{"action":"created","issue":{"url":"https://api.github.com/repos/alekseyzimin/masurca/issues/66","repository_url":"https://api.github.com/repos/alekseyzimin/masurca","labels_url":"https://api.github.com/repos/alekseyzimin/masurca/issues/66/labels{/name}","comments_url":"https://api.github.com/repos/alekseyzimin/masurca/issues/66/comments","events_url":"https://api.github.com/repos/alekseyzimin/masurca/issues/66/events","html_url":"https://github.com/alekseyzimin/masurca/issues/66","id":364300306,"node_id":"MDU6SXNzdWUzNjQzMDAzMDY=","number":66,"title":"buildPosMap segmentation fault","user":{"login":"TimothyStephens","id":5172407,"node_id":"MDQ6VXNlcjUxNzI0MDc=","avatar_url":"https://avatars0.githubusercontent.com/u/5172407?v=4","gravatar_id":"","url":"https://api.github.com/users/TimothyStephens","html_url":"https://github.com/TimothyStephens","followers_url":"https://api.github.com/users/TimothyStephens/followers","following_url":"https://api.github.com/users/TimothyStephens/following{/other_user}","gists_url":"https://api.github.com/users/TimothyStephens/gists{/gist_id}","starred_url":"https://api.github.com/users/TimothyStephens/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TimothyStephens/subscriptions","organizations_url":"https://api.github.com/users/TimothyStephens/orgs","repos_url":"https://api.github.com/users/TimothyStephens/repos","events_url":"https://api.github.com/users/TimothyStephens/events{/privacy}","received_events_url":"https://api.github.com/users/TimothyStephens/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-09-27T04:25:57Z","updated_at":"2018-10-25T07:53:32Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI am getting the below segmentation fault from buildPosMap. I am running MaSuRCA 3.2.6.\r\nThe assembler continues despite this issue and appears to complete correctly so I assume it is not a critical problem. \r\n\r\nThanks.\r\n\r\n----------------------------------------END Tue Sep 18 01:31:50 2018 (1201 seconds)\r\nERROR: Failed with signal SEGV (11)\r\n================================================================================\r\n\r\nrunCA failed.\r\n\r\n----------------------------------------\r\nStack trace:\r\n\r\n at /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/bin/../CA8/Linux-amd64/bin/runCA line 1613.\r\n\tmain::caFailure(\"buildPosMap failed\", \"/30days/uqtstep3/POLARELLA_GLACIALIS/CCMP1383/GENOME_ASSEMBLI\"...) called at /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/bin/../CA8/Linux-amd64/bin/runCA line 5905\r\n\tmain::terminate() called at /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/bin/../CA8/Linux-amd64/bin/runCA line 6532\r\n\r\n----------------------------------------\r\nLast few lines of the relevant log file (/30days/uqtstep3/POLARELLA_GLACIALIS/CCMP1383/GENOME_ASSEMBLIES/MaSuRCA/ASSEMBLY/CA.mr.41.15.17.0.029/9-terminator/buildPosMap.err):\r\n\r\n\r\nFailed with 'Segmentation fault'\r\n\r\nBacktrace (mangled):\r\n\r\n/gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap[0x407185]\r\n/lib64/libpthread.so.0[0x3fbe40f7e0]\r\n/gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap[0x403fa3]\r\n/gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap[0x406008]\r\n/lib64/libc.so.6(__libc_start_main+0xfd)[0x3fbd81ed1d]\r\n/gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap[0x401ef9]\r\n\r\nBacktrace (demangled):\r\n\r\n[0] /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap() [0x407185]\r\n[1] /lib64/libpthread.so.0() [0x3fbe40f7e0]\r\n[2] /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap() [0x403fa3]\r\n[3] /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap() [0x406008]\r\n[4] /lib64/libc.so.6::(null) + 0xfd  [0x3fbd81ed1d]\r\n[5] /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap() [0x401ef9]\r\n\r\nGDB:\r\n\r\n\r\n\r\n----------------------------------------\r\nFailure message:\r\n\r\nbuildPosMap