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"scout update omim" not working

See original GitHub issue

Worked a few weeks ago… I don’t have time to debug this at the moment. If no one else cares about this I will take a look at it next week!

$ scout update omim --institute CMD --api-key xxxxxxxxxxxxxxxxxxxxx

2019-11-21 15:17:13 cmdscout2 scout.commands.base[16298] INFO Running scout version 4.8.3
2019-11-21 15:17:13 cmdscout2 scout.commands.base[16298] DEBUG Debug logging enabled.
2019-11-21 15:17:13 cmdscout2 scout.commands.update.omim[16298] INFO Running scout update omim
2019-11-21 15:17:13 cmdscout2 scout.adapter.mongo.institute[16298] DEBUG Fetch institute CMD
2019-11-21 15:17:13 cmdscout2 scout.adapter.mongo.panel[16298] INFO Fetching gene panels OMIM-AUTO from database
2019-11-21 15:17:13 cmdscout2 scout.adapter.mongo.panel[16298] INFO Setting version to 3.0
2019-11-21 15:17:13 cmdscout2 scout.utils.requests[16298] INFO Fetching OMIM files from https://omim.org/
2019-11-21 15:17:13 cmdscout2 scout.utils.requests[16298] INFO Requesting https://omim.org/static/omim/data/mim2gene.txt
2019-11-21 15:17:14 cmdscout2 scout.utils.requests[16298] INFO Requesting https://data.omim.org/downloads/xxxxxxxxxxxxxxxxx/genemap2.txt
2019-11-21 15:17:15 cmdscout2 scout.adapter.mongo.hgnc[16298] INFO Fetching all genes by alias
2019-11-21 15:17:16 cmdscout2 scout.parse.omim[16298] INFO Get the mim genes
2019-11-21 15:17:16 cmdscout2 scout.parse.omim[16298] INFO Parsing mim2gene
2019-11-21 15:17:16 cmdscout2 scout.parse.omim[16298] INFO Number of genes without hgnc symbol 175
2019-11-21 15:17:16 cmdscout2 scout.parse.omim[16298] INFO Parsing the omim genemap2
2019-11-21 15:17:16 cmdscout2 scout.commands.update.omim[16298] ERROR 'Mim Number'
Aborted!

Issue Analytics

State:
Created 4 years ago
Comments:9 (7 by maintainers)

Top GitHub Comments

2reactions

moonsocommented, Nov 22, 2019

Haha yes you can always hire mine, just swish me

1reaction

northwestwitchcommented, Nov 22, 2019

It might actually take some more time, because after some attempts my omim key has been blocked, and instead of the definitions I get this message This data account exceeded its download cap, please contact us at https://omim.org/contact if this is an issue

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