{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio.variation.recall/issues/12","repository_url":"https://api.github.com/repos/chapmanb/bcbio.variation.recall","labels_url":"https://api.github.com/repos/chapmanb/bcbio.variation.recall/issues/12/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio.variation.recall/issues/12/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio.variation.recall/issues/12/events","html_url":"https://github.com/chapmanb/bcbio.variation.recall/issues/12","id":165401289,"number":12,"title":"merge vcf","user":{"login":"DiyaVaka","id":5193033,"avatar_url":"https://avatars.githubusercontent.com/u/5193033?v=3","gravatar_id":"","url":"https://api.github.com/users/DiyaVaka","html_url":"https://github.com/DiyaVaka","followers_url":"https://api.github.com/users/DiyaVaka/followers","following_url":"https://api.github.com/users/DiyaVaka/following{/other_user}","gists_url":"https://api.github.com/users/DiyaVaka/gists{/gist_id}","starred_url":"https://api.github.com/users/DiyaVaka/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DiyaVaka/subscriptions","organizations_url":"https://api.github.com/users/DiyaVaka/orgs","repos_url":"https://api.github.com/users/DiyaVaka/repos","events_url":"https://api.github.com/users/DiyaVaka/events{/privacy}","received_events_url":"https://api.github.com/users/DiyaVaka/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2016-07-13T19:25:22Z","updated_at":"2016-07-20T19:29:08Z","closed_at":"2016-07-13T20:19:54Z","body":"Hi Brad,\r\n\r\nAttached is the script I am using and the error it says is below. Also I attached the vcf file which it is complaining\r\n[n201-1017_test.vcf.txt](https://github.com/chapmanb/bcbio.variation.recall/files/362286/n201-1017_test.vcf.txt)\r\n[bcbiomerge.sh.txt](https://github.com/chapmanb/bcbio.variation.recall/files/362288/bcbiomerge.sh.txt)\r\n\r\n\r\n about.\r\n\r\n2016-07-13 12:20:03 ihg-headnode-1 INFO [bcbio.run.itx] - [E::vcf_hdr_read] no sample line\r\n2016-07-13 12:20:03 ihg-headnode-1 INFO [bcbio.run.itx] - Failed to open /coldstorage/U19_project/U19_vcf/n201-1017_93g.vcf: could not parse header\r\n2016-07-13 12:20:03 ihg-headnode-1 ERROR [bcbio.run.itx] - \r\njava.lang.Exception: Shell command failed: bcftools view -f 'PASS,.' /coldstorage/U19_project/U19_vcf/n201-1017_93g.vcf | bgzip -c > /coldstorage/U19_project/U19_vcf/results_UG/inprep/txtmp1500156387816019744/n201-1017_93g-qprep-passonly.vcf.gz\r\n                     Failed to open /coldstorage/U19_project/U19_vcf/n201-1017_93g.vcf: could not parse header\r\n                     [E::vcf_hdr_read] no sample line\r\n                         bcbio.run.itx/check-run       itx.clj:  168\r\nbcbio.variation.ensemble.prep/bgzip-index-vcf/fn      prep.clj:   47\r\n   bcbio.variation.ensemble.prep/bgzip-index-vcf      prep.clj:   47\r\n                      clojure.lang.RestFn.invoke   RestFn.java:  559\r\n  bcbio.variation.recall.merge/prep-by-region/fn     merge.clj:  135\r\n                             clojure.core/map/fn      core.clj: 2622\r\n                       clojure.lang.LazySeq.sval  LazySeq.java:   40\r\n                        clojure.lang.LazySeq.seq  LazySeq.java:   49\r\n                             clojure.lang.RT.seq       RT.java:  507\r\n                                clojure.core/seq      core.clj:  137\r\n                             clojure.core/map/fn      core.clj: 2616\r\n                       clojure.lang.LazySeq.sval  LazySeq.java:   40\r\n                        clojure.lang.LazySeq.seq  LazySeq.java:   49\r\n                             clojure.lang.RT.seq       RT.java:  507\r\n                                clojure.core/seq      core.clj:  137\r\n                              clojure.core/apply      core.clj:  630\r\n                             clojure.core/mapcat      core.clj: 2660\r\n                      clojure.lang.RestFn.invoke   RestFn.java:  423\r\n  bcbio.variation.recall.split/group-breakpoints     split.clj:   67\r\n     bcbio.variation.recall.split/group-pregions     split.clj:   87\r\n     bcbio.variation.recall.merge/prep-by-region     merge.clj:  138\r\n       bcbio.variation.recall.merge/combine-vcfs     merge.clj:  152\r\n              bcbio.variation.recall.merge/-main     merge.clj:  193\r\n                     clojure.lang.RestFn.applyTo   RestFn.java:  137\r\n                              clojure.core/apply      core.clj:  630\r\n            bcbio.variation.recall.main/-main/fn      