failed\r\n"},"comment":{"url":"https://api.github.com/repos/alekseyzimin/masurca/issues/comments/432950894","html_url":"https://github.com/alekseyzimin/masurca/issues/66#issuecomment-432950894","issue_url":"https://api.github.com/repos/alekseyzimin/masurca/issues/66","id":432950894,"node_id":"MDEyOklzc3VlQ29tbWVudDQzMjk1MDg5NA==","user":{"login":"tong2200","id":18298354,"node_id":"MDQ6VXNlcjE4Mjk4MzU0","avatar_url":"https://avatars3.githubusercontent.com/u/18298354?v=4","gravatar_id":"","url":"https://api.github.com/users/tong2200","html_url":"https://github.com/tong2200","followers_url":"https://api.github.com/users/tong2200/followers","following_url":"https://api.github.com/users/tong2200/following{/other_user}","gists_url":"https://api.github.com/users/tong2200/gists{/gist_id}","starred_url":"https://api.github.com/users/tong2200/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tong2200/subscriptions","organizations_url":"https://api.github.com/users/tong2200/orgs","repos_url":"https://api.github.com/users/tong2200/repos","events_url":"https://api.github.com/users/tong2200/events{/privacy}","received_events_url":"https://api.github.com/users/tong2200/received_events","type":"User","site_admin":false},"created_at":"2018-10-25T07:53:32Z","updated_at":"2018-10-25T07:53:32Z","author_association":"NONE","body":"I also caught the error from buildPosMap when I ran MaSuRCA-3.2.8. The error message caught by strace is:\r\n\r\nwrite(11, \"3069480\\t7180044060193\\t0\\t150\\tf\\n71\"..., 4096) = 4096\r\nread(3, \"GAATAGATATGGCAGGTTTCAGGACACTGA\\nT\"..., 4096) = 4096\r\nread(3, \"llllllllllllllllllllll\\nlllllllll\"..., 4096) = 4096\r\nread(3, \"\\n{CCO\\nacc:(7180044060323,1342148\"..., 4096) = 4096\r\nwrite(10, \"\\t0\\t150\\tf\\naa197810158\\t71800440602\"..., 4096) = 4096\r\nwrite(21, \"044060096\\t150\\n7180044060097\\t150\\n\"..., 4096) = 4096\r\nread(3, \"GTCTCCGCACTGGTCCTCTTCCACG\\nTCCTCT\"..., 4096) = 4096\r\nread(3, \"\\ndln:0\\ndel:\\n}\\n{MPS\\ntyp:R\\nmid:ba6\"..., 4096) = 4096\r\nread(3, \"``\\n``````````\\n.\\nfor:0\\nnpc:2\\nnou:\"..., 4096) = 4096\r\nread(3, \"os:0,150\\ndln:0\\ndel:\\n}\\n{UPS\\ntyp:s\"..., 4096) = 4096\r\nread(3, \"el:\\n}\\n}\\n{CCO\\nacc:(7180044060359,\"..., 4096) = 4096\r\nread(3, \"````````````````````````\\n```````\"..., 4096) = 4096\r\nread(3, \"50\\ndln:0\\ndel:\\n}\\n{MPS\\ntyp:R\\nmid:a\"..., 4096) = 4096\r\nwrite(10, \"44060323\\t0\\t150\\tf\\naa197889886\\t718\"..., 4096) = 4096\r\nread(3, \"ATACAGAATGGTGTCGTCTGTGTAGAGGTAGA\"..., 4096) = 4096\r\n--- SIGSEGV {si_signo=SIGSEGV, si_code=SEGV_ACCERR, si_addr=0x7f7eed33e1f0} ---\r\n+++ killed by SIGSEGV (core dumped) +++\r\n% time     seconds  usecs/call     calls    errors syscall\r\n------ ----------- ----------- --------- --------- ----------------\r\n 57.57   58.434596           9   6836159           write\r\n 33.08   33.579053           2  15915194           read\r\n  7.73    7.840929      270377        29           open\r\n  1.57    1.590790       79540        20           munmap\r\n  0.04    0.045191         284       159           mremap\r\n  0.00    0.001822          83        22           fstat\r\n  0.00    0.000880          10        84           mmap\r\n  0.00    0.000186           5        36           brk\r\n  0.00    0.000156          10        16           mprotect\r\n  0.00    0.000066           8         8           close\r\n  0.00    0.000047          47         1           execve\r\n  0.00    0.000038          38         1         1 access\r\n  0.00    0.000012           6         2           rt_sigaction\r\n  0.00    0.000006           6         1           rt_sigprocmask\r\n  0.00    0.000005           5         1           getrlimit\r\n  0.00    0.000005           5         1           set_tid_address\r\n  0.00    0.000004           4         1           arch_prctl\r\n  0.00    0.000004           4         1           set_robust_list\r\n------ ----------- ----------- --------- --------- ----------------\r\n100.00  101.493790              22751736         1 total\r\n\r\nstrace command line:\r\n\r\nstrace -C -d -v -o strace.log ~/MaSuRCA-3.2.8/CA/Linux-amd64/bin/buildPosMap -i genome.asm -o genome"}}
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