{"action":"created","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/307","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/307/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/307/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/307/events","html_url":"https://github.com/marbl/canu/issues/307","id":193679716,"number":307,"title":"Assertion `aovl > 0' failed","user":{"login":"prince26121991","id":13187771,"avatar_url":"https://avatars.githubusercontent.com/u/13187771?v=3","gravatar_id":"","url":"https://api.github.com/users/prince26121991","html_url":"https://github.com/prince26121991","followers_url":"https://api.github.com/users/prince26121991/followers","following_url":"https://api.github.com/users/prince26121991/following{/other_user}","gists_url":"https://api.github.com/users/prince26121991/gists{/gist_id}","starred_url":"https://api.github.com/users/prince26121991/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/prince26121991/subscriptions","organizations_url":"https://api.github.com/users/prince26121991/orgs","repos_url":"https://api.github.com/users/prince26121991/repos","events_url":"https://api.github.com/users/prince26121991/events{/privacy}","received_events_url":"https://api.github.com/users/prince26121991/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-12-06T04:19:51Z","updated_at":"2016-12-06T08:36:08Z","closed_at":null,"body":"Graph error threshold = 0.050 (5.000%)\r\nBubble error threshold = 0.062 (6.250%)\r\nMerge error threshold = 0.037 (3.750%)\r\nRepeat error threshold = 0.050 (5.000%)\r\n\r\nMinimum overlap length = 3000 bases\r\n\r\nSPURIOUS_COVERAGE_THRESHOLD 6\r\nISECT_NEEDED_TO_BREAK 269\r\nREGION_END_WEIGHT 15\r\n\r\nnumber of threads = 16 (command line)\r\n\r\nFragmentInfo()-- Loading fragment information for 8514477 fragments and 1 libraries from cache '/home/scbbcluster/nitesh_mpi/pacbio_assembly/canu-1.2/Linux-amd64/bin/6th_trial/unitigging/4-unitigger/6th_try.fragmentInfo'\r\n\r\nOverlapCache()-- limited to 64512MB memory (user supplied).\r\nPHYS_PAGES = 33047400\r\nPAGE_SIZE = 4096\r\nMEMORY = 135362150400\r\nOverlapCache()-- 97MB for fragment data.\r\nOverlapCache()-- 129MB for best edges.\r\nOverlapCache()-- 129MB for best containments.\r\nOverlapCache()-- 259MB for unitig layouts.\r\nOverlapCache()-- 2MB for unitigs.\r\nOverlapCache()-- 64MB for id maps.\r\nOverlapCache()-- 97MB for overlap cache pointers.\r\nOverlapCache()-- 56MB for overlap cache initial bucket.\r\nOverlapCache()-- 512MB for overlap cache thread data.\r\nOverlapCache()-- 32MB for number of overlaps per read.\r\nOverlapCache()-- 0MB for other processes.\r\nOverlapCache()-- ---------\r\nOverlapCache()-- 1382MB for data structures (sum of above).\r\nOverlapCache()-- 63129MB available for overlaps.\r\n\r\nOverlapCache()-- Loading number of overlaps per fragment.\r\nOverlapCache()-- Initial guess at _maxPer=485 (max of 202529) from (memLimit=66196567385 - memUsed=0) / (numFrags=8514477 * sizeof(OVL)=16)\r\nOverlapCache()-- _maxPer= 485 (numBelow=4645599 numEqual=1045 numAbove=3867833 totalLoad=2249577350 -- 0 + 2249577350 = 35993237600 <? 66196567385\r\nOverlapCache()-- (28804 MB free, adjust by 488)\r\nOverlapCache()-- _maxPer= 973 (numBelow=5029374 numEqual=586 numAbove=3484517 totalLoad=4034530747 -- 0 + 4034530747 = 64552491952 <? 66196567385\r\nOverlapCache()-- (1567 MB free, adjust by 29)\r\nOverlapCache()-- _maxPer= 1002 (numBelow=5045299 numEqual=513 numAbove=3468665 totalLoad=4135358202 -- 0 + 4135358202 = 66165731232 <? 66196567385\r\nOverlapCache()-- (29 MB free, adjust by 0)\r\n\r\nOverlapCache()-- blockSize = 64645085 (986MB)\r\n\r\nOverlapCache()-- _maxPer = 1002 overlaps/reads\r\nOverlapCache()-- numBelow = 5045299 reads (all overlaps loaded)\r\nOverlapCache()-- numEqual = 513 reads (all overlaps loaded)\r\nOverlapCache()-- numAbove = 3468665 reads (some overlaps loaded)\r\nOverlapCache()-- totalLoad = 4135358202 overlaps ( 6.69%)\r\n\r\nOverlapCache()-- availForOverlaps = 63129MB\r\nOverlapCache()-- totalMemory = 0MB for organization\r\nOverlapCache()-- totalMemory = 63100MB for overlaps\r\nOverlapCache()-- totalMemory = 63100MB used\r\n\r\nOverlapCache()-- Loading overlap information\r\nOverlapCache()-- Loading overlap information: overlaps processed 8157 (000.00%) loaded 0 (000.00%) (at read iid 1)\r\nWARNING: bogus overlap found for A=403787 B=450908\r\nWARNING: A len=2158 hang=-3042 ovl=-112\r\nWARNING: B len=3630 hang=-2270 ovl=588\r\nbogart: bogart/AS_BAT_Datatypes.H:306: uint32 FragmentInfo::overlapLength(uint32, uint32, int32, int32): Assertion `aovl > 0' failed.