stamatak
commented
9 years ago Dear Florent,
Could you re-post this message in the RAxML google group, please and maybe also send me the input files that produced the above error?
Thanks,
Alexis
On 10/16/2014 06:29 AM, Florent Angly wrote:
Hi,
I get an error / core dump when running the EPA in RAxML version 7.3.0. I included a backtrace below, but I get the same error with 8.1.1 also.
$ gdb raxmlHPC GNU gdb (Ubuntu/Linaro 7.4-2012.04-0ubuntu2.1) 7.4-2012.04 Copyright (C) 2012 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-linux-gnu". For bug reporting instructions, please see: <http://bugs.launchpad.net/gdb-linaro/>... Reading symbols from /srv/sw/RAxML/7.3.0/bin/raxmlHPC...(no debugging symbols found)...done. (gdb) run -f v -R RAxML_binaryModelParameters.PARAMS -t gg_97_otus_indented.tree -s papara_alignment.phyml -m GTRCAT -n RESULTS Starting program: /srv/sw/RAxML/7.3.0/bin/raxmlHPC -f v -R RAxML_binaryModelParameters.PARAMS -t gg_97_otus_indented.tree -s papara_alignment.phyml -m GTRCAT -n RESULTS warning: no loadable sections found in added symbol-file system-supplied DSO at 0x7ffff7ffa000 RAxML output files with the run ID <RESULTS> already exist in directory /srv/home/uqfangly/Olga_sediments/Illumina-2timepoints-Hitman/phylo_tree/ ...... exiting [Inferior 1 (process 19531) exited with code 0377] (gdb) run -f v -R RAxML_binaryModelParameters.PARAMS -t gg_97_otus_indented.tree -s papara_alignment.phyml -m GTRCAT -n RESULTS Starting program: /srv/sw/RAxML/7.3.0/bin/raxmlHPC -f v -R RAxML_binaryModelParameters.PARAMS -t gg_97_otus_indented.tree -s papara_alignment.phyml -m GTRCAT -n RESULTS warning: no loadable sections found in added symbol-file system-supplied DSO at 0x7ffff7ffa000 IMPORTANT WARNING: Sequences 4315144 and 4410017 are exactly identical IMPORTANT WARNING Found 1 sequence that is exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. An alignment file with sequence duplicates removed has already been printed to file papara_alignment.phyml.reduced Found a total of 99322 taxa in tree file gg_97_otus_indented.tree This is RAxML version 7.3.0 released by Alexandros Stamatakis in June 2011. With greatly appreciated code contributions by: Andre Aberer (HITS) Simon Berger (HITS) Nick Pattengale (Sandia) Wayne Pfeiffer (SDSC) Akifumi S. Tanabe (Univ. Tsukuba) Alignment has 1517 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 20.61% RAxML likelihood-based placement algorithm Using 1 distinct models/data partitions with joint branch length optimization All free model parameters will be estimated by RAxML ML estimate of 25 per site rate categories Partition: 0 Alignment Patterns: 1517 Name: No Name Provided DataType: DNA Substitution Matrix: GTR RAxML was called as follows: /srv/sw/RAxML/7.3.0/bin/raxmlHPC -f v -R RAxML_binaryModelParameters.PARAMS -t gg_97_otus_indented.tree -s papara_alignment.phyml -m GTRCAT -n RESULTS RAxML placement algorithm: You provided a reference tree with 99322 taxa; alignmnet has 99340 taxa 18 query taxa will be placed using maximum likelihood RAxML Evolutionary Placement Algorithm raxmlHPC: optimizeModel.c:2411: modOpt: Assertion `!adef->useBinaryModelFile' failed. Program received signal SIGABRT, Aborted. 0x00007ffff77550d5 in __GI_raise (sig=<optimised out>) at ../nptl/sysdeps/unix/sysv/linux/raise.c:64 64 ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory. (gdb) bt #0 0x00007ffff77550d5 in __GI_raise (sig=<optimised out>) at ../nptl/sysdeps/unix/sysv/linux/raise.c:64 #1 0x00007ffff775883b in __GI_abort () at abort.c:91 #2 0x00007ffff774dd9e in __assert_fail_base (fmt=<optimised out>, assertion=0x4dba98 "!adef->useBinaryModelFile", file=0x4dba10 "optimizeModel.c", line=<optimised out>, function=<optimised out>) at assert.c:94 #3 0x00007ffff774de42 in __GI___assert_fail (assertion=0x4dba98 "!adef->useBinaryModelFile", file=0x4dba10 "optimizeModel.c", line=2411, function=0x4dc1a3 "modOpt") at assert.c:103 #4 0x000000000041f387 in modOpt () #5 0x00000000004b0b12 in classifyML () #6 0x0000000000439c43 in treeReadLen () #7 0x000000000043a9f9 in getStartingTree () #8 0x00000000004052d9 in main ()Any idea what is wrong? I could send you the data if needed. Cheers, Florent
Reply to this email directly or view it on GitHub: https://github.com/stamatak/standard-RAxML/issues/15
Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University of Arizona at Tucson
www.exelixis-lab.org
fangly
Hi,
I get an error / core dump when running the EPA in RAxML version 7.3.0. I included a backtrace below, but I get the same error with 8.1.1 also.
Any idea what is wrong? I could send you the data if needed. Cheers, Florent