ExaBayes error parsing

[Angélica Gallego Narbón]

Hello everyone!

I just compiled ExaBayes and there seems to be a problem to run partitioned alignments. Any ideas on what the problem could be?

#!/bin/bash
#SBATCH -p long #particion(cola)
#SBATCH -N 8#numero de nodos
#SBATCH -n 80 #numero de cores(CPUs)
#SBATCH -e ExaBayesCpTot.err
#SBATCH -o ExaBayesCpTot.out

cd /lustre/home/rjb/mfmazuecos/HybSeq_AGN/0_Arboles/plasto/CpTot_ExaBayes
mpirun -np 80 /lustre/home/rjb/mfmazuecos/applications/exabayes-1.5/exabayes -f CpTot.phy -q CpTot_annotations.txt -n ExaBayes_CpTot -s $RANDOM -m DNA -c modelpar.nex -R 2 -C 2

I also send a link to the alignment. I extracted the loci through Hyb-Seq, concatenated them in Geneious and exported the alignment in phillip format

https://www.dropbox.com/s/di00pnsyqnqkwiq/CpTot.phy?dl=0 

[Alexandros Stamatakis]

Hi Angelica,

I don't see any evident error what kind of error message are you getting?

Alexis

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--
Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)

[Angélica Gallego Narbón]

Thank you for trying to help. That is the error:

Error while opening/reading file CpTot_annotations.txt
exabayes: ./src/contrib/AlignmentPLL.cpp:208: void AlignmentPLL::initPartitions(std::string): Assertion `0' failed.
[drago31020064:4042645] *** Process received signal ***
[drago31020064:4042645] Signal: Aborted (6)
[drago31020064:4042645] Signal code:  (-6)
[drago31020064:4042645] [ 0] /lib64/libpthread.so.0(+0x12ce0)[0x7f99c3ac6ce0]
[drago31020064:4042645] [ 1] /lib64/libc.so.6(gsignal+0x10f)[0x7f99c373da9f]
[drago31020064:4042645] [ 2] /lib64/libc.so.6(abort+0x127)[0x7f99c3710e05]
[drago31020064:4042645] [ 3] /lib64/libc.so.6(+0x21cd9)[0x7f99c3710cd9]
[drago31020064:4042645] [ 4] /lib64/libc.so.6(+0x473f6)[0x7f99c37363f6]
[drago31020064:4042645] [ 5] /lustre/home/rjb/mfmazuecos/applications/exabayes-1.5/exabayes[0x48de75]
[drago31020064:4042645] [ 6] /lustre/home/rjb/mfmazuecos/applications/exabayes-1.5/exabayes[0x45630e]
[drago31020064:4042645] [ 7] /lustre/home/rjb/mfmazuecos/applications/exabayes-1.5/exabayes[0x457d36]
[drago31020064:4042645] [ 8] /lustre/home/rjb/mfmazuecos/applications/exabayes-1.5/exabayes[0x436ab2]
[drago31020064:4042645] [ 9] /lustre/home/rjb/mfmazuecos/applications/exabayes-1.5/exabayes[0x437ad9]
[drago31020064:4042645] [10] /lustre/home/rjb/mfmazuecos/applications/exabayes-1.5/exabayes[0x4321fd]
[drago31020064:4042645] [11] /lib64/libc.so.6(__libc_start_main+0xf3)[0x7f99c3729cf3]
[drago31020064:4042645] [12] /lustre/home/rjb/mfmazuecos/applications/exabayes-1.5/exabayes[0x433c6e]
[drago31020064:4042645] *** End of error message ***
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node drago31020064 exited on signal 6 (Aborted).
--------------------------------------------------------------------------

[Alexandros Stamatakis]

Hi Angelica,

So for some reason you are not seeing the full error message, presumably
because you are using the MPI version on a cluster.

The full error message that is printed looks like this:

std::cout << "\n\nError: parsing file " << partitionFile << " failed. \n\n"
"Please double-check, whether each site is assigned a
partition. \n"
"Side note: the notation for choosing every n-th (e.g.,
triplet) \n"
"character has changed from '\\3' to '/3'.";
assert(0);

So it might well be that some sites have not been assigned a partition,
or maybe that some sites have been assigned to two partitions or that
not all sites of the MSA have been assigned to a partition.

The best way to figure out what the problem is, is to test with the
sequential version of ExaBayes on some laptop or Desktop what the error
is, as this will let you see the error message immediately.

Alexis

> https://groups.google.com/d/msgid/exabayes/ee8a2128-3b6d-4d98-8489-00eb3686df60n%40googlegroups.com <https://groups.google.com/d/msgid/exabayes/ee8a2128-3b6d-4d98-8489-00eb3686df60n%40googlegroups.com> <https://groups.google.com/d/msgid/exabayes/ee8a2128-3b6d-4d98-8489-00eb3686df60n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/exabayes/ee8a2128-3b6d-4d98-8489-00eb3686df60n%40googlegroups.com?utm_medium=email&utm_source=footer>>.

>
> --
> Alexandros (Alexis) Stamatakis
>
> ERA Chair, Institute of Computer Science, Foundation for Research and
> Technology - Hellas
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
>

> www.biocomp.gr <http://www.biocomp.gr> (Crete lab)
> www.exelixis-lab.org <http://www.exelixis-lab.org> (Heidelberg lab)

>
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[Angélica Gallego Narbón]

I´ll give it a try, thank you!