{"action":"created","issue":{"url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/56","labels_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/56/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/56/comments","events_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/56/events","html_url":"https://github.com/arq5x/lumpy-sv/issues/56","id":56438138,"number":56,"title":"lumpy error removing reads","user":{"login":"mbourgey","id":5649914,"avatar_url":"https://avatars.githubusercontent.com/u/5649914?v=3","gravatar_id":"","url":"https://api.github.com/users/mbourgey","html_url":"https://github.com/mbourgey","followers_url":"https://api.github.com/users/mbourgey/followers","following_url":"https://api.github.com/users/mbourgey/following{/other_user}","gists_url":"https://api.github.com/users/mbourgey/gists{/gist_id}","starred_url":"https://api.github.com/users/mbourgey/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mbourgey/subscriptions","organizations_url":"https://api.github.com/users/mbourgey/orgs","repos_url":"https://api.github.com/users/mbourgey/repos","events_url":"https://api.github.com/users/mbourgey/events{/privacy}","received_events_url":"https://api.github.com/users/mbourgey/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-02-03T21:13:42Z","updated_at":"2015-02-03T21:15:16Z","closed_at":null,"body":"Hi \r\nwhen I was running lumpy v0.2.9 I get this error message:\r\n\r\nRunning  lumpy-sv 2015-01-29 13:38:26\r\n466\t0\r\n491\t0\r\nchr10\t1000000\r\nchr10\t2000000\r\nchr10\t4000000\r\nchr11\t1000000\r\nchr11\t2000000\r\nchr11\t4000000\r\nchr12\t1000000\r\nchr12\t2000000\r\nchr12\t4000000\r\nchr13\t1000000\r\nchr13\t2000000\r\nchr13\t4000000\r\nchr14\t1000000\r\nchr14\t2000000\r\nchr14\t4000000\r\nchr15\t1000000\r\nchr15\t2000000\r\nchr15\t4000000\r\nchr16\t1000000\r\nchr16\t2000000\r\nchr16\t4000000\r\nchr17\t1000000\r\nchr17\t2000000\r\nchr17\t4000000\r\nchr18\t1000000\r\nchr18\t2000000\r\nchr18\t4000000\r\nchr19\t1000000\r\nchr19\t2000000\r\nchr19\t4000000\r\nchr1\t1000000\r\nchr1\t2000000\r\nchr1\t4000000\r\nchr2\t1000000\r\nchr2\t2000000\r\nchr2\t4000000\r\nchr3\t1000000\r\nchr3\t2000000\r\nchr3\t4000000\r\nchr4\t1000000\r\nchr4\t2000000\r\nchr4\t4000000\r\nchr5\t1000000\r\nchr5\t2000000\r\nchr5\t4000000\r\nchr6\t1000000\r\nchr6\t2000000\r\nchr6\t4000000\r\nError removing element:chr6,91016653,91016653,+\tchr6,91016674,91016674,-\t1\r\n./runLumpy.sh: line 38: 1906358 Aborted                 (core dumped) lumpy -mw 4 -tt 0.0 -pe bam_file:${TUMOR_PE},histo_file:${TUMOR_PE%.bam}.histo,mean:$tumorMean,stdev:$tumorStdev,read_length:$READ_LENGTH,min_non_overlap:$READ_LENGTH,discordant_z:4,back_distance:20,weight:1,id:10,min_mapping_threshold:1 -pe bam_file:${BLOOD_PE},histo_file:${BLOOD_PE%.bam}.histo,mean:$bloodMean,stdev:$bloodStdev,read_length:$READ_LENGTH,min_non_overlap:$READ_LENGTH,discordant_z:4,back_distance:20,weight:1,id:20,min_mapping_threshold:1 -sr bam_file:${TUMOR_SR},back_distance:20,weight:1,id:11,min_mapping_threshold:20 -sr bam_file:${BLOOD_SR},back_distance:20,weight:1,id:21,min_mapping_threshold:20 > $OUTPUT\r\n\r\nIt looks like what was discussed in the issue #33 but first you seems to have corrected this issue and second I don't see in any of the reads from the region a cigar string with no base matched.\r\n\r\ndo you have an idea ? do you want me to send you a slice of bams ?\r\n\r\nthanks in advance\r\n\r\nMathieu "},"comment":{"url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/comments/72736255","html_url":"https://github.com/arq5x/lumpy-sv/issues/56#issuecomment-72736255","issue_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/56","id":72736255,"user":{"login":"mbourgey","id":5649914,"avatar_url":"https://avatars.githubusercontent.com/u/5649914?v=3","gravatar_id":"","url":"https://api.github.com/users/mbourgey","html_url":"https://github.com/mbourgey","followers_url":"https://api.github.com/users/mbourgey/followers","following_url":"https://api.github.com/users/mbourgey/following{/other_user}","gists_url":"https://api.github.com/users/mbourgey/gists{/gist_id}","starred_url":"https://api.github.com/users/mbourgey/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mbourgey/subscriptions","organizations_url":"https://api.github.com/users/mbourgey/orgs","repos_url":"https://api.github.com/users/mbourgey/repos","events_url":"https://api.github.com/users/mbourgey/events{/privacy}","received_events_url":"https://api.github.com/users/mbourgey/received_events","type":"User","site_admin":false},"created_at":"2015-02-03T21:15:16Z","updated_at":"2015-02-03T21:15:16Z","body":"FYI, here is the list of all the cigar string from read mapped in the region surounding the problem (chr6:91016000-91018000) :\r\n100M\r\n12S88M\r\n17S83M\r\n22S75M\r\n22S78M\r\n28M24D72M\r\n29S70M\r\n30M1D25M34S\r\n33M24D57M\r\n36M24D64M\r\n38M43H\r\n38S43M\r\n39M24D56M\r\n39M54H\r\n39M61H\r\n39S54M\r\n39S61M\r\n44M56H\r\n44S56M\r\n45M51H\r\n45S51M\r\n46H36M\r\n46M24D51M\r\n46M24D54M\r\n48M24D52M\r\n49M34D50M\r\n4S96M\r\n51M34D43M\r\n52M24D48M\r\n55H34M\r\n57H33M\r\n57M33S\r\n58M\r\n62H38M\r\n62M38S\r\n64H32M\r\n65H35M\r\n67H33M\r\n75M21S\r\n76M24S\r\n78M22S\r\n83M\r\n84M\r\n87M13S\r\n88M\r\n92M\r\n93M\r\n94M\r\n95M\r\n97M\r\n98M\r\n99M"}}