{"action":"opened","issue":{"url":"https://api.github.com/repos/opencb/opencga/issues/789","repository_url":"https://api.github.com/repos/opencb/opencga","labels_url":"https://api.github.com/repos/opencb/opencga/issues/789/labels{/name}","comments_url":"https://api.github.com/repos/opencb/opencga/issues/789/comments","events_url":"https://api.github.com/repos/opencb/opencga/issues/789/events","html_url":"https://github.com/opencb/opencga/issues/789","id":296458894,"number":789,"title":"WriteError with code 11000 does not match with the pattern","user":{"login":"nicholsn","id":463344,"avatar_url":"https://avatars3.githubusercontent.com/u/463344?v=4","gravatar_id":"","url":"https://api.github.com/users/nicholsn","html_url":"https://github.com/nicholsn","followers_url":"https://api.github.com/users/nicholsn/followers","following_url":"https://api.github.com/users/nicholsn/following{/other_user}","gists_url":"https://api.github.com/users/nicholsn/gists{/gist_id}","starred_url":"https://api.github.com/users/nicholsn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nicholsn/subscriptions","organizations_url":"https://api.github.com/users/nicholsn/orgs","repos_url":"https://api.github.com/users/nicholsn/repos","events_url":"https://api.github.com/users/nicholsn/events{/privacy}","received_events_url":"https://api.github.com/users/nicholsn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-02-12T17:23:43Z","updated_at":"2018-02-12T17:23:43Z","closed_at":null,"author_association":"NONE","body":"I think this might be related to #766, while running the variant index pipeline (built from the opencga-1.3-rc at commit 358a4326f091016bdeb5206893f11d14a7766f67) I see the following error:\r\n\r\n```\r\n2018-02-11 18:00:11 [pool-1-thread-9] ERROR MongoDBVariantStageLoader:192 - WriteError with code 11000 does not match with the pattern ^.*dup key: \\{ : \"([^\"]*)\" \\}$\r\n2018-02-11 18:00:11 [pool-1-thread-9] ERROR ParallelTaskRunner:830 - Error writing batch 38209\r\ncom.mongodb.MongoBulkWriteException: Bulk write operation error on server localhost:27017. Write errors: [BulkWriteError{index=98, code=11000, message='E11000 duplicate key error collection: opencga_gneva_hgi.stage index: _id_ dup key: { : \" 2:  76585772::��2\r\n�0', details={ }}].\r\n        at com.mongodb.connection.BulkWriteBatchCombiner.getError(BulkWriteBatchCombiner.java:176)\r\n        at com.mongodb.connection.BulkWriteBatchCombiner.throwOnError(BulkWriteBatchCombiner.java:205)\r\n        at com.mongodb.connection.BulkWriteBatchCombiner.getResult(BulkWriteBatchCombiner.java:146)\r\n        at com.mongodb.operation.MixedBulkWriteOperation$1.call(MixedBulkWriteOperation.java:188)\r\n        at com.mongodb.operation.MixedBulkWriteOperation$1.call(MixedBulkWriteOperation.java:168)\r\n        at com.mongodb.operation.OperationHelper.withConnectionSource(OperationHelper.java:422)\r\n        at com.mongodb.operation.OperationHelper.withConnection(OperationHelper.java:413)\r\n        at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:168)\r\n        at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:74)\r\n        at com.mongodb.Mongo.execute(Mongo.java:845)\r\n        at com.mongodb.Mongo$2.execute(Mongo.java:828)\r\n        at com.mongodb.MongoCollectionImpl.bulkWrite(MongoCollectionImpl.java:301)\r\n        at org.opencb.commons.datastore.mongodb.MongoDBNativeQuery.update(MongoDBNativeQuery.java:259)\r\n        at org.opencb.commons.datastore.mongodb.MongoDBCollection.update(MongoDBCollection.java:404)\r\n        at org.opencb.opencga.storage.mongodb.variant.load.stage.MongoDBVariantStageLoader.updateMongo(MongoDBVariantStageLoader.java:168)\r\n        at org.opencb.opencga.storage.mongodb.variant.load.stage.MongoDBVariantStageLoader.insert(MongoDBVariantStageLoader.java:102)\r\n        at org.opencb.opencga.storage.mongodb.variant.load.stage.MongoDBVariantStageLoader.write(MongoDBVariantStageLoader.java:93)\r\n        at org.opencb.commons.run.ParallelTaskRunner$WriterRunnable.call(ParallelTaskRunner.java:828)\r\n        at org.opencb.commons.run.ParallelTaskRunner$WriterRunnable.call(ParallelTaskRunner.java:811)\r\n        at java.util.concurrent.FutureTask.run(FutureTask.java:266)\r\n        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)\r\n        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)\r\n        at java.lang.Thread.run(Thread.java:745)\r\n```"}}
{"actor":{"display_login":"nicholsn"}}