{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/pbalign/issues/8","labels_url":"https://api.github.com/repos/PacificBiosciences/pbalign/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/pbalign/issues/8/comments","events_url":"https://api.github.com/repos/PacificBiosciences/pbalign/issues/8/events","html_url":"https://github.com/PacificBiosciences/pbalign/issues/8","id":63677014,"number":8,"title":"samtoh5: double free or corruption","user":{"login":"fbemm","id":8361254,"avatar_url":"https://avatars.githubusercontent.com/u/8361254?v=3","gravatar_id":"","url":"https://api.github.com/users/fbemm","html_url":"https://github.com/fbemm","followers_url":"https://api.github.com/users/fbemm/followers","following_url":"https://api.github.com/users/fbemm/following{/other_user}","gists_url":"https://api.github.com/users/fbemm/gists{/gist_id}","starred_url":"https://api.github.com/users/fbemm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fbemm/subscriptions","organizations_url":"https://api.github.com/users/fbemm/orgs","repos_url":"https://api.github.com/users/fbemm/repos","events_url":"https://api.github.com/users/fbemm/events{/privacy}","received_events_url":"https://api.github.com/users/fbemm/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-03-23T09:35:10Z","updated_at":"2015-03-23T11:51:14Z","closed_at":null,"body":"I am trying to run pbalign using data from a single SMRT cell (P6-C4). samFilter crashes with the following error:\r\n\r\n*** glibc detected *** samtoh5: double free or corruption (!prev): 0x0000000000b4b6d0 ***\r\n======= Backtrace: =========\r\n[0x7077c2]\r\n[0x410d70]\r\n[0x415697]\r\n[0x402c09]\r\n[0x6e9584]\r\n[0x404161]\r\n======= Memory map: ========\r\n00400000-008b3000 r-xp 00000000 00:15 2273052                            /software/pacbio/blasr2/tools/samtoh5\r\n00ab3000-00ac2000 rw-p 004b3000 00:15 2273052                            /software/pacbio/blasr2/tools/samtoh5\r\n00ac2000-118d7000 rw-p 00000000 00:00 0                                  [heap]\r\n7fe5b2045000-7fe5d71d8000 rw-p 00000000 00:00 0\r\n7fe5d741a000-7fe5d749c000 rw-p 00000000 00:00 0\r\n7fe5d749c000-7fe6030d5000 r--p 00000000 00:1c 19506024463                p_ctg.fa\r\n7fff05c65000-7fff05c88000 rw-p 00000000 00:00 0                          [stack]\r\n7fff05ddf000-7fff05de0000 r-xp 00000000 00:00 0                          [vdso]\r\nffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]\r\n\r\nHappens with blasr-I and blasr-II. I tried to run it on the 3 bax.h5 from the SMRT cell and on an individual bax.h5 file. The reference is 800Mb in size in about 1000 contigs. Each bax.h5 is about 1.3G. The machine has plenty of memory (512G) available. blasr was compiled with gcc 4.9.1 and hdf 1.8.13 and works fine in general. Seems to be a problem with samFilter. "},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/pbalign/issues/comments/84963632","html_url":"https://github.com/PacificBiosciences/pbalign/issues/8#issuecomment-84963632","issue_url":"https://api.github.com/repos/PacificBiosciences/pbalign/issues/8","id":84963632,"user":{"login":"fbemm","id":8361254,"avatar_url":"https://avatars.githubusercontent.com/u/8361254?v=3","gravatar_id":"","url":"https://api.github.com/users/fbemm","html_url":"https://github.com/fbemm","followers_url":"https://api.github.com/users/fbemm/followers","following_url":"https://api.github.com/users/fbemm/following{/other_user}","gists_url":"https://api.github.com/users/fbemm/gists{/gist_id}","starred_url":"https://api.github.com/users/fbemm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fbemm/subscriptions","organizations_url":"https://api.github.com/users/fbemm/orgs","repos_url":"https://api.github.com/users/fbemm/repos","events_url":"https://api.github.com/users/fbemm/events{/privacy}","received_events_url":"https://api.github.com/users/fbemm/received_events","type":"User","site_admin":false},"created_at":"2015-03-23T11:51:14Z","updated_at":"2015-03-23T11:51:14Z","body":"backtrace:\r\n\r\n#0  0x0000000000773f75 in raise ()\r\n#1  0x000000000070123b in abort ()\r\n#2  0x000000000070de8e in __libc_message ()\r\n#3  0x0000000000715d62 in malloc_printerr ()\r\n#4  0x0000000000434f71 in HDFAlnInfoGroup::~HDFAlnInfoGroup() ()\r\n#5  0x00000000004070fa in HDFCmpFile<AlignmentCandidate<FASTASequence, FASTASequence> >::~HDFCmpFile() () at /software/pacbio/blasr2/libcpp/hdf/HDFCmpFile.hpp:42\r\n#6  0x00000000004040a2 in main () at SamToCmpH5.cpp:88"}}