main.clj:   34\r\n               bcbio.variation.recall.main/-main      main.clj:   33\r\n                     clojure.lang.RestFn.applyTo   RestFn.java:  137\r\n                bcbio.variation.recall.main.main              :     \r\n\r\n2016-07-13 12:20:03 ihg-headnode-1 ERROR [bcbio.variation.recall.main] - \r\njava.lang.Exception: Shell command failed: bcftools view -f 'PASS,.' /coldstorage/U19_project/U19_vcf/n201-1017_93g.vcf | bgzip -c > /coldstorage/U19_project/U19_vcf/results_UG/inprep/txtmp1500156387816019744/n201-1017_93g-qprep-passonly.vcf.gz\r\n                     Failed to open /coldstorage/U19_project/U19_vcf/n201-1017_93g.vcf: could not parse header\r\n                     [E::vcf_hdr_read] no sample line\r\n                         bcbio.run.itx/check-run       itx.clj:  168\r\nbcbio.variation.ensemble.prep/bgzip-index-vcf/fn      prep.clj:   47\r\n   bcbio.variation.ensemble.prep/bgzip-index-vcf      prep.clj:   47\r\n                      clojure.lang.RestFn.invoke   RestFn.java:  559\r\n  bcbio.variation.recall.merge/prep-by-region/fn     merge.clj:  135\r\n                             clojure.core/map/fn      core.clj: 2622\r\n                       clojure.lang.LazySeq.sval  LazySeq.java:   40\r\n                        clojure.lang.LazySeq.seq  LazySeq.java:   49\r\n                             clojure.lang.RT.seq       RT.java:  507\r\n                                clojure.core/seq      core.clj:  137\r\n                             clojure.core/map/fn      core.clj: 2616\r\n                       clojure.lang.LazySeq.sval  LazySeq.java:   40\r\n                        clojure.lang.LazySeq.seq  LazySeq.java:   49\r\n                             clojure.lang.RT.seq       RT.java:  507\r\n                                clojure.core/seq      core.clj:  137\r\n                              clojure.core/apply      core.clj:  630\r\n                             clojure.core/mapcat      core.clj: 2660\r\n                      clojure.lang.RestFn.invoke   RestFn.java:  423\r\n  bcbio.variation.recall.split/group-breakpoints     split.clj:   67\r\n     bcbio.variation.recall.split/group-pregions     split.clj:   87\r\n     bcbio.variation.recall.merge/prep-by-region     merge.clj:  138\r\n       bcbio.variation.recall.merge/combine-vcfs     merge.clj:  152\r\n              bcbio.variation.recall.merge/-main     merge.clj:  193\r\n                     clojure.lang.RestFn.applyTo   RestFn.java:  137\r\n                              clojure.core/apply      core.clj:  630\r\n            bcbio.variation.recall.main/-main/fn      main.clj:   34\r\n               bcbio.variation.recall.main/-main      main.clj:   33\r\n                     clojure.lang.RestFn.applyTo   RestFn.java:  137\r\n                bcbio.variation.recall.main.main              :     \r\n\r\nStop Date       = Wed Jul 13 12:20:03 PDT 2016"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio.variation.recall/issues/comments/234055849","html_url":"https://github.com/chapmanb/bcbio.variation.recall/issues/12#issuecomment-234055849","issue_url":"https://api.github.com/repos/chapmanb/bcbio.variation.recall/issues/12","id":234055849,"user":{"login":"DiyaVaka","id":5193033,"avatar_url":"https://avatars.githubusercontent.com/u/5193033?v=3","gravatar_id":"","url":"https://api.github.com/users/DiyaVaka","html_url":"https://github.com/DiyaVaka","followers_url":"https://api.github.com/users/DiyaVaka/followers","following_url":"https://api.github.com/users/DiyaVaka/following{/other_user}","gists_url":"https://api.github.com/users/DiyaVaka/gists{/gist_id}","starred_url":"https://api.github.com/users/DiyaVaka/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DiyaVaka/subscriptions","organizations_url":"https://api.github.com/users/DiyaVaka/orgs","repos_url":"https://api.github.com/users/DiyaVaka/repos","events_url":"https://api.github.com/users/DiyaVaka/events{/privacy}","received_events_url":"https://api.github.com/users/DiyaVaka/received_events","type":"User","site_admin":false},"created_at":"2016-07-20T19:29:08Z","updated_at":"2016-07-20T19:29:08Z","body":"Thank you Brad. Now its giving an \"Exception in thread \"main\" java.lang.OutOfMemeoryError: GC overhead limit exceeded..\r\n\r\nI tried to change -Xmx to 10g but of no use. When I read forums they say that lot of stuff is getting written to garbage collection. Did you encounter this issue before?\r\n\r\nThanks,"}}
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