNA DELETIONS,AUTOSOMAL DOMINANT, 4; PEOA4;;PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA, AUTOSOMAL DOMINANT, 4	HP:0100704	Cortical visual impairment			HP:0040283				OMIM-CS:HEAD AND NECK_EYES > CORTICAL BLINDNESS (1 PATIENT)	OMIM:610131	TAS	HPO:skoehler[2013-04-02]
2018-10-09 10:00:31.822 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Generalized seizures instead of Generalized-onset seizure for Generalized-onset seizure: see following line
2018-10-09 10:00:31.823 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:300842	#300842 MCLEOD SYNDROME; MCLDS;;MCLEOD PHENOTYPE;;NEUROACANTHOCYTOSIS, MCLEOD TYPEMCLEOD SYNDROME WITH CHRONIC GRANULOMATOUS DISEASE, INCLUDED	HP:0002197	Generalized seizures								OMIM:300842	IEA	HPO:skoehler[2013-01-11]
2018-10-09 10:00:31.823 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0011146] for TermId [prefix=TermPrefix [value=HP], id=0002384] (Focal impaired awareness seizure): see following line
2018-10-09 10:00:31.823 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:607745	SEIZURES, BENIGN FAMILIAL NEONATAL-INFANTILE	HP:0011146	Dialeptic seizures								OMIM:607745	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.823 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Dialeptic seizures instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.823 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:607745	SEIZURES, BENIGN FAMILIAL NEONATAL-INFANTILE	HP:0011146	Dialeptic seizures								OMIM:607745	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.823 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.824 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:607745	SEIZURES, BENIGN FAMILIAL NEONATAL-INFANTILE	HP:0007359	Focal seizures								OMIM:607745	TAS	HPO:iea[2012-07-20]
2018-10-09 10:00:31.824 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.824 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:609056	#609056 AMISH INFANTILE EPILEPSY SYNDROME;;EPILEPSY SYNDROME, INFANTILE-ONSET SYMPTOMATIC;;GM3 SYNTHASE DEFICIENCY	HP:0100704	Cortical visual impairment								OMIM:609056	TAS	HPO:skoehler[2013-06-04]
2018-10-09 10:00:31.824 ERROR main [main] (V2LineQualityController.java:428) - Invalid frequency term (see next line): 96.7% 
2018-10-09 10:00:31.824 ERROR main [main] (V2LineQualityController.java:428) - Bad frequency [96.7% ]: OMIM:146255	HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE	HP:0000407	Sensorineural hearing impairment			96.7% 					PMID:29663634	PCS	HPO:nvasilevsky;HPO:nvasilevsky[2018-08-02]
2018-10-09 10:00:31.824 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.824 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:613608	%613608 EPILEPSY, FAMILIAL ADULT MYOCLONIC, 3; FAME3;;CORTICAL MYOCLONIC TREMOR WITH EPILEPSY, FAMILIAL, 3; FCMTE3	HP:0007359	Focal seizures							OMIM-CS:NEUROLOGIC > PARTIAL SEIZURES	OMIM:613608	TAS	HPO:skoehler[2012-10-17]
2018-10-09 10:00:31.824 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Abnormality of the temporal bone instead of Abnormal temporal bone morphology for Abnormal temporal bone morphology: see following line
2018-10-09 10:00:31.824 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:613703	MICROPHTHALMIA, ISOLATED, WITH COLOBOMA 6	HP:0009911	Abnormality of the temporal bone			1/2				anomalous right temporal bone	PMID:19864492	PCS	HPO:iea[2012-04-24]
2018-10-09 10:00:31.824 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.824 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:605543	PARKINSON DISEASE 4, AUTOSOMAL DOMINANT LEWY BODY	HP:0002459	Abnormal autonomic nervous system physiology								OMIM:605543	TAS	HPO:probinson[2012-07-19]
2018-10-09 10:00:31.824 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Abnormality of the eyelashes instead of Abnormal eyelash morphology for Abnormal eyelash morphology: see following line
2018-10-09 10:00:31.825 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:180730	ROMBO SYNDROME	HP:0000499	Abnormality of the eyelashes								OMIM:180730	PCS	HPO:iea[2012-02-21]
2018-10-09 10:00:31.825 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0007782] for TermId [prefix=TermPrefix [value=HP], id=0007769] (Peripheral retinal degeneration): see following line
2018-10-09 10:00:31.825 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:609021	PERIPHERAL CONE DYSTROPHY	HP:0007782	Peripheral retinal degeneration								OMIM:609021	TAS	HPO:probinson[2012-04-28]
2018-10-09 10:00:31.825 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.825 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:617599	EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 55; EIEE55	HP:0100704	Cortical visual impairment							OMIM-CS:headAndNeckEyes > CORTICAL VISUAL IMPAIRMENT	OMIM:617599	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.825 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Abnormality of the eyelashes instead of Abnormal eyelash morphology for Abnormal eyelash morphology: see following line
2018-10-09 10:00:31.825 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:147791	#147791 JACOBSEN SYNDROME; JBS;;CHROMOSOME 11q DELETION SYNDROME;;PARTIAL 11q MONOSOMY SYNDROME	HP:0000499	Abnormality of the eyelashes							OMIM-CS:HEAD AND NECK_EYES > ABNORMAL EYELASHES	OMIM:147791	TAS	HPO:skoehler[2014-11-27]
2018-10-09 10:00:31.825 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Abnormality of the eyelashes instead of Abnormal eyelash morphology for Abnormal eyelash morphology: see following line
2018-10-09 10:00:31.825 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:147791	#147791 JACOBSEN SYNDROME; JBS;;CHROMOSOME 11q DELETION SYNDROME;;PARTIAL 11q MONOSOMY SYNDROME	HP:0000499	Abnormality of the eyelashes							OMIM-CS:SKIN, NAILS, HAIR_HAIR > ABNORMAL EYELASHES	OMIM:147791	TAS	HPO:skoehler[2014-11-27]
2018-10-09 10:00:31.825 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.825 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616034	#616034 2,4-@DIENOYL-CoA REDUCTASE DEFICIENCY; DECRD	HP:0100704	Cortical visual impairment							OMIM-CS:HEAD AND NECK_EYES > CORTICAL BLINDNESS	OMIM:616034	TAS	HPO:skoehler[2015-01-04]
