Assertion `tr->ntips == tr->mxtips' failed

[jodyphelan]

Hi,

I am getting an error but not sure what it means:

Examl-OMP-AVX: treeIO.c:907: treeReadLen: Assertion `tr->ntips == tr->mxtips' failed. [s4:161245] Process received signal [s4:161245] Signal: Aborted (6) [s4:161245] Signal code: (-6) [s4:161245] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10330) [0x7f257a1b2330] [s4:161245] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37) [0x7f2579e10c37] [s4:161245] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x148) [0x7f2579e14028] [s4:161245] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x2fbf6) [0x7f2579e09bf6] [s4:161245] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x2fca2) [0x7f2579e09ca2] [s4:161245] [ 5] /mnt/storage/jody/software/ExaML/examl/examl-OMP-AVX() [0x424810] [s4:161245] [ 6] /mnt/storage/jody/software/ExaML/examl/examl-OMP-AVX() [0x4252b2] [s4:161245] [ 7] /mnt/storage/jody/software/ExaML/examl/examl-OMP-AVX() [0x4047a6] [s4:161245] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f2579dfbf45] [s4:161245] [ 9] /mnt/storage/jody/software/ExaML/examl/examl-OMP-AVX() [0x404987] [s4:161245] End of error message Aborted (core dumped)

The command I am running is this:

raxmlHPC-PTHREADS-AVX -y -m GTRCAT -p 12345 -s all_samples.phylip -n StartingTree -T 40
parse-examl -s all_samples.phylip -n all_samples -m DNA
examl-OMP-AVX -s all_samples.binary -n examl -m PSR -D -t RAxML_parsimonyTree.StartingTree

RAxML runs fine but ExaML throws an error... Any ideas on how to troubleshoot?

Thanks, Jody

[stamatak]

Hi Jody,

Could you please post such questions on the raxml google group in the future?

The error means that apparently the tree you provide contains less taxa than the respective alignment you provide which is not allowed in ExaML.

However, your sequence of command lines looks correct and it seems to always use the same alignment file.

As I don't know if all of this was executed on the same system, it could be that the copies of the alignment files differ.

Another possible source of error is that you are using the OpenMP version which could be generating the bug.

Finally, please consider switching to RAxML-NG which will replace both RAxML and ExaML this year:

https://github.com/amkozlov/raxml-ng

Alexis

On 18.01.2018 20:32, jodyphelan wrote:

Hi,

I am getting an error but not sure what it means:

Examl-OMP-AVX: treeIO.c:907: treeReadLen: Assertion `tr->ntips == tr->mxtips' failed. [s4:161245] Process received signal [s4:161245] Signal: Aborted (6) [s4:161245] Signal code: (-6) [s4:161245] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10330) [0x7f257a1b2330] [s4:161245] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37) [0x7f2579e10c37] [s4:161245] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x148) [0x7f2579e14028] [s4:161245] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x2fbf6) [0x7f2579e09bf6] [s4:161245] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x2fca2) [0x7f2579e09ca2] [s4:161245] [ 5] /mnt/storage/jody/software/ExaML/examl/examl-OMP-AVX() [0x424810] [s4:161245] [ 6] /mnt/storage/jody/software/ExaML/examl/examl-OMP-AVX() [0x4252b2] [s4:161245] [ 7] /mnt/storage/jody/software/ExaML/examl/examl-OMP-AVX() [0x4047a6] [s4:161245] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f2579dfbf45] [s4:161245] [ 9] /mnt/storage/jody/software/ExaML/examl/examl-OMP-AVX() [0x404987] [s4:161245] End of error message Aborted (core dumped)

The command I am running is this:

|raxmlHPC-PTHREADS-AVX -y -m GTRCAT -p 12345 -s all_samples.phylip -n StartingTree -T 40 parse-examl -s all_samples.phylip -n all_samples -m DNA examl-OMP-AVX -s all_samples.snps.binary -n examl -m PSR -D -t RAxML_parsimonyTree.StartingTree |

RAxML runs fine but ExaML throws an error... Any ideas on how to troubleshoot?

Thanks, Jody

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/stamatak/ExaML/issues/11, or mute the thread https://github.com/notifications/unsubscribe-auth/AA1w-gIXpjrhsKHc9HteUMgBYCx5aHlsks5tL5nKgaJpZM4RjbxZ.

-- Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

[jodyphelan]

Ok. I will use the raxml google group. It works with raxml-ng.

Thanks, Jody