{"action":"created","issue":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1150","repository_url":"https://api.github.com/repos/bigdatagenomics/adam","labels_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1150/labels{/name}","comments_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1150/comments","events_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1150/events","html_url":"https://github.com/bigdatagenomics/adam/issues/1150","id":174915703,"number":1150,"title":"File _rgdict.avro does not exist","user":{"login":"ooliynyk","id":11317736,"avatar_url":"https://avatars.githubusercontent.com/u/11317736?v=3","gravatar_id":"","url":"https://api.github.com/users/ooliynyk","html_url":"https://github.com/ooliynyk","followers_url":"https://api.github.com/users/ooliynyk/followers","following_url":"https://api.github.com/users/ooliynyk/following{/other_user}","gists_url":"https://api.github.com/users/ooliynyk/gists{/gist_id}","starred_url":"https://api.github.com/users/ooliynyk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ooliynyk/subscriptions","organizations_url":"https://api.github.com/users/ooliynyk/orgs","repos_url":"https://api.github.com/users/ooliynyk/repos","events_url":"https://api.github.com/users/ooliynyk/events{/privacy}","received_events_url":"https://api.github.com/users/ooliynyk/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2016-09-03T20:27:22Z","updated_at":"2016-10-26T23:30:52Z","closed_at":null,"body":"I have converted vcf file to adam format using the command `# adam-submit vcf2adam file:///tmp/A7VAGPU.vcf.gz file:///tmp/a7.adam`\r\n\r\nWhen I tried to run `# adam-submit count_kmers file:///tmp/a7.adam/ file:///tmp/kmers.adam 10` I got error:\r\n```\r\nCommand body threw exception:\r\njava.io.FileNotFoundException: File file:/tmp/a7.adam/_rgdict.avro does not exist\r\nException in thread \"main\" java.io.FileNotFoundException: File file:/tmp/a7.adam/_rgdict.avro does not exist\r\n\tat org.apache.hadoop.fs.RawLocalFileSystem.deprecatedGetFileStatus(RawLocalFileSystem.java:534)\r\n\tat org.apache.hadoop.fs.RawLocalFileSystem.getFileLinkStatusInternal(RawLocalFileSystem.java:747)\r\n\tat org.apache.hadoop.fs.RawLocalFileSystem.getFileStatus(RawLocalFileSystem.java:524)\r\n\tat org.apache.hadoop.fs.FilterFileSystem.getFileStatus(FilterFileSystem.java:409)\r\n\tat org.apache.hadoop.fs.ChecksumFileSystem$ChecksumFSInputChecker.<init>(ChecksumFileSystem.java:140)\r\n\tat org.apache.hadoop.fs.ChecksumFileSystem.open(ChecksumFileSystem.java:341)\r\n\tat org.apache.hadoop.fs.FileSystem.open(FileSystem.java:766)\r\n\tat org.bdgenomics.adam.rdd.ADAMContext.loadAvro(ADAMContext.scala:442)\r\n\tat org.bdgenomics.adam.rdd.ADAMContext.loadAvroReadGroupMetadata(ADAMContext.scala:160)\r\n\tat org.bdgenomics.adam.rdd.ADAMContext.loadParquetAlignments(ADAMContext.scala:520)\r\n\tat org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadAlignments$1.apply(ADAMContext.scala:1023)\r\n\tat org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadAlignments$1.apply(ADAMContext.scala:1002)\r\n\tat scala.Option.fold(Option.scala:157)\r\n\tat org.apache.spark.rdd.Timer.time(Timer.scala:48)\r\n\tat org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:1000)\r\n\tat org.bdgenomics.adam.cli.CountReadKmers.run(CountReadKmers.scala:63)\r\n\tat org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:55)\r\n\tat org.bdgenomics.adam.cli.CountReadKmers.run(CountReadKmers.scala:54)\r\n\tat org.bdgenomics.adam.cli.ADAMMain.apply(ADAMMain.scala:132)\r\n\tat org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:72)\r\n\tat org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala)\r\n\tat sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r\n\tat sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)\r\n\tat sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\r\n\tat java.lang.reflect.Method.invoke(Method.java:498)\r\n\tat org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:674)\r\n\tat org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:180)\r\n\tat org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:205)\r\n\tat org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)\r\n\tat org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)\r\n```\r\n\r\nFiles in .adam directory:\r\n```\r\nroot@2ef6c96e995a:/tmp# ls -la /tmp/a7.adam/\r\ntotal 2044\r\ndrwxr-xr-x  2 root root    4096 Sep  3 20:03 .\r\ndrwxrwxrwt 75 root root    4096 Sep  3 20:04 ..\r\n-rw-r--r--  1 root root       8 Sep  3 20:03 ._SUCCESS.crc\r\n-rw-r--r--  1 root root     108 Sep  3 20:03 ._common_metadata.crc\r\n-rw-r--r--  1 root root     140 Sep  3 20:03 ._metadata.crc\r\n-rw-r--r--  1 root root      20 Sep  3 20:03 ._samples.avro.crc\r\n-rw-r--r--  1 root root      20 Sep  3 20:03 ._seqdict.avro.crc\r\n-rw-r--r--  1 root root   15628 Sep  3 20:03 .part-r-00000.gz.parquet.crc\r\n-rw-r--r--  1 root root       0 Sep  3 20:03 _SUCCESS\r\n-rw-r--r--  1 root root   12467 Sep  3 20:03 _common_metadata\r\n-rw-r--r--  1 root root   16770 Sep  3 20:03 _metadata\r\n-rw-r--r--  1 root root    1301 Sep  3 20:03 _samples.avro\r\n-rw-r--r--  1 root root    1402 Sep  3 20:03 _seqdict.avro\r\n-rw-r--r--  1 root root 1999220 Sep  3 20:03 part-r-00000.gz.parquet\r\n```\r\n[A7VAGPU.vcf.gz](https://github.com/bigdatagenomics/adam/files/453616/A7VAGPU.vcf.gz)\r\n"},"comment":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/comments/256506678","html_url":"https://github.com/bigdatagenomics/adam/issues/1150#issuecomment-256506678","issue_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1150","id":256506678,"user":{"login":"heuermh","id":35293,"avatar_url":"https://avatars.githubusercontent.com/u/35293?v=3","gravatar_id":"","url":"https://api.github.com/users/heuermh","html_url":"https://github.com/heuermh","followers_url":"https://api.github.com/users/heuermh/followers","following_url":"https://api.github.com/users/heuermh/following{/other_user}","gists_url":"https://api.github.com/users/heuermh/gists{/gist_id}","starred_url":"https://api.github.com/users/heuermh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/heuermh/subscriptions","organizations_url":"https://api.github.com/users/heuermh/orgs","repos_url":"https://api.github.com/users/heuermh/repos","events_url":"https://api.github.com/users/heuermh/events{/privacy}","received_events_url":"https://api.github.com/users/heuermh/received_events","type":"User","site_admin":false},"created_at":"2016-10-26T23:30:52Z","updated_at":"2016-10-26T23:30:52Z","body":"@BrandonColbyMD ADAM is kind of like the swiss-army knife for getting data in traditional bioinformatics file formats ready for analysis on Spark; most of the interesting bits can be found in downstream repositories or in workbooks. I'll let others chime in with specific examples."}}
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