2018-10-09 10:00:31.825 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.825 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:617268	Neurodevelopmental disorder with hypotonia, seizures, and absent language	HP:0100704	Cortical visual impairment			3/7					PMID:27389779	PCS	HP:probinson[2018-07-05]
2018-10-09 10:00:31.826 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.826 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:615548	#615548 NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE VII; HSAN7;;HSAN VII;;INSENSITIVITY TO PAIN, CONGENITAL, WITH GASTROINTESTINAL DYSFUNCTIONAND HYPERHIDROSIS	HP:0002459	Abnormal autonomic nervous system physiology							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > AUTONOMIC DYSFUNCTION	OMIM:615548	TAS	HPO:skoehler[2014-01-28]
2018-10-09 10:00:31.826 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0008024] for TermId [prefix=TermPrefix [value=HP], id=0100018] (Nuclear cataract): see following line
2018-10-09 10:00:31.826 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:604307	#604307 CATARACT, COPPOCK-LIKE; CCL;;CATARACT, EMBRYONIC NUCLEAR	HP:0008024	Nuclear cataract								OMIM:604307	TAS	HPO:probinson[2013-02-19]
2018-10-09 10:00:31.826 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.826 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:614652	#614652 COENZYME Q10 DEFICIENCY, PRIMARY, 3; COQ10D3	HP:0100704	Cortical visual impairment							OMIM-CS:HEAD AND NECK_EYES > CORTICAL BLINDNESS	OMIM:614652	TAS	HPO:skoehler[2012-10-17]
2018-10-09 10:00:31.826 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.826 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:105210	AMYLOIDOSIS VII	HP:0002459	Abnormal autonomic nervous system physiology								OMIM:105210	IEA	HPO:skoehler[2012-10-12]
2018-10-09 10:00:31.826 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Generalized seizures instead of Generalized-onset seizure for Generalized-onset seizure: see following line
2018-10-09 10:00:31.826 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:300912	MENTAL RETARDATION, X-LINKED 98; MRX98	HP:0002197	Generalized seizures							OMIM-CS:neurologicCentralNervousSystem > GENERALIZED SEIZURES	OMIM:300912	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.826 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Severe visual impairment instead of Severe vision loss for Severe vision loss: see following line
2018-10-09 10:00:31.827 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:613794	RETINITIS PIGMENTOSA 20	HP:0001141	Severe visual impairment							OMIM-CS:headandneckeyes > SEVERE VISUAL IMPAIRMENT	OMIM:613794	TAS	HPO:skoehler[2017-07-13]
2018-10-09 10:00:31.827 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.827 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:540000	MITOCHONDRIAL MYOPATHY, ENCEPHALOPATHY, LACTIC ACIDOSIS, AND STROKE-LIKEEPISODES	HP:0100704	Cortical visual impairment								OMIM:540000	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.827 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.827 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:617516	STANKIEWICZ-ISIDOR SYNDROME; STISS	HP:0100704	Cortical visual impairment							OMIM-CS:headAndNeckEyes > CORTICAL VISUAL IMPAIRMENT	OMIM:617516	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.827 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Severe visual impairment instead of Severe vision loss for Severe vision loss: see following line
2018-10-09 10:00:31.827 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:613826	#613826 LEBER CONGENITAL AMAUROSIS 6; LCA6	HP:0001141	Severe visual impairment								OMIM:613826	TAS	HPO:probinson[2013-08-10]
2018-10-09 10:00:31.827 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.827 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:604403	#604403 GENERALIZED EPILEPSY WITH FEBRILE SEIZURES PLUS, TYPE 2; GEFSP2;;GEFS+, TYPE 2; GEFS+2FEBRILE SEIZURES, FAMILIAL, 3A, INCLUDED; FEB3A, INCLUDED	HP:0007359	Focal seizures							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > PARTIAL SEIZURES	OMIM:604403	TAS	HPO:skoehler[2012-10-17]
2018-10-09 10:00:31.827 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.827 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:300868	#300868 MULTIPLE CONGENITAL ANOMALIES-HYPOTONIA-SEIZURES SYNDROME 2; MCAHS2;;EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 20; EIEE20	HP:0100704	Cortical visual impairment							OMIM-CS:HEAD AND NECK_EYES > CORTICAL BLINDNESS	OMIM:300868	TAS	HPO:skoehler[2014-06-24]
2018-10-09 10:00:31.827 ERROR main [main] (V2LineQualityController.java:428) - Invalid frequency term (see next line): Occasional
2018-10-09 10:00:31.827 ERROR main [main] (V2LineQualityController.java:428) - Bad frequency [Occasional]: OMIM:139500	HAIRY EARS	HP:0000819	Diabetes mellitus			Occasional					PMID:2364572	PCS	HPO:nvasilevsky[2018-08-30]
2018-10-09 10:00:31.827 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0008033] for TermId [prefix=TermPrefix [value=HP], id=0000577] (Exotropia): see following line
2018-10-09 10:00:31.828 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:133705	EXTERNAL AUDITORY CANAL, BILATERAL ATRESIA OF, WITH CONGENITAL VERTICALTALUS	HP:0008033	Exotropia								OMIM:133705	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.828 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Generalized seizures instead of Generalized-onset seizure for Generalized-onset seizure: see following line
2018-10-09 10:00:31.828 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:615501	#615501 MOLYBDENUM COFACTOR DEFICIENCY, COMPLEMENTATION GROUP C; MOCODC	HP:0002197	Generalized seizures							OMIM-TX: 'g difficulties, and generalized seizures. brainmri showed c'	OMIM:615501	IEA	HPO:skoehler[2015-08-30]
