"Core Dumped" Error

109 views
Skip to first unread message

CapitaineRex69

unread,
Jun 14, 2016, 8:43:22 AM6/14/16
to raxml
Hello,

I am trying to run raxml on a .aln file generated by Roary, but I always get an error : "... (core dumped)."

I type : raxmlHPC-AVX -m GTRGAMMA -p 12345 -s alignment.aln -n CF_ATCC_bootstrap -f a -x 12345 -N 100

I'm using the 8.2.8 version of raxml.

Thanks for your help !

Jeremy.

Alexandros Stamatakis

unread,
Jun 14, 2016, 8:58:29 AM6/14/16
to ra...@googlegroups.com
what's the format of that alignment file?

does raxml print out anything else?

alexis
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.

--
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

CapitaineRex69

unread,
Jun 14, 2016, 9:11:32 AM6/14/16
to raxml
Thank you for your answer.
My file looks like this, so basically fasta format with 6 total sequences :
>12040
ATGATCCCGCGCGAAATCGCGATTCTCGATGCGTACATGCCCACGGTCGTGCTGATGTTC
GTCGTCGGCGCGCTCGCGACCTGGGCCGTCGACCGCCTGCTCGCCTATACGGGCCTCTAC
CGTGTCGTCTGGCACCCGTCGCTGTTCCGGGCCTGCCTGCTCGTCTGCATATGCGGCGGA
CTCAGTCTCGCCGTTTACCGTTGAATGTCGAAGACAACGTATTAC
...
>12041
ATGATCCCGCGCGAAATCGCGATTCTCGATGCGTACATGCCCACGGTCGTGCTGATGTTC
GTCGTCGGCGCGCTCGCGACCTGGGCCGTCGACCGCCTGCTCGCCTATACGGGCCTCTAC
CGTGTCGTCTGGCACCCGTCGCTGTTCCGGGCCTGCCTGCTCGTCTGCATATGCGGCGGA
...

Here is all what raxml prints after I type the command :

Alignment has 386 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 0.77%
RAxML rapid hill-climbing mode
Using 1 distinct models/data partitions with joint branch length optimization
Executing 1 inferences on the original alignment using 1 distinct randomized MP trees
All free model parameters will be estimated by RAxML
GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 386
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
raxmlHPC-PTHREADS-AVX -m GTRGAMMA -p 12345 -s core_gene_alignment.aln -n CF_ATCC_basic
Partition: 0 with name: No Name Provided
Base frequencies: 0.159 0.338 0.344 0.158
Instruction non permise (core dumped)

Alexandros Stamatakis

unread,
Jun 14, 2016, 9:14:46 AM6/14/16
to ra...@googlegroups.com
does your CPU support AVX instructions?

the error message:

"Instruction non permise (core dumped)"

indicates that it most probably doesn't, please try the SSE3 version and
check if it works,

alexis
> > an email to raxml+un...@googlegroups.com <javascript:>
> > <mailto:raxml+un...@googlegroups.com <javascript:>>.
> > For more options, visit https://groups.google.com/d/optout
> <https://groups.google.com/d/optout>.
>
> --
> 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 <http://www.exelixis-lab.org>

CapitaineRex69

unread,
Jun 14, 2016, 9:29:44 AM6/14/16
to raxml
Worked perfectly. Thank you for poiting out my mistake !
Reply all
Reply to author
Forward
0 new messages