\r\n\r\nFailed with 'Aborted'\r\n\r\nBacktrace (mangled):\r\n\r\n/home/scbbcluster/nitesh_mpi/pacbio_assembly/canu-1.2/Linux-amd64/bin/bogart[0x4f269d]\r\n/lib64/libpthread.so.0[0x3b9660f500]\r\n/lib64/libc.so.6(gsignal+0x35)[0x3b95e328a5]\r\n/lib64/libc.so.6(abort+0x175)[0x3b95e34085]\r\n/lib64/libc.so.6[0x3b95e2ba1e]\r\n/lib64/libc.so.6(__assert_perror_fail+0x0)[0x3b95e2bae0]\r\n/home/scbbcluster/nitesh_mpi/pacbio_assembly/canu-1.2/Linux-amd64/bin/bogart[0x4be1e6]\r\n/home/scbbcluster/nitesh_mpi/pacbio_assembly/canu-1.2/Linux-amd64/bin/bogart[0x4be6f4]\r\n/home/scbbcluster/nitesh_mpi/pacbio_assembly/canu-1.2/Linux-amd64/bin/bogart[0x4bf8e8]\r\n/home/scbbcluster/nitesh_mpi/pacbio_assembly/canu-1.2/Linux-amd64/bin/bogart[0x403593]\r\n/lib64/libc.so.6(__libc_start_main+0xfd)[0x3b95e1ecdd]\r\n/home/scbbcluster/nitesh_mpi/pacbio_assembly/canu-1.2/Linux-amd64/bin/bogart[0x404999]\r\n\r\nBacktrace (demangled):\r\n\r\n[0] /home/scbbcluster/nitesh_mpi/pacbio_assembly/canu-1.2/Linux-amd64/bin/bogart() [0x4f269d]\r\n[1] /lib64/libpthread.so.0() [0x3b9660f500]\r\n[2] /lib64/libc.so.6::(null) + 0x35 [0x3b95e328a5]\r\n[3] /lib64/libc.so.6::(null) + 0x175 [0x3b95e34085]\r\n[4] /lib64/libc.so.6() [0x3b95e2ba1e]\r\n[5] /lib64/libc.so.6::(null) + 0 [0x3b95e2bae0]\r\n[6] /home/scbbcluster/nitesh_mpi/pacbio_assembly/canu-1.2/Linux-amd64/bin/bogart() [0x4be1e6]\r\n[7] /home/scbbcluster/nitesh_mpi/pacbio_assembly/canu-1.2/Linux-amd64/bin/bogart() [0x4be6f4]\r\n[8] /home/scbbcluster/nitesh_mpi/pacbio_assembly/canu-1.2/Linux-amd64/bin/bogart() [0x4bf8e8]\r\n[9] /home/scbbcluster/nitesh_mpi/pacbio_assembly/canu-1.2/Linux-amd64/bin/bogart() [0x403593]\r\n[10] /lib64/libc.so.6::(null) + 0xfd [0x3b95e1ecdd]\r\n[11] /home/scbbcluster/nitesh_mpi/pacbio_assembly/canu-1.2/Linux-amd64/bin/bogart() [0x404999]\r\n\r\nGDB:\r\n\r\nPlease suggest what should I do?"},"comment":{"url":"https://api.github.com/repos/marbl/canu/issues/comments/265091445","html_url":"https://github.com/marbl/canu/issues/307#issuecomment-265091445","issue_url":"https://api.github.com/repos/marbl/canu/issues/307","id":265091445,"user":{"login":"brianwalenz","id":8249720,"avatar_url":"https://avatars.githubusercontent.com/u/8249720?v=3","gravatar_id":"","url":"https://api.github.com/users/brianwalenz","html_url":"https://github.com/brianwalenz","followers_url":"https://api.github.com/users/brianwalenz/followers","following_url":"https://api.github.com/users/brianwalenz/following{/other_user}","gists_url":"https://api.github.com/users/brianwalenz/gists{/gist_id}","starred_url":"https://api.github.com/users/brianwalenz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brianwalenz/subscriptions","organizations_url":"https://api.github.com/users/brianwalenz/orgs","repos_url":"https://api.github.com/users/brianwalenz/repos","events_url":"https://api.github.com/users/brianwalenz/events{/privacy}","received_events_url":"https://api.github.com/users/brianwalenz/received_events","type":"User","site_admin":false},"created_at":"2016-12-06T08:36:08Z","updated_at":"2016-12-06T08:36:08Z","body":"It's complaining there is an overlap that makes no sense, the alignment described extends past the end of one of the reads.  I've never seen this happen before.\r\n\r\nI'd rather not spend time trying to figure out what happened, because in the end, the options are the same:\r\n\r\n1)  Modify the code to ignore both of these reads.  I do not recommend this, because if the data on disk is corrupt, the problem will keep occurring.\r\n\r\n2)  Upgrade to the latest non-released code.  This has many benefits.  The 1.2 release is 8 months old, and we've made significant improvements to the algorithms.  You'll be able to painlessly update to the 1.4 release when it is ready (soon).  If it does fail again, we can easily patch the current code, letting you just update to the latest and rerun, instead of manually patching the old version.\r\n\r\nThe downside of using the latest code is that you need to start the assembly potion again.  You can use the same corrected and trimmed reads (supply `-pacbio-corrected <path-to>/6th_trial/trimmedReads.fasta.gz`).  I would, however, suggest starting completely from scratch, to correct the reads again as repeat handling was improved."}}
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