{"action":"created","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/277","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/277/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/277/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/277/events","html_url":"https://github.com/marbl/canu/issues/277","id":184119369,"number":277,"title":"unitigger.sh: segmentation fault while running bogart","user":{"login":"aseetharam","id":4835524,"avatar_url":"https://avatars.githubusercontent.com/u/4835524?v=3","gravatar_id":"","url":"https://api.github.com/users/aseetharam","html_url":"https://github.com/aseetharam","followers_url":"https://api.github.com/users/aseetharam/followers","following_url":"https://api.github.com/users/aseetharam/following{/other_user}","gists_url":"https://api.github.com/users/aseetharam/gists{/gist_id}","starred_url":"https://api.github.com/users/aseetharam/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aseetharam/subscriptions","organizations_url":"https://api.github.com/users/aseetharam/orgs","repos_url":"https://api.github.com/users/aseetharam/repos","events_url":"https://api.github.com/users/aseetharam/events{/privacy}","received_events_url":"https://api.github.com/users/aseetharam/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-10-20T02:19:52Z","updated_at":"2016-10-24T20:28:00Z","closed_at":null,"body":"Hi,\r\nSorry, not sure if this is the issue with the program or just incorrect compiling, but I have problem running the `canu`\r\nAFAIK, the installation went smoothly without errors and I have enough RAM /processing power in the maching (2Tb RAM, 40 procs). The porgram fails at unitiggging step. I am using the CCS reads. \r\nThe log just says:\r\n```\r\n-- Unitigger failed.\r\n--\r\n================================================================================\r\nDon't panic, but a mostly harmless error occurred and canu failed.\r\n\r\ncanu failed with 'failed to generate unitigs.  Made 2 attempts, jobs still failed'.\r\n``` \r\nbut when I run the script, I get this error:\r\n```\r\nbogart \\\r\n>  -G /data021/GIF/arnstrm/Baum/Assembly_HgCamtech_20161014/02_falcon/canu_assembly/unitigging/canu_assembly.gkpStore \\\r\n>  -O /data021/GIF/arnstrm/Baum/Assembly_HgCamtech_20161014/02_falcon/canu_assembly/unitigging/canu_assembly.ovlStore \\\r\n>  -o /data021/GIF/arnstrm/Baum/Assembly_HgCamtech_20161014/02_falcon/canu_assembly/unitigging/4-unitigger/canu_assembly \\\r\n>  -gs 100000000 \\\r\n>  -eg 0.045 \\\r\n>  -eM 0.045 \\\r\n>  -el 500 \\\r\n>  -dg 6 \\\r\n>  -db 6 \\\r\n>  -dr 3 \\\r\n>  -ca 2100 \\\r\n>  -cp 200 \\\r\n>  -threads 8 \\\r\n>  -M 64 \\\r\n>  -unassembled 2 1000 0.75 0.75 2\r\n\r\nGraph  error threshold  = 0.045 (4.500%)\r\nMax    error threshold  = 0.045 (4.500%)\r\n\r\nMinimum overlap length = 500 bases\r\n\r\nnumber of threads     = 8 (command line)\r\n\r\n\r\n==> LOADING AND FILTERING OVERLAPS.\r\n\r\nReadInfo()-- Using 88811 reads, no minimum read length used.\r\n\r\nOverlapCache()-- limited to 65536MB memory (user supplied).\r\nPHYS_PAGES = 529411203\r\nPAGE_SIZE  = 4096\r\nMEMORY     = 2168468287488\r\nOverlapCache()--       1MB for read data.\r\nOverlapCache()--       1MB for best edges.\r\nOverlapCache()--       2MB for unitig layouts.\r\nOverlapCache()--       0MB for tigs.\r\nOverlapCache()--       0MB for id maps.\r\nOverlapCache()--       5MB for error profiles.\r\nOverlapCache()--       1MB for overlap cache pointers.\r\nOverlapCache()--      56MB for overlap cache initial bucket.\r\nOverlapCache()--     128MB for overlap cache thread data.\r\nOverlapCache()--       0MB for number of overlaps per read.\r\nOverlapCache()--       0MB for other processes.\r\nOverlapCache()-- ---------\r\nOverlapCache()--     190MB for data structures (sum of above).\r\nOverlapCache()--   65345MB available for overlaps.\r\n\r\nOverlapCache()-- Loading number of overlaps per read.\r\nOverlapCache()--  Initial guess at _maxPer=48219 (max of 6882) from (memLimit=68519411630 - memUsed=0) / (numReads=88811 * sizeof(OVL)=16)\r\nOverlapCache()-- _maxPer=  48219 (numBelow=88808 numEqual=0 numAbove=0 totalLoad=27715290 -- 0 + 27715290 = 443444640 <? 