2018-10-09 10:00:31.828 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures with impairment of consciousness or awareness instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.828 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:610003	CEROID LIPOFUSCINOSIS, NEURONAL, 8, NORTHERN EPILEPSY VARIANT	HP:0002384	Focal seizures with impairment of consciousness or awareness								OMIM:610003	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.828 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures with impairment of consciousness or awareness instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.828 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:607208	SEVERE MYOCLONIC EPILEPSY OF INFANCY	HP:0002384	Focal seizures with impairment of consciousness or awareness								OMIM:607208	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.828 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.828 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:607208	#607208 DRAVET SYNDROME;;EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 6; EIEE6;;SEVERE MYOCLONIC EPILEPSY OF INFANCY; SMEI	HP:0100704	Cortical visual impairment								OMIM:607208	TAS	HPO:skoehler[2013-01-22]
2018-10-09 10:00:31.828 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Moderate visual impairment instead of Moderate vision loss for Moderate vision loss: see following line
2018-10-09 10:00:31.828 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616151	#616151 MACULAR DYSTROPHY, VITELLIFORM, 4; VMD4	HP:0030515	Moderate visual impairment							OMIM-TX: 'rized by late-onset moderate visual impairment, smallsatellite dr'	OMIM:616151	IEA	HPO:skoehler[2015-09-15]
2018-10-09 10:00:31.829 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.829 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616268	#616268 MENTAL RETARDATION, AUTOSOMAL DOMINANT 32; MRD32	HP:0100704	Cortical visual impairment							OMIM-CS:HEAD AND NECK_EYES > CORTICAL VISUAL IMPAIRMENT	OMIM:616268	TAS	HPO:skoehler[2015-05-31]
2018-10-09 10:00:31.829 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.829 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:231550	ACHALASIA-ADDISONIANISM-ALACRIMA SYNDROME	HP:0002459	Abnormal autonomic nervous system physiology								OMIM:231550	TAS	HPO:probinson[2012-04-11]
2018-10-09 10:00:31.829 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0000655] for TermId [prefix=TermPrefix [value=HP], id=0007773] (Vitreoretinopathy): see following line
2018-10-09 10:00:31.829 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:267750	KNOBLOCH SYNDROME, TYPE I	HP:0000655	Vitreoretinal degeneration								OMIM:267750	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.829 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Vitreoretinal degeneration instead of Vitreoretinopathy for Vitreoretinopathy: see following line
2018-10-09 10:00:31.829 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:267750	KNOBLOCH SYNDROME, TYPE I	HP:0000655	Vitreoretinal degeneration								OMIM:267750	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.829 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Abnormality of the eyelashes instead of Abnormal eyelash morphology for Abnormal eyelash morphology: see following line
2018-10-09 10:00:31.829 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:300042	ALOPECIA, CONGENITAL	HP:0000499	Abnormality of the eyelashes					NOT			OMIM:300042	TAS	HPO:probinson[2012-07-19]
2018-10-09 10:00:31.829 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.829 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:615552	#615552 EPISODIC PAIN SYNDROME, FAMILIAL, 3; FEPS3	HP:0002459	Abnormal autonomic nervous system physiology			HP:0040282				OMIM-CS:NEUROLOGIC > AUTONOMIC DYSFUNCTION, VARIABLE	OMIM:615552	TAS	HPO:skoehler[2014-11-26]
2018-10-09 10:00:31.829 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.830 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:614254	NEURODEVELOPMENTAL DISORDER WITH OR WITHOUT HYPERKINETIC MOVEMENTS AND SEIZURES, AUTOSOMAL DOMINANT; NDHMSD	HP:0100704	Cortical visual impairment			HP:0040284				OMIM-CS:headAndNeckEyes > CORTICAL BLINDNESS (IN SOME PATIENTS)	OMIM:614254	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.830 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.830 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:613863	#613863 GENERALIZED EPILEPSY WITH FEBRILE SEIZURES PLUS, TYPE 7; GEFSP7;;GEFS+, TYPE 7; GEFS+7FEBRILE SEIZURES, FAMILIAL, 3B, INCLUDED; FEB3B, INCLUDED	HP:0007359	Focal seizures							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > PARTIAL SEIZURES	OMIM:613863	TAS	HPO:skoehler[2012-10-17]
2018-10-09 10:00:31.830 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Increased mean corpuscular hemoglobin instead of Increased mean corpuscular hemoglobin concentration for Increased mean corpuscular hemoglobin concentration: see following line
2018-10-09 10:00:31.830 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:194380	DEHYDRATED HEREDITARY STOMATOCYTOSIS 1 WITH OR WITHOUT PSEUDOHYPERKALEMIA AND/OR PERINATAL EDEMA; DHS1	HP:0025548	Increased mean corpuscular hemoglobin							OMIM-CS:hematology > INCREASED MEAN CORPUSCULAR HEMOGLOBIN CONCENTRATION	OMIM:194380	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.830 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures with impairment of consciousness or awareness instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.830 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616193	#616193 MENTAL RETARDATION, AUTOSOMAL RECESSIVE 47; MRT47	HP:0002384	Focal seizures with impairment of consciousness or awareness			HP:0040283				OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > COMPLEX PARTIAL SEIZURES (IN SOME PATIENTS)	OMIM:616193	TAS	HPO:skoehler[2015-02-22]
2018-10-09 10:00:31.830 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.830 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: DECIPHER:59	Adult-onset autosomal dominant leukodystrophy (ADLD)	HP:0002459	Abnormal autonomic nervous system physiology								DECIPHER:59	IEA	HPO:skoehler[2013-05-29]
