{"action":"opened","issue":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/18","labels_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/18/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/18/comments","events_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/18/events","html_url":"https://github.com/PacificBiosciences/FALCON/issues/18","id":57578372,"number":18,"title":"falcon running failed,help!","user":{"login":"AnWD","id":10287901,"avatar_url":"https://avatars.githubusercontent.com/u/10287901?v=3","gravatar_id":"","url":"https://api.github.com/users/AnWD","html_url":"https://github.com/AnWD","followers_url":"https://api.github.com/users/AnWD/followers","following_url":"https://api.github.com/users/AnWD/following{/other_user}","gists_url":"https://api.github.com/users/AnWD/gists{/gist_id}","starred_url":"https://api.github.com/users/AnWD/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AnWD/subscriptions","organizations_url":"https://api.github.com/users/AnWD/orgs","repos_url":"https://api.github.com/users/AnWD/repos","events_url":"https://api.github.com/users/AnWD/events{/privacy}","received_events_url":"https://api.github.com/users/AnWD/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-02-13T09:44:05Z","updated_at":"2015-02-13T09:44:05Z","closed_at":null,"body":"To assemble human genome with pacbio-only sequencing data, we tried to apply FALCON software. We installed the software following the instructions, and no error turned up in the process of installation, the installation information is attached.Here is our sever environment which is satisfied with the installation requirement too. \r\n\r\n[smrtanalysis@node4 FALCON-master]$ uname -a \r\nLinux node4.bnu.edu.cn 2.6.32-279.el6.x86_64 #1 SMP Wed Jun 13 18:24:36 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux \r\n\r\n[smrtanalysis@node4 FALCON-master]$ gcc --version \r\ngcc (GCC) 4.8.2 \r\n\r\n[smrtanalysis@node4 FALCON-master]$ python --version \r\nPython 2.7.3 \r\n\r\nHowever, when I ran the FALCON following the instructions, it failed and the running error information is also attched.\r\n\r\nfc_run.cfg:\r\n[General]\r\n# list of files of the initial bas.h5 files\r\ninput_fofn = input.fofn\r\n#input_fofn = preads.fofn\r\n\r\ninput_type = raw\r\n#input_type = preads\r\n\r\n# The length cutoff used for seed reads used for initial mapping\r\nlength_cutoff = 12000\r\n\r\n# The length cutoff used for seed reads usef for pre-assembly\r\nlength_cutoff_pr = 12000\r\n\r\n\r\nsge_option_da = -l h=nodesuper -pe openmp 4 -q all.q\r\nsge_option_la = -l h=nodesuper -pe openmp 4 -q all.q\r\nsge_option_pda = -l h=nodesuper -pe openmp 2 -q all.q\r\nsge_option_pla = -l h=nodesuper -pe openmp 2 -q all.q\r\nsge_option_fc = -l h=nodesuper -pe openmp 4 -q all.q\r\nsge_option_cns = -l h=nodesuper -pe openmp 4 -q all.q\r\n\r\n\r\npa_concurrent_jobs = 16\r\ncns_concurrent_jobs = 16\r\novlp_concurrent_jobs = 16\r\n\r\npa_HPCdaligner_option =  -v -dal4 -t16 -e.70 -l1000 -s400\r\novlp_HPCdaligner_option = -v -dal4 -t32 -h60 -e.96 -l500 -s400\r\n\r\npa_DBsplit_option = -x50 -s50\r\novlp_DBsplit_option = -x50 -s50\r\n\r\nfalcon_sense_option = --output_multi --min_idt 0.70 --min_cov 2 --local_match_count_threshold 1 --max_n_read 10 --n_core 2\r\n\r\noverlap_filtering_setting = --max_diff 50 --max_cov 30 --min_cov 20 --bestn 10\r\n\r\n\r\n\r\nERROR 1(input_type = raw)：\r\n  command:  vi  ./0-rawreads/job_10684559/rj_10684559.log\r\n\r\n\"15079 vs 15111 :   3\r\n15104 vs 15111 :   4\r\n\r\n     18,604,978 14-mers (7.440891e-09 of matrix)\r\n          5,100 seed hits (2.039698e-12 of matrix)\r\n            560 confirmed hits (2.239669e-13 of matrix)\r\n*** glibc detected *** daligner: double free or corruption (out): 0x0000003ea0c04b30 ***\r\n======= Backtrace: =========\r\n/lib64/libc.so.6[0x3ea0c75366]\r\n/lib64/libc.so.6[0x3ea0c77e93]\r\ndaligner[0x401ea6]\r\n/lib64/libc.so.6(__libc_start_main+0xfd)[0x3ea0c1ecdd]\r\ndaligner[0x401339]\r\n======= Memory map: ========\r\n00400000-0041f000 r-xp 00000000 00:1c 113118876                          /home/nfs_UserData_220/falcon/installation_dir/FALCON-master/fc_env/bin/daligner\r\n0061e000-0061f000 rw-p 0001e000 00:1c 113118876                          /home/nfs_UserData_220/falcon/installation_dir/FALCON-master/fc_env/bin/daligner\"\r\n\r\ncommand:    gdb ./0-rawreads/job_58132038/core.9839\r\n\"[New Thread 9839]\r\nCore was generated by `daligner -v -t16 -H3000 -e0.7 -s1000 raw_reads.1 raw_reads.1'.\r\nProgram terminated with signal 6, Aborted.\"\r\n\r\n\r\nERROR 2(input_type = preads)：\r\nwhen run the command \"fc_run.py fc_run.cfg\",it shows\r\n\r\n\"No target specified, assuming \"assembly\" as target \r\nException in thread Thread-2:\r\nTraceback (most recent call last):\r\n  File \"/home/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/python2.7/lib/python2.7/threading.py\", line 551, in __bootstrap_inner\r\n    self.run()\r\n  File \"/home/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/python2.7/lib/python2.7/threading.py\", line 504, in run\r\n    self.__target(*self.__args, **self.__kwargs)\r\n  File \"/home/nfs_UserData_220/falcon/installation_dir/FALCON-master/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/task.py\", line 317, in __call__\r\n    runFlag = self._getRunFlag()\r\n  File \"/home/nfs_UserData_220/falcon/installation_dir/FALCON-master/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/task.py\", line 147, in _getRunFlag\r\n    runFlag = any( [ f(self.inputDataObjs, self.outputDataObjs, self.parameters) for f in self._compareFunctions] )\r\n  File \"/home/nfs_UserData_220/falcon/installation_dir/FALCON-master/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/task.py\", line 812, in timeStampCompare\r\n    if min(outputDataObjsTS) < max(inputDataObjsTS):\r\nValueError: max() arg is an empty sequence\r\n\r\nException in thread Thread-4:\r\nTraceback (most recent call last):\r\n  File \"/home/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/python2.7/lib/python2.7/threading.py\", line 551, in __bootstrap_inner\r\n    self.run()\r\n  File \"/home/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/python2.7/lib/python2.7/threading.py\", line 504, in run\r\n    self.__target(*self.__args, **self.__kwargs)\r\n  File \"/home/nfs_UserData_220/falcon/installation_dir/FALCON-master/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/task.py\", line 317, in __call__\r\n    runFlag = self._getRunFlag()\r\n  File \"/home/nfs_UserData_220/falcon/installation_dir/FALCON-master/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/task.py\", line 147, in _getRunFlag\r\n    runFlag = any( [ f(self.inputDataObjs, self.outputDataObjs, self.parameters) for f in self._compareFunctions] )\r\n  File \"/home/nfs_UserData_220/falcon/installation_dir/FALCON-master/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/task.py\", line 812, in timeStampCompare\r\n    if min(outputDataObjsTS) < max(inputDataObjsTS):\r\nValueError: max() arg is an empty sequence\"\r\n\r\nand also the sge_log/falcon-ea66cd36.o9615    shows :\"/home/sgeadmin/node10/node10/job_scripts/9615: line 3: 42517               core dumped)DB2Falcon preads\"  \r\n\"in <module>  for res in exe_pool.imap(filter_stage1, inputs): File  '/home/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/python2.7/lib/python2.7/multiprocessing/pool.py', line 626, in next raise value\r\nOSError: [Errno 2] No such file or directory\"\r\n\r\nps:\r\nwe have also run the ecoli example descriped in the manual,the same error  above.\r\n\r\nhardware environment:\r\nsupernode: 48 cores  2.7GHz ,600G memory * 1\r\nnode : 24 cores 2.1GHz, 64G memory * 8\r\n\r\nWould you like to help us about this? "}}