{"issue":{"milestone":null,"user":{"id":275483,"login":"yp","url":"https://api.github.com/users/yp","avatar_url":"https://secure.gravatar.com/avatar/ceeee22eff014a93ef44a53f7adb1556?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png","gravatar_id":"ceeee22eff014a93ef44a53f7adb1556"},"title":"Segmentation fault during suffix-tree preprocessing","created_at":"2011-12-16T16:25:27Z","updated_at":"2011-12-16T16:48:34Z","labels":[{"name":"bug","url":"https://api.github.com/repos/AlgoLab/PIntron/labels/bug","color":"e10c02"}],"state":"closed","id":2581384,"pull_request":{"patch_url":null,"html_url":null,"diff_url":null},"html_url":"https://github.com/AlgoLab/PIntron/issues/10","closed_at":"2011-12-16T16:48:34Z","body":"If PIntron is built with `STATUS=debug`, the first step of PIntron (`est-fact`) gives a segmentation fault during the suffix-tree preprocessing phase on [these sequences](https://gist.github.com/34f17cde21fddfb5e993).\r\nStep `est-fact` correctly completes if it is compiled with `STATUS=production`.\r\nIn particular, the last messages of the log are:\r\n\r\n````\r\n* INFO (main              ) Creating the suffix tree  (src/main-est-fact.c:276)\r\n* INFO (log_info          ) log-information gst-construction-begin      1324051456      4210 239 167 81 0 2556 0  (src/util.c:220)\r\n* INFO (log_info          ) log-information gst-preprocessing-begin     1324051474      4210 239 167 81 0 2556 0  (src/util.c:220)\r\n* DEBUG(main              ) Preprocessing the GST  (src/main-est-fact.c:293)\r\n* DEBUG(preprocess_text   ) Alphabet: |ACGNT|  (src/aug_suffix_tree.c:112)\r\n* DEBUG(preprocess_text   ) Occurrences of A:       2086  (           0)  (src/aug_suffix_tree.c:115)\r\n* DEBUG(preprocess_text   ) Occurrences of C:       2122  (        2086)  (src/aug_suffix_tree.c:115)\r\n* DEBUG(preprocess_text   ) Occurrences of G:       1896  (        4208)  (src/aug_suffix_tree.c:115)\r\n* DEBUG(preprocess_text   ) Occurrences of N:      50001  (        6104)  (src/aug_suffix_tree.c:115)\r\n* DEBUG(preprocess_text   ) Occurrences of T:       1984  (       56105)  (src/aug_suffix_tree.c:115)\r\n* INFO (stree_preprocess..) Starting the suffix-tree preprocessing phase with 1 strings  (src/aug_suffix_tree.c:227)\r\nSegmentation fault                                                                                                                                           \r\n````\r\n\r\nPIntron version: `v1.2.24`\r\nInput files: https://gist.github.com/34f17cde21fddfb5e993\r\nCommand-line:\r\n\r\n````\r\n./bin-debug/pintron --bin-dir=./bin-debug/ -k --genomic=genomic.txt --EST=ests.txt --organism=human --gene=issue10 --output=pintron-full-output.json --gtf=pintron-cds-annotated-isoforms.gtf --extended-gtf=pintron-all-isoforms.gtf --logfile=pintron-pipeline-log.txt --general-logfile=pintron-log.txt\r\n````","number":10,"url":"https://api.github.com/repos/AlgoLab/PIntron/issues/10","comments":1,"assignee":{"id":275483,"login":"yp","url":"https://api.github.com/users/yp","avatar_url":"https://secure.gravatar.com/avatar/ceeee22eff014a93ef44a53f7adb1556?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png","gravatar_id":"ceeee22eff014a93ef44a53f7adb1556"}},"action":"closed"}