2018-10-09 10:00:31.830 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.830 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:610954	#610954 PITT-HOPKINS SYNDROME; PTHS;;ENCEPHALOPATHY, SEVERE EPILEPTIC, WITH AUTONOMIC DYSFUNCTION;;MENTAL RETARDATION, SYNDROMAL, WITH INTERMITTENT HYPERVENTILATION	HP:0002459	Abnormal autonomic nervous system physiology							Disease name contained:ere epileptic, with autonomic dysfunction;;mental retardation	OMIM:610954	IEA	HPO:skoehler[2015-01-21]
2018-10-09 10:00:31.830 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.830 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:610042	PITT-HOPKINS-LIKE SYNDROME 1; PTHSL1	HP:0007359	Focal seizures							OMIM-CS:neurologicCentralNervousSystem > FOCAL SEIZURES	OMIM:610042	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.830 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Generalized seizures instead of Generalized-onset seizure for Generalized-onset seizure: see following line
2018-10-09 10:00:31.831 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:610042	PITT-HOPKINS-LIKE SYNDROME 1; PTHSL1	HP:0002197	Generalized seizures							OMIM-CS:neurologicCentralNervousSystem > GENERALIZED SEIZURES	OMIM:610042	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.831 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.831 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:614255	#614255 MENTAL RETARDATION, AUTOSOMAL DOMINANT 9; MRD9	HP:0100704	Cortical visual impairment			HP:0040283				OMIM-CS:HEAD AND NECK_EYES > CORTICAL VISUAL IMPAIRMENT (IN SOME PATIENTS)	OMIM:614255	TAS	HPO:skoehler[2015-10-05]
2018-10-09 10:00:31.831 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Generalized seizures instead of Generalized-onset seizure for Generalized-onset seizure: see following line
2018-10-09 10:00:31.831 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:271900	CANAVAN DISEASE	HP:0002197	Generalized seizures							Early	OMIM:264470	PCS	HPO:probinson[2012-04-11]
2018-10-09 10:00:31.831 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.831 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:243000	INDIFFERENCE TO PAIN, CONGENITAL, AUTOSOMAL RECESSIVE; CIP	HP:0002459	Abnormal autonomic nervous system physiology								OMIM:243000	TAS	HPO:skoehler[2015-12-30]
2018-10-09 10:00:31.831 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.831 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:301500	FABRY DISEASE	HP:0002459	Abnormal autonomic nervous system physiology								OMIM:301500	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.831 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.831 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:606232	CHROMOSOME 22q13.3 DELETION SYNDROME	HP:0100704	Cortical visual impairment			6%					http://www.ncbi.nlm.nih.gov/books/NBK1198/	PCS	HPO:iea[2012-04-24]
2018-10-09 10:00:31.831 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures with impairment of consciousness or awareness instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.831 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:612691	#612691 POLYMICROGYRIA, BILATERAL TEMPOROOCCIPITAL; BTOP	HP:0002384	Focal seizures with impairment of consciousness or awareness							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > COMPLEX FOCAL SEIZURES	OMIM:612691	TAS	HPO:skoehler[2014-10-06]
2018-10-09 10:00:31.832 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.832 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:614961	#614961 PONTOCEREBELLAR HYPOPLASIA, TYPE 8; PCH8	HP:0100704	Cortical visual impairment			HP:0040283				OMIM-CS:HEAD AND NECK_EYES > CORTICAL VISUAL IMPAIRMENT (IN SOME PATIENTS)	OMIM:614961	TAS	HPO:skoehler[2012-12-30]
2018-10-09 10:00:31.832 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Generalized seizures instead of Generalized-onset seizure for Generalized-onset seizure: see following line
2018-10-09 10:00:31.832 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:601764	CONVULSIONS, BENIGN FAMILIAL INFANTILE, 1	HP:0002197	Generalized seizures								OMIM:601764	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.832 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0011146] for TermId [prefix=TermPrefix [value=HP], id=0002384] (Focal impaired awareness seizure): see following line
2018-10-09 10:00:31.832 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:601764	CONVULSIONS, BENIGN FAMILIAL INFANTILE, 1	HP:0011146	Dialeptic seizures								OMIM:601764	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.832 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Dialeptic seizures instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.832 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:601764	CONVULSIONS, BENIGN FAMILIAL INFANTILE, 1	HP:0011146	Dialeptic seizures								OMIM:601764	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.832 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.832 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:601764	CONVULSIONS, BENIGN FAMILIAL INFANTILE, 1	HP:0007359	Focal seizures								OMIM:601764	TAS	HPO:probinson[2013-02-27]
2018-10-09 10:00:31.832 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0001226] for TermId [prefix=TermPrefix [value=HP], id=0006121] (Acral ulceration): see following line
2018-10-09 10:00:31.833 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:256860	NEUROPATHY, HEREDITARY SENSORY, ATYPICAL	HP:0001226	Acral ulceration					NOT			OMIM:256860	TAS	HPO:skoehler[2009-02-17]
2018-10-09 10:00:31.833 ERROR main [main] (V2LineQualityController.java:428) - Invalid frequency term (see next line): Very frequent
2018-10-09 10:00:31.833 ERROR main [main] (V2LineQualityController.java:428) - Bad frequency [Very frequent]: OMIM:614266	#614266 BARRETT ESOPHAGUS;;BARRETT METAPLASIAADENOCARCINOMA OF ESOPHAGUS, INCLUDED	HP:0004791	Esophageal ulceration			Very frequent					PMID:14791960	PCS	HPO:lccarmody[2018-10-04]
