{"action":"created","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/888","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/888/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/888/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/888/events","html_url":"https://github.com/marbl/canu/issues/888","id":318781159,"node_id":"MDU6SXNzdWUzMTg3ODExNTk=","number":888,"title":"Overlap jobs failed, job trimming/1-overlapper/001/000057.ovb FAILED","user":{"login":"psur9757","id":37357172,"node_id":"MDQ6VXNlcjM3MzU3MTcy","avatar_url":"https://avatars2.githubusercontent.com/u/37357172?v=4","gravatar_id":"","url":"https://api.github.com/users/psur9757","html_url":"https://github.com/psur9757","followers_url":"https://api.github.com/users/psur9757/followers","following_url":"https://api.github.com/users/psur9757/following{/other_user}","gists_url":"https://api.github.com/users/psur9757/gists{/gist_id}","starred_url":"https://api.github.com/users/psur9757/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/psur9757/subscriptions","organizations_url":"https://api.github.com/users/psur9757/orgs","repos_url":"https://api.github.com/users/psur9757/repos","events_url":"https://api.github.com/users/psur9757/events{/privacy}","received_events_url":"https://api.github.com/users/psur9757/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2018-04-30T04:04:47Z","updated_at":"2018-06-04T14:09:52Z","closed_at":"2018-06-04T14:09:52Z","author_association":"NONE","body":"Error when running overlap jobs. \r\n\r\n> BEGIN TRIMMING\r\n> \r\n> Overlap jobs failed, tried 2 times, giving up.\r\n> job trimming/1-overlapper/001/000057.ovb FAILED.\r\n> \r\n> ABORT:\r\n> ABORT: Canu 1.7\r\n> ABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.\r\n> ABORT: Try restarting. If that doesn't work, ask for help.\r\n> ABORT:\r\n\r\nI tried `sh overlap.sh 000057` but it was aborted with the following error.\r\n\r\n> Running job 57 based on command line options.\r\n> \r\n> STRING_NUM_BITS 31\r\n> OFFSET_BITS 31\r\n> STRING_NUM_MASK 2147483647\r\n> OFFSET_MASK 2147483647\r\n> MAX_STRING_NUM 2147483647\r\n> \r\n> Hash_Mask_Bits 23\r\n> Max_Hash_Strings 12180\r\n> Max_Hash_Data_Len 170639703\r\n> Max_Hash_Load 0.750000\r\n> Kmer Length 22\r\n> Min Overlap Length 500\r\n> Max Error Rate 0.150000\r\n> Min Kmer Matches 0\r\n> \r\n> Num_PThreads 4\r\n> \r\n> HASH_TABLE_SIZE 8388608\r\n> sizeof(Hash_Bucket_t) 216\r\n> hash table size: 1728 MB\r\n> \r\n> terminate called after throwing an instance of 'std::bad_alloc'\r\n> what(): std::bad_alloc\r\n> \r\n> Failed with 'Aborted'; backtrace (libbacktrace):\r\n> AS_UTL/AS_UTL_stackTrace.C::97 in _Z17AS_UTL_catchCrashiP7siginfoPv()\r\n> (null)::0 in (null)()\r\n> (null)::0 in (null)()\r\n> (null)::0 in (null)()\r\n> ../../gcc-4.8.2/libstdc++-v3/libsupc++/vterminate.cc::95 in _ZN9__gnu_cxx27__verbose_terminate_handlerEv()\r\n> ../../gcc-4.8.2/libstdc++-v3/libsupc++/eh_terminate.cc::38 in _ZN10__cxxabiv111__terminateEPFvvE()\r\n> ../../gcc-4.8.2/libstdc++-v3/libsupc++/eh_terminate.cc::48 in _ZSt9terminatev()\r\n> ../../gcc-4.8.2/libstdc++-v3/libsupc++/eh_throw.cc::84 in __cxa_throw()\r\n> ../../gcc-4.8.2/libstdc++-v3/libsupc++/new_op.cc::56 in _Znwm()\r\n> ../../gcc-4.8.2/libstdc++-v3/libsupc++/new_opv.cc::32 in _Znam()\r\n> overlapInCore/overlapInCore.C::527 in main()\r\n> (null)::0 in (null)()\r\n> (null)::0 in (null)()\r\n> overlap.sh: line 794: 44317 Aborted (core dumped) $bin/overlapInCore -G -t 4 -k 22 -k ../0-mercounts/OSR_512_canu2.ms22.frequentMers.fasta --hashbits 23 --hashload 0.75 --maxerate 0.15 --minlength 500 $opt -o ./$job.ovb.WORKING -s ./$job.stats ../OSR_512_canu2.gkpStore\r\n\r\n@brianwalenz suggested \r\n> It looks like you need to request more memory, or increase your memory limit. The job seems to be failing to allocate a relatively small (1.7GB) array.\r\n\r\nCan I get further details? Thanks!"},"comment":{"url":"https://api.github.com/repos/marbl/canu/issues/comments/394367998","html_url":"https://github.com/marbl/canu/issues/888#issuecomment-394367998","issue_url":"https://api.github.com/repos/marbl/canu/issues/888","id":394367998,"node_id":"MDEyOklzc3VlQ29tbWVudDM5NDM2Nzk5OA==","user":{"login":"skoren","id":923478,"node_id":"MDQ6VXNlcjkyMzQ3OA==","avatar_url":"https://avatars2.githubusercontent.com/u/923478?v=4","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":"2018-06-04T14:09:52Z","updated_at":"2018-06-04T14:09:52Z","author_association":"MEMBER","body":"Original issue appears fixed, if there are other errors in this run open a new issue."}}
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