{"action":"created","issue":{"url":"https://api.github.com/repos/nf-core/deepvariant/issues/5","repository_url":"https://api.github.com/repos/nf-core/deepvariant","labels_url":"https://api.github.com/repos/nf-core/deepvariant/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/nf-core/deepvariant/issues/5/comments","events_url":"https://api.github.com/repos/nf-core/deepvariant/issues/5/events","html_url":"https://github.com/nf-core/deepvariant/issues/5","id":372490221,"node_id":"MDU6SXNzdWUzNzI0OTAyMjE=","number":5,"title":"Issues with Exomes","user":{"login":"apeltzer","id":2359510,"node_id":"MDQ6VXNlcjIzNTk1MTA=","avatar_url":"https://avatars3.githubusercontent.com/u/2359510?v=4","gravatar_id":"","url":"https://api.github.com/users/apeltzer","html_url":"https://github.com/apeltzer","followers_url":"https://api.github.com/users/apeltzer/followers","following_url":"https://api.github.com/users/apeltzer/following{/other_user}","gists_url":"https://api.github.com/users/apeltzer/gists{/gist_id}","starred_url":"https://api.github.com/users/apeltzer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/apeltzer/subscriptions","organizations_url":"https://api.github.com/users/apeltzer/orgs","repos_url":"https://api.github.com/users/apeltzer/repos","events_url":"https://api.github.com/users/apeltzer/events{/privacy}","received_events_url":"https://api.github.com/users/apeltzer/received_events","type":"User","site_admin":false},"labels":[{"id":1079220592,"node_id":"MDU6TGFiZWwxMDc5MjIwNTky","url":"https://api.github.com/repos/nf-core/deepvariant/labels/bug","name":"bug","color":"d73a4a","default":true}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":20,"created_at":"2018-10-22T11:56:40Z","updated_at":"2018-10-30T12:56:20Z","closed_at":"2018-10-26T13:38:20Z","author_association":"MEMBER","body":"Double checked already that exome bam and my BED file have compatible contigs but no success unfortunately:\r\n\r\n```\r\nleus/io/sam_reader.cc:537] Unrecognized SAM header type, ignoring: \r\n  I1022 11:53:51.789329 47582124862080 genomics_reader.py:213] Reading hroc113_0.md.bam with NativeSamReader\r\n  I1022 11:53:51.808645 47582124862080 make_examples.py:991] Common contigs are [u'1', u'2', u'3', u'4', u'5', u'6', u'7', u'8', u'9', u'10', u'11', u'12', u'13', u'14', u'15', u'16', u'17', u'18', u'19', u'20', u'21', u'22', u'X', u'Y']\r\n  I1022 11:53:51.819024 47582124862080 genomics_reader.py:213] Reading exons_padded50bp_ucsc_hg19_grch37.bed with NativeBedReader\r\n  I1022 11:54:03.196350 47582124862080 ranges.py:121] Adding interval chr6:117127483-117128419 to intervaltree\r\n  I1022 11:54:14.932882 47582124862080 ranges.py:121] Adding interval chr14:24034765-24034960 to intervaltree\r\n  Traceback (most recent call last):\r\n    File \"/scratch/5306779/Bazel.runfiles_7WvCJa/runfiles/com_google_deepvariant/deepvariant/make_examples.py\", line 1188, in <module>\r\n      tf.app.run()\r\n    File \"/opt/conda/envs/nf-core-deepvariant-1.0dev/lib/python2.7/site-packages/tensorflow/python/platform/app.py\", line 125, in run\r\n      _sys.exit(main(argv))\r\n    File \"/scratch/5306779/Bazel.runfiles_7WvCJa/runfiles/com_google_deepvariant/deepvariant/make_examples.py\", line 1178, in main\r\n      make_examples_runner(options)\r\n    File \"/scratch/5306779/Bazel.runfiles_7WvCJa/runfiles/com_google_deepvariant/deepvariant/make_examples.py\", line 1076, in make_examples_runner\r\n      regions = processing_regions_from_options(options)\r\n    File \"/scratch/5306779/Bazel.runfiles_7WvCJa/runfiles/com_google_deepvariant/deepvariant/make_examples.py\", line 995, in processing_regions_from_options\r\n      raise ValueError('The regions to call is empty. Check your --regions and '\r\n  ValueError: The regions to call is empty. Check your --regions and --exclude_regions flags to make sure they are not resulting in set of empty region to process. This also happens if you use \"chr20\" for a BAM where contig names don't have \"chr\"s (or vice versa).\r\n  parallel: This job failed:\r\n  /opt/conda/envs/nf-core-deepvariant-1.0dev/bin/python /opt/conda/envs/nf-core-deepvariant-1.0dev/share/deepvariant-0.7.0-0/binaries/DeepVariant/0.7.0/DeepVariant-0.7.0+cl-208818123/make_examples.zip --mode calling --ref human_g1k_v37_decoy.fasta.gz --reads hroc113_0.md.bam --regions exons_padded50bp_ucsc_hg19_grch37.bed --examples hroc113_0.md_shardedExamples/hroc113_0.md.bam.tfrecord@1.gz --task 0\r\n  Warning: unable to close filehandle properly: Remote I/O error during global destruction.\r\n```"},"comment":{"url":"https://api.github.com/repos/nf-core/deepvariant/issues/comments/434290181","html_url":"https://github.com/nf-core/deepvariant/issues/5#issuecomment-434290181","issue_url":"https://api.github.com/repos/nf-core/deepvariant/issues/5","id":434290181,"node_id":"MDEyOklzc3VlQ29tbWVudDQzNDI5MDE4MQ==","user":{"login":"apeltzer","id":2359510,"node_id":"MDQ6VXNlcjIzNTk1MTA=","avatar_url":"https://avatars3.githubusercontent.com/u/2359510?v=4","gravatar_id":"","url":"https://api.github.com/users/apeltzer","html_url":"https://github.com/apeltzer","followers_url":"https://api.github.com/users/apeltzer/followers","following_url":"https://api.github.com/users/apeltzer/following{/other_user}","gists_url":"https://api.github.com/users/apeltzer/gists{/gist_id}","starred_url":"https://api.github.com/users/apeltzer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/apeltzer/subscriptions","organizations_url":"https://api.github.com/users/apeltzer/orgs","repos_url":"https://api.github.com/users/apeltzer/repos","events_url":"https://api.github.com/users/apeltzer/events{/privacy}","received_events_url":"https://api.github.com/users/apeltzer/received_events","type":"User","site_admin":false},"created_at":"2018-10-30T12:56:20Z","updated_at":"2018-10-30T12:56:20Z","author_association":"MEMBER","body":"No laptop and I can just have a look at this tomorrow - our Cluster where I ran this is in maintenance till Friday, so can try this then. \n\nI’ll also have a look in detail, traveling atm and mobile phone is not enough to carefully look etc ... "}}
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