2018-10-09 10:00:31.833 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.833 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:600072	FATAL FAMILIAL INSOMNIA	HP:0002459	Abnormal autonomic nervous system physiology								OMIM:600072	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.833 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Generalized seizures instead of Generalized-onset seizure for Generalized-onset seizure: see following line
2018-10-09 10:00:31.833 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:300672	#300672 EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 2; EIEE2;;INFANTILE SPASM SYNDROME, X-LINKED 2; ISSX2	HP:0002197	Generalized seizures							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > GENERALIZED SEIZURES	OMIM:300672	TAS	HPO:skoehler[2013-06-23]
2018-10-09 10:00:31.833 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.833 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:300672	#300672 EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 2; EIEE2;;INFANTILE SPASM SYNDROME, X-LINKED 2; ISSX2	HP:0100704	Cortical visual impairment								PMID:22264704	PCS	HP:probinson[2018-05-13]
2018-10-09 10:00:31.833 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.833 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:613722	#613722 EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 12; EIEE12	HP:0007359	Focal seizures							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > FOCAL SEIZURES	OMIM:613722	TAS	HPO:skoehler[2012-10-17]
2018-10-09 10:00:31.833 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Generalized seizures instead of Generalized-onset seizure for Generalized-onset seizure: see following line
2018-10-09 10:00:31.833 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:613722	#613722 EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 12; EIEE12	HP:0002197	Generalized seizures							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > GENERALIZED SEIZURES	OMIM:613722	TAS	HPO:skoehler[2012-10-17]
2018-10-09 10:00:31.833 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Severe visual impairment instead of Severe vision loss for Severe vision loss: see following line
2018-10-09 10:00:31.833 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:262300	ACHROMATOPSIA 3	HP:0001141	Severe visual impairment								OMIM:262300	TAS	HPO:probinson[2012-08-01]
2018-10-09 10:00:31.834 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Abnormality of the eyelashes instead of Abnormal eyelash morphology for Abnormal eyelash morphology: see following line
2018-10-09 10:00:31.834 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:206920	#206920 MICROPHTHALMIA WITH LIMB ANOMALIES;;WAARDENBURG ANOPHTHALMIA SYNDROME;;ANOPHTHALMIA-SYNDACTYLY;;OPHTHALMOACROMELIC SYNDROME; OAS	HP:0000499	Abnormality of the eyelashes					NOT		OMIM-CS:SKIN, NAILS, HAIR_HAIR > NORMAL EYELASHES	OMIM:206920	TAS	HPO:skoehler[2014-11-27]
2018-10-09 10:00:31.834 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Abnormality of esophagus morphology instead of Abnormal esophagus morphology for Abnormal esophagus morphology: see following line
2018-10-09 10:00:31.834 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:164330	ODONTOMA-DYSPHAGIA SYNDROME	HP:0002031	Abnormality of esophagus morphology								OMIM:164330	TAS	HPO:probinson[2015-06-02]
2018-10-09 10:00:31.834 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.834 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:617140	ZTTK SYNDROME	HP:0100704	Cortical visual impairment							OMIM-CS:headandneckeyes > CORTICAL VISUAL IMPAIRMENT	OMIM:617140	TAS	HPO:skoehler[2017-07-13]
2018-10-09 10:00:31.834 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.834 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616900	HYPOTONIA, INFANTILE, WITH PSYCHOMOTOR RETARDATION AND CHARACTERISTIC FACIES 3	HP:0100704	Cortical visual impairment			4/5					PMID:27040692	PCS	HPO:probinson[2017-06-24]
2018-10-09 10:00:31.834 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0000655] for TermId [prefix=TermPrefix [value=HP], id=0007773] (Vitreoretinopathy): see following line
2018-10-09 10:00:31.834 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:183900	SPONDYLOEPIPHYSEAL DYSPLASIA CONGENITA	HP:0000655	Vitreoretinal degeneration								OMIM:183900	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.834 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Vitreoretinal degeneration instead of Vitreoretinopathy for Vitreoretinopathy: see following line
2018-10-09 10:00:31.834 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:183900	SPONDYLOEPIPHYSEAL DYSPLASIA CONGENITA	HP:0000655	Vitreoretinal degeneration								OMIM:183900	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.834 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0000655] for TermId [prefix=TermPrefix [value=HP], id=0007773] (Vitreoretinopathy): see following line
2018-10-09 10:00:31.835 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:614284	#614284 STICKLER SYNDROME, TYPE V; STL5	HP:0000655	Vitreoretinal degeneration							OMIM-CS:HEAD AND NECK_EYES > VITREORETINAL DEGENERATION	OMIM:614284	TAS	HPO:skoehler[2012-10-17]
2018-10-09 10:00:31.835 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Vitreoretinal degeneration instead of Vitreoretinopathy for Vitreoretinopathy: see following line
2018-10-09 10:00:31.835 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:614284	#614284 STICKLER SYNDROME, TYPE V; STL5	HP:0000655	Vitreoretinal degeneration							OMIM-CS:HEAD AND NECK_EYES > VITREORETINAL DEGENERATION	OMIM:614284	TAS	HPO:skoehler[2012-10-17]
2018-10-09 10:00:31.835 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.835 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:615476	#615476 EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 18; EIEE18	HP:0007359	Focal seizures							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > FOCAL SEIZURES	OMIM:615476	TAS	HPO:skoehler[2013-11-18]
