{"action":"closed","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/1262","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1262/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1262/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1262/events","html_url":"https://github.com/broadinstitute/gatk/issues/1262","id":120529755,"number":1262,"title":"Spark on CRAM complains about seq dictionary when non-spark does not ","user":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/broadinstitute/gatk/labels/Spark","name":"Spark","color":"FFD700"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-12-05T05:07:39Z","updated_at":"2015-12-05T12:12:20Z","closed_at":"2015-12-05T12:12:20Z","body":"spark complains but non-spark does not\r\n\r\n```\r\nCollectQualityYieldMetricsSpark  --output a.metrics --useOriginalQualities true --reference src/test/resources/Homo_sapiens_assembly19_chr1_1M.fasta --input src/test/resources/org/broadinstitute/hellbender/tools/picard/analysis/CollectQualityYieldMetrics/collect_quality_yield_metrics.cram  --disableSequenceDictionaryValidation false\r\n\r\norg.broadinstitute.hellbender.exceptions.UserException$IncompatibleSequenceDictionaries: A USER ERROR has occurred: Input files reference and reads have incompatible contigs: Found contigs with the same name but different lengths:\r\n  contig reference = 1 / 1000000\r\n  contig reads = 1 / 249250621.\r\n  reference contigs = [1]\r\n  reads contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000207.1, GL000226.1, GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, GL000201.1, GL000247.1, GL000245.1, GL000197.1, GL000203.1, GL000246.1, GL000249.1, GL000196.1, GL000248.1, GL000244.1, GL000238.1, GL000202.1, GL000234.1, GL000232.1, GL000206.1, GL000240.1, GL000236.1, GL000241.1, GL000243.1, GL000242.1, GL000230.1, GL000237.1, GL000233.1, GL000204.1, GL000198.1, GL000208.1, GL000191.1, GL000227.1, GL000228.1, GL000214.1, GL000221.1, GL000209.1, GL000218.1, GL000220.1, GL000213.1, GL000211.1, GL000199.1, GL000217.1, GL000216.1, GL000215.1, GL000205.1, GL000219.1, GL000224.1, GL000223.1, GL000195.1, GL000212.1, GL000222.1, GL000200.1, GL000193.1, GL000194.1, GL000225.1, GL000192.1, NC_007605]\r\n```\r\n\r\nOnce fixed, reenable 2 tests in CollectQualityYieldMetricsSparkIntegrationTest"}}