68519411630\r\n\r\nOverlapCache()-- blockSize        = 66913487 (1021MB)\r\n\r\nOverlapCache()-- _maxPer          = 48219 overlaps/reads\r\nOverlapCache()-- numBelow         = 88808 reads (all overlaps loaded)\r\nOverlapCache()-- numEqual         = 0 reads (all overlaps loaded)\r\nOverlapCache()-- numAbove         = 0 reads (some overlaps loaded)\r\nOverlapCache()-- totalLoad        = 27715290 overlaps (100.00%)\r\n\r\nOverlapCache()-- availForOverlaps = 65345MB\r\nOverlapCache()-- totalMemory      = 0MB for organization\r\nOverlapCache()-- totalMemory      = 422MB for overlaps\r\nOverlapCache()-- totalMemory      = 422MB used\r\n\r\nOverlapCache()-- Loading: overlaps processed         4175 (000.02%) loaded         4143 (000.01%) droppeddupe            4 (000.00%) (at read iid 2)\r\nOverlapCache()-- Loading: overlaps processed     27722174 (100.02%) loaded     27431494 (098.98%) droppeddupe        61490 (000.22%)\r\n\r\nBestOverlapGraph()-- allocating best edges (2MB)\r\nBestOverlapGraph()-- analyzing 88811 reads for best contains, with 8 threads.\r\nBestOverlapGraph()-- analyzing 88811 reads for best edges, with 8 threads.\r\nBestOverlapGraph()-- removing suspicious reads from graph, with 8 threads.\r\nBestOverlapGraph()-- marked 41275 reads as suspicious.\r\nBestOverlapGraph()-- analyzing 88811 reads for best contains, with 8 threads.\r\nBestOverlapGraph()-- analyzing 88811 reads for best edges, with 8 threads.\r\nBestOverlapGraph()-- analyzing best edges to find useful edge error rate\r\nBestOverlapGraph()-- analyzing 88811 reads for best contains, with 8 threads.\r\nBestOverlapGraph()-- analyzing 88811 reads for best edges, with 8 threads.\r\nBestOverlapGraph()-- removing suspicious edges from graph, with 8 threads.\r\nBestOverlapGraph()-- analyzing 88811 reads for best contains, with 8 threads.\r\nBestOverlapGraph()-- analyzing 88811 reads for best edges, with 8 threads.\r\nBestOverlapGraph()-- detecting spur reads.\r\nBestOverlapGraph()-- detected 22404 spur reads.\r\nBestOverlapGraph()-- analyzing 88811 reads for best contains, with 8 threads.\r\nBestOverlapGraph()-- analyzing 88811 reads for best edges, with 8 threads.\r\nBestOverlapGraph()-- removing best edges for contained reads.\r\n\r\n==> BUILDING GREEDY TIGS.\r\n\r\nbreakSingletonTigs()-- Removed 29256 singleton tigs; reads are now unplaced.\r\n\r\n==> PLACE CONTAINED READS.\r\n\r\ncomputeErrorProfiles()-- Computing error profiles for 30739 tigs, with 8 threads.\r\n\r\nFailed with 'Segmentation fault'\r\n\r\nBacktrace (mangled):\r\n\r\nbogart[0x517e3d]\r\n/lib64/libpthread.so.0[0x3d8dc0f710]\r\nbogart[0x50289c]\r\nbogart[0x4fdcd1]\r\n/usr/lib64/libgomp.so.1[0x31e420e0c5]\r\n/lib64/libpthread.so.0[0x3d8dc079d1]\r\n/lib64/libc.so.6(clone+0x6d)[0x3d8d8e88fd]\r\n\r\nBacktrace (demangled):\r\n\r\n[0] bogart() [0x517e3d]\r\n[1] /lib64/libpthread.so.0() [0x3d8dc0f710]\r\n[2] bogart() [0x50289c]\r\n[3] bogart() [0x4fdcd1]\r\n[4] /usr/lib64/libgomp.so.1() [0x31e420e0c5]\r\n[5] /lib64/libpthread.so.0() [0x3d8dc079d1]\r\n[6] /lib64/libc.so.6::(null) + 0x6d  [0x3d8d8e88fd]\r\n\r\nGDB:\r\n\r\n\r\nSegmentation fault\r\n```\r\nPlease help!\r\nThanks very much!"},"comment":{"url":"https://api.github.com/repos/marbl/canu/issues/comments/255856109","html_url":"https://github.com/marbl/canu/issues/277#issuecomment-255856109","issue_url":"https://api.github.com/repos/marbl/canu/issues/277","id":255856109,"user":{"login":"skoren","id":923478,"avatar_url":"https://avatars.githubusercontent.com/u/923478?v=3","gravatar_id":"","url":"https://api.github.com/users/skoren","html_url":"https://github.com/skoren","followers_url":"https://api.github.com/users/skoren/followers","following_url":"https://api.github.com/users/skoren/following{/other_user}","gists_url":"https://api.github.com/users/skoren/gists{/gist_id}","starred_url":"https://api.github.com/users/skoren/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/skoren/subscriptions","organizations_url":"https://api.github.com/users/skoren/orgs","repos_url":"https://api.github.com/users/skoren/repos","events_url":"https://api.github.com/users/skoren/events{/privacy}","received_events_url":"https://api.github.com/users/skoren/received_events","type":"User","site_admin":false},"created_at":"2016-10-24T20:27:59Z","updated_at":"2016-10-24T20:27:59Z","body":"Are these errors with the latest code or the 1.3 release? If with the latest code you could try going back to 1.3 to see if it is fixed."}}
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