2018-10-09 10:00:31.835 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Generalized seizures instead of Generalized-onset seizure for Generalized-onset seizure: see following line
2018-10-09 10:00:31.835 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:615476	#615476 EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 18; EIEE18	HP:0002197	Generalized seizures							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > GENERALIZED SEIZURES	OMIM:615476	TAS	HPO:skoehler[2013-11-18]
2018-10-09 10:00:31.835 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.835 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:133020	#133020 ERYTHERMALGIA, PRIMARY;;ERYTHROMELALGIA, PRIMARY;;ERYTHROMELALGIA, FAMILIALNEUROPATHY, SMALL FIBER, INCLUDED; SFNP, INCLUDED	HP:0002459	Abnormal autonomic nervous system physiology			HP:0040283				OMIM-CS:NEUROLOGIC_PERIPHERAL NERVOUS SYSTEM > AUTONOMIC DYSFUNCTION (IN SOME PATIENTS)	OMIM:133020	TAS	HPO:skoehler[2014-11-26]
2018-10-09 10:00:31.835 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.835 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:224000	DYSAUTONOMIA-LIKE DISORDER	HP:0002459	Abnormal autonomic nervous system physiology							Disease name contained:dysautonomia-like disorder	OMIM:224000	IEA	HPO:skoehler[2015-01-27]
2018-10-09 10:00:31.835 ERROR main [main] (V2LineQualityController.java:428) - Invalid frequency term (see next line): Obligate
2018-10-09 10:00:31.835 ERROR main [main] (V2LineQualityController.java:428) - Bad frequency [Obligate]: OMIM:228400	FEVER, FAMILIAL LIFELONG PERSISTENT	HP:0001945	Fever			Obligate				Persistent	OMIM:228400	TAS	HPO:probinson[2009-02-17];HPO:lccarmody[2018-10-04]
2018-10-09 10:00:31.835 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:117100	CENTRALOPATHIC EPILEPSY	HP:0007359	Focal seizures								OMIM:117100	TAS	HPO:probinson[2013-12-15]
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616954	YOU-HOOVER-FONG SYNDROME	HP:0100704	Cortical visual impairment			HP:0040283				OMIM-CS:headandneckeyes > CORTICAL VISUAL IMPAIRMENT (IN SOME PATIENTS)	OMIM:616954	TAS	HPO:skoehler[2017-07-13]
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Invalid frequency term (see next line): Obligate
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Bad frequency [Obligate]: OMIM:164230	OBSESSIVE-COMPULSIVE DISORDER 1	HP:0000722	Obsessive-compulsive behavior			Obligate					OMIM:164230	IEA	HPO:iea[2009-02-17];HPO:lccarmody[2018-10-02]
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Invalid frequency term (see next line): Obligate
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Bad frequency [Obligate]: OMIM:613285	#613285 DEAFNESS, AUTOSOMAL RECESSIVE 25; DFNB25	HP:0000365	Hearing impairment	HP:0011463	Childhood onset	Obligate					PMID:20137778	TAS	HPO:skoehler[2015-01-21];HPO:lccarmody[2018-10-04]
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures without impairment of consciousness or awareness instead of Focal aware seizure for Focal aware seizure: see following line
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:611630	EPILEPSY, FAMILIAL MESIAL TEMPORAL LOBE	HP:0002349	Focal seizures without impairment of consciousness or awareness								OMIM:611630	TAS	HPO:probinson[2009-02-17]
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures with impairment of consciousness or awareness instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:611630	EPILEPSY, FAMILIAL MESIAL TEMPORAL LOBE	HP:0002384	Focal seizures with impairment of consciousness or awareness								OMIM:611630	TAS	HPO:probinson[2009-02-17]
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0000655] for TermId [prefix=TermPrefix [value=HP], id=0007773] (Vitreoretinopathy): see following line
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:193230	VITREORETINAL DEGENERATION, SNOWFLAKE TYPE	HP:0000655	Vitreoretinal degeneration							Disease name contained:vitreoretinal degeneration, snowflake type	OMIM:193230	IEA	HPO:skoehler[2015-01-27]
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Vitreoretinal degeneration instead of Vitreoretinopathy for Vitreoretinopathy: see following line
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:193230	VITREORETINAL DEGENERATION, SNOWFLAKE TYPE	HP:0000655	Vitreoretinal degeneration							Disease name contained:vitreoretinal degeneration, snowflake type	OMIM:193230	IEA	HPO:skoehler[2015-01-27]
2018-10-09 10:00:31.836 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:105120	AMYLOIDOSIS V	HP:0002459	Abnormal autonomic nervous system physiology					NOT			OMIM:105120	IEA	HPO:skoehler[2010-06-20]
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:105120	AMYLOIDOSIS V	HP:0002459	Abnormal autonomic nervous system physiology					NOT			OMIM:105120	IEA	HPO:skoehler[2012-10-11]
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:615859	#615859 EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 23; EIEE23	HP:0100704	Cortical visual impairment							OMIM-CS:HEAD AND NECK_EYES > CORTICAL BLINDNESS	OMIM:615859	TAS	HPO:skoehler[2014-07-11]
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:615859	#615859 EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 23; EIEE23	HP:0100704	Cortical visual impairment							OMIM-CS:HEAD AND NECK_EYES > CORTICAL VISUAL IMPAIRMENT	OMIM:615859	TAS	HPO:skoehler[2014-07-11]
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Invalid frequency term (see next line): Very rare
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Bad frequency [Very rare]: OMIM:305400	FACIOGENITAL DYSPLASIA	HP:0001256	Intellectual disability, mild			Very rare					PMID:20082460	IEA	HP:probinson[2018-09-23]
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616973	MENTAL RETARDATION, AUTOSOMAL DOMINANT 42	HP:0100704	Cortical visual impairment			HP:0040283				OMIM-CS:headandneckeyes > CORTICAL VISUAL IMPAIRMENT (IN SOME PATIENTS)	OMIM:616973	TAS	HPO:skoehler[2017-07-13]
