Building gene trees: IQ-TREE CRASHES WITH SIGNAL ABORTED

[Gregg Thomas]

Hello,

I am using version:

IQ-TREE multicore version 2.0-rc1 for Linux 64-bit built Nov 21 2019
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

I am trying to run the command:

iqtree -S aln/ --prefix loci -T AUTO

This runs for a while and then exits with:

ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: ***    Log file: loci.log
ERROR: ***    Alignment files (if possible)

I can see no other info in the log file that pertains to this error, so I don't even know where to start to try and figure this out (hopefully I didn't miss something simple!).

Just for reference, the command:

iqtree -p aln/ --prefix concat -B 1000 -T AUTO

completes successfully.

The logfile is attached. I can send the alignments as well, but they were too large to attach here. Please let me know how to send those and if you need anything else.

Thanks!

-Gregg

[Minh Bui]

Hi Gregg,

Can you try rc2 version here: https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0-rc2

Let me know if that works or not.

Thanks,

Minh

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<loci.log>

[Gregg Thomas]

Hi Minh,

Thanks for the reply. Unfortunately that didn't work either. I'm now getting a segmentation fault.

Version:

IQ-TREE multicore version 2.0-rc2 for Linux 64-bit built Feb 19 2020

Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Error in the log file:

ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT

ERROR: *** For bug report please send to developers:
ERROR: ***    Log file: loci.log
ERROR: ***    Alignment files (if possible)

The logfile is attached, and I can send the alignments if necessary.

Thanks!

-Gregg

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[jigyasa arora]

Hey Minh and Gregg

I am facing exactly the same problem with iqtree-1.6.12-Linux version.

Error in the log file-

"ERROR: splitgraph.h:235: int SplitGraph::getNTaxa(): Assertion `size() > 0' failed.

ERROR: STACK TRACE FOR DEBUGGING:

ERROR:

ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED

ERROR: *** For bug report please send to developers:

ERROR: ***    Log file: iqtree-FcC_smatrix.log

ERROR: ***    Alignment files (if possible)"

Any suggestions?

[Gregg Thomas]

Hi Minh,

I wanted to follow up on this. This appears to occur only when specifying -T > 1 (or -T AUTO). Running this analysis on a single thread completes successfully, though obviously takes longer.
I have tried this on both SLURM and TORQUE managed systems with the same result. Here is the log file from my latest attempt yesterday, with the latest release of IQ-Tree.

Version:

IQ-TREE multicore version 2.0.4 for Linux 64-bit built Apr 27 2020

Command I ran:

iqtree -S aln-windows/125kb-0.5-0.5-aln/ --prefix 125kb-0.5-0.5-loci -T AUTO

Error:

ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:

ERROR: ***    Log file: 125kb-0.5-0.5-loci.log

ERROR: ***    Alignment files (if possible)

Log file is attached. Happy to send alignments, though I should note that I have tried this on multiple datasets now to no avail.

Thanks,
-Gregg

[Minh Bui]

Hi Gregg,

Sorry for the delay — At the moment I really have limited time to support users. In this case, you can alternatively do a for-loop to run IQ-TREE for each alignment instead of -S option. So I suggest that you do this for the moment. Before I can get to fix the issue. Nevertheless, pls send me the alignments and I will come to that when time permits.

Thanks for your understanding,

Minh

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<125kb-0.5-0.5-loci.log>

[Narfusala]

Hey there,

I'm experiencing the exact same problem on 1.6.12 on a slurm HPC with a ~200x SNP array multi fasta using the command
$ iqtree -s input_multi.fasta -st DNA -keep-ident -mem 450G -nt 32 -m MF -bb 1000 -wbtl

Since gregg also works on slurm, maybe it's a slurm issue rather than iqtree issue? Anyway, trying to run it on one thread now to see if that helps :P

Cheers,
Lesley

Op woensdag 6 mei 2020 om 03:14:42 UTC+2 schreef Minh Bui:

[Marcus Teixeira]

I had the same problems.

But change the  -T AUTO to -T 16 and so far so good.

Marcus