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0008024] for TermId [prefix=TermPrefix [value=HP], id=0100018] (Nuclear cataract): see following line
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:601701	ARTHROGRYPOSIS AND ECTODERMAL DYSPLASIA	HP:0008024	Nuclear cataract								OMIM:601701	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:616840	PARKINSON DISEASE 23	HP:0002459	Abnormal autonomic nervous system physiology			2/3					PMID:26942284	PCS	HPO:probinson[2017-06-20]
2018-10-09 10:00:31.837 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.838 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:613870	#613870 HIRSCHSPRUNG DISEASE, CARDIAC DEFECTS, AND AUTONOMIC DYSFUNCTION	HP:0002459	Abnormal autonomic nervous system physiology								OMIM:613870	TAS	HPO:probinson[2013-08-10]
2018-10-09 10:00:31.838 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Generalized seizures instead of Generalized-onset seizure for Generalized-onset seizure: see following line
2018-10-09 10:00:31.838 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:159950	#159950 SPINAL MUSCULAR ATROPHY WITH PROGRESSIVE MYOCLONIC EPILEPSY; SMAPME;;MYOCLONUS, HEREDITARY, WITH PROGRESSIVE DISTAL MUSCULAR ATROPHY	HP:0002197	Generalized seizures							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > GENERALIZED SEIZURES	OMIM:159950	TAS	HPO:skoehler[2012-10-17]
2018-10-09 10:00:31.838 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.838 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:168600	#168600 PARKINSON DISEASE, LATE-ONSET; PD;;PARK	HP:0002459	Abnormal autonomic nervous system physiology			HP:0040283				OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > DYSAUTONOMIA MAY OCCUR	OMIM:168600	TAS	HPO:skoehler[2012-11-21]
2018-10-09 10:00:31.838 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.838 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:608105	EPILEPSY, ROLANDIC, WITH PAROXYSMAL EXERCISE-INDUCED DYSTONIA ANDWRITER'S CRAMP	HP:0007359	Focal seizures								OMIM:608105	TAS	HPO:probinson[2013-02-27]
2018-10-09 10:00:31.838 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.838 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:617162	EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 46	HP:0100704	Cortical visual impairment							OMIM-CS:headandneckeyes > CORTICAL VISUAL IMPAIRMENT (PATIENT A)	OMIM:617162	TAS	HPO:skoehler[2017-07-13]
2018-10-09 10:00:31.838 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Abnormality of the eyelashes instead of Abnormal eyelash morphology for Abnormal eyelash morphology: see following line
2018-10-09 10:00:31.838 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:613981	HYPOTRICHOSIS 3; HYPT3	HP:0000499	Abnormality of the eyelashes					NOT		OMIM-CS:headAndNeckEyes > NORMAL EYELASHES	OMIM:613981	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.838 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.838 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:304700	MOHR-TRANEBJAERG SYNDROME	HP:0100704	Cortical visual impairment								OMIM:304700	PCS	HPO:probinson[2012-03-30]
2018-10-09 10:00:31.838 ERROR main [main] (V2LineQualityController.java:428) - Invalid frequency term (see next line): Obligate
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Bad frequency [Obligate]: OMIM:155350	MEGALENCEPHALY	HP:0001355	Megalencephaly			Obligate					PMID:7274594	PCS	HPO:iea[2009-02-17];HPO:lccarmody[2018-10-02]
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Generalized seizures instead of Generalized-onset seizure for Generalized-onset seizure: see following line
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:159700	MYOCLONUS AND ATAXIA	HP:0002197	Generalized seizures			HP:0040283					OMIM:159700	TAS	HPO:skoehler[2010-06-20]
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616364	WHITE-SUTTON SYNDROME	HP:0100704	Cortical visual impairment							OMIM-CS:headandneckeyes > CORTICAL BLINDNESS	OMIM:616364	TAS	HPO:skoehler[2017-07-13]
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures with impairment of consciousness or awareness instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616461	#616461 EPILEPSY, FAMILIAL TEMPORAL LOBE, 8; ETL8	HP:0002384	Focal seizures with impairment of consciousness or awareness							OMIM-CS:NEUROLOGIC_CENTRAL NERVOUS SYSTEM > COMPLEX PARTIAL SEIZURES	OMIM:616461	TAS	HPO:skoehler[2015-08-02]
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures without impairment of consciousness or awareness instead of Focal aware seizure for Focal aware seizure: see following line
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:611631	EPILEPSY, FAMILIAL TEMPORAL LOBE, 4	HP:0002349	Focal seizures without impairment of consciousness or awareness								OMIM:611631	TAS	HPO:probinson[2012-09-20]
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures with impairment of consciousness or awareness instead of Focal impaired awareness seizure for Focal impaired awareness seizure: see following line
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:611631	EPILEPSY, FAMILIAL TEMPORAL LOBE, 4	HP:0002384	Focal seizures with impairment of consciousness or awareness								OMIM:611631	TAS	HPO:skoehler[2012-09-20]
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Invalid frequency term (see next line): Obligate
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Bad frequency [Obligate]: OMIM:615072	#615072 BRACHYDACTYLY, TYPE A1, C; BDA1C	HP:0001156	Brachydactyly			Obligate				Disease name contained:#615072 brachydactyly, type a1,	OMIM:615072	IEA	HPO:skoehler[2015-01-19];HPO:lccarmody[2018-10-02]
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:615005	#615005 EPILEPSY, NOCTURNAL FRONTAL LOBE, 5; ENFL5	HP:0007359	Focal seizures								OMIM:615005	IEA	HPO:skoehler[2013-01-11]
2018-10-09 10:00:31.839 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Moderate visual impairment instead of Moderate vision loss for Moderate vision loss: see following line
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616152	#616152 MACULAR DYSTROPHY, VITELLIFORM, 5; VMD5	HP:0030515	Moderate visual impairment							OMIM-TX: 'rized by late-onset moderate visual impairment, preservationof re'	OMIM:616152	IEA	HPO:skoehler[2015-09-15]
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:617669	ENCEPHALOPATHY, PROGRESSIVE, EARLY-ONSET, WITH BRAIN ATROPHY AND SPASTICITY; PEBAS	HP:0100704	Cortical visual impairment							OMIM-CS:headAndNeckEyes > CORTICAL VISUAL IMPAIRMENT	OMIM:617669	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0008024] for TermId [prefix=TermPrefix [value=HP], id=0100018] (Nuclear cataract): see following line
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:600886	HYPERFERRITINEMIA-CATARACT SYNDROME	HP:0008024	Nuclear cataract								OMIM:600886	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Cortical visual impairment instead of Cerebral visual impairment for Cerebral visual impairment: see following line
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:615722	BOSCH-BOONSTRA-SCHAAF OPTIC ATROPHY SYNDROME; BBSOAS	HP:0100704	Cortical visual impairment							OMIM-CS:headAndNeckEyes > CEREBRAL VISUAL IMPAIRMENT	OMIM:615722	IEA	HPO:skoehler[2018-10-08]
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:146500	MULTIPLE SYSTEM ATROPHY 1, SUSCEPTIBILITY TO; MSA1	HP:0002459	Abnormal autonomic nervous system physiology								OMIM:146500	IEA	HPO:skoehler[2010-06-18]
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Focal seizures instead of Focal-onset seizure for Focal-onset seizure: see following line
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:616645	EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 34	HP:0007359	Focal seizures								PMID:26333769	PCS	HPO:probinson[2017-06-17]
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0000655] for TermId [prefix=TermPrefix [value=HP], id=0007773] (Vitreoretinopathy): see following line
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:172870	PIGMENTED PARAVENOUS CHORIORETINAL ATROPHY	HP:0000655	Vitreoretinal degeneration								OMIM:172870	TAS	HPO:probinson[2009-02-17]
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Vitreoretinal degeneration instead of Vitreoretinopathy for Vitreoretinopathy: see following line
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:172870	PIGMENTED PARAVENOUS CHORIORETINAL ATROPHY	HP:0000655	Vitreoretinal degeneration								OMIM:172870	TAS	HPO:probinson[2009-02-17]
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0000655] for TermId [prefix=TermPrefix [value=HP], id=0007773] (Vitreoretinopathy): see following line
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:268100	ENHANCED S-CONE SYNDROME	HP:0000655	Vitreoretinal degeneration								OMIM:268100	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Vitreoretinal degeneration instead of Vitreoretinopathy for Vitreoretinopathy: see following line
2018-10-09 10:00:31.840 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:268100	ENHANCED S-CONE SYNDROME	HP:0000655	Vitreoretinal degeneration								OMIM:268100	IEA	HPO:iea[2009-02-17]
2018-10-09 10:00:31.841 ERROR main [main] (V2LineQualityController.java:428) - Found usage of alt_id TermId [prefix=TermPrefix [value=HP], id=0002459] for TermId [prefix=TermPrefix [value=HP], id=0012332] (Abnormal autonomic nervous system physiology): see following line
2018-10-09 10:00:31.841 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotypeId: OMIM:252320	MOTOR NEUROPATHY, PERIPHERAL, WITH DYSAUTONOMIA	HP:0002459	Abnormal autonomic nervous system physiology								OMIM:252320	PCS	HPO:probinson[2012-04-11]
2018-10-09 10:00:31.841 ERROR main [main] (V2LineQualityController.java:428) - Found usage of wrong term label Severe visual impairment instead of Severe vision loss for Severe vision loss: see following line
2018-10-09 10:00:31.841 ERROR main [main] (V2LineQualityController.java:428) - Bad phenotype label: OMIM:203300	HERMANSKY-PUDLAK SYNDROME	HP:0001141	Severe visual impairment								OMIM:203300	IEA	HPO:iea[2009-02-17]
V2 orph about to write this many od3246
2018-10-09 10:00:32.068 ERROR main [main] (Orphanet2BigFile.java:57) - Could not make annotation for term HP:0000118 of disorder Leydig cell hypoplasia 
2018-10-09 10:00:32.068 ERROR main [main] (Orphanet2BigFile.java:58) - Will skip this line: Could not get aspect for term Phenotypic abnormality [HP:0000118]
2018-10-09 10:00:32.483 ERROR main [main] (Orphanet2BigFile.java:57) - Could not make annotation for term HP:0000118 of disorder Male infertility with teratozoospermia due to single gene mutation 
2018-10-09 10:00:32.483 ERROR main [main] (Orphanet2BigFile.java:58) - Will skip this line: Could not get aspect for term Phenotypic abnormality [HP:0000118]
2018-10-09 10:00:32.483 ERROR main [main] (Orphanet2BigFile.java:57) - Could not make annotation for term HP:0000118 of disorder Male infertility with azoospermia or oligozoospermia due to single gene mutation 
2018-10-09 10:00:32.484 ERROR main [main] (Orphanet2BigFile.java:58) - Will skip this line: Could not get aspect for term Phenotypic abnormality [HP:0000118]
2018-10-09 10:00:32.500 ERROR main [main] (Orphanet2BigFile.java:57) - Could not make annotation for term HP:0000118 of disorder Normosmic congenital hypogonadotropic hypogonadism 
2018-10-09 10:00:32.500 ERROR main [main] (Orphanet2BigFile.java:58) - Will skip this line: Could not get aspect for term Phenotypic abnormality [HP:0000118]
2018-10-09 10:00:32.631 ERROR main [main] (Orphanet2BigFile.java:57) - Could not make annotation for term HP:0000118 of disorder Autosomal recessive spastic paraplegia type 15 
2018-10-09 10:00:32.631 ERROR main [main] (Orphanet2BigFile.java:58) - Will skip this line: Could not get aspect for term Phenotypic abnormality [HP:0000118]
We output a total of 68646 orphanet annotations from 3246 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
Sending e-mails to: sebastian.koehler@charite.de peter.robinson@jax.org
Finished: SUCCESS