IQTree 1.3.13 crashes during tree search with partitioned dataset

[Joaquim Martins Junior]

Hi all,

I am trying to construct a tree using partitioned scheme and model by codon. At every attempt to run, it crashes after few minutes.

Command line: iqtree-omp -s citri_67_taxons_aln.phy -spp partition_PF.nex -nt 3 -vvv -bb 1000 -numpars 500 -toppars 200 -numcand 100

It is running on a server with 1TB RAM and 80 cores.

Please, find bellow the log file.

https://drive.google.com/file/d/0B2w8d6nWlwqKeXU2YXdnVlVBdTA/view?usp=sharing

Any idea about what should be happening?

Best regards,

Joaquim

  

[Bui Quang Minh]

Hi Joaquim, 

Thanks for the report. The crash looks weird, but I could not see what the problem was from the log file. Therefore can you pls send me your input data files via personal email? 

Cheers, Minh

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Bui Quang Minh

Center for Integrative Bioinformatics Vienna (CIBIV)

Campus Vienna Biocenter 5, VBC5, Ebene 1

A-1030 Vienna, Austria

Phone: ++43 1 4277 74326

Email: minh.bui (AT) univie.ac.at

[Joaquim Martins Junior]

Hi Minh,

Unfortunately, my supervisor did not allowed me to send the dataset to you. We performed the same run with the same dataset using Windows version 1.3.12 and it ends ok! Now we will try Windows version 1.3.13. Maybe It could be a bug on linux version...?

Thank you for helping.

Best regards,

Joaquim

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…

Joaquim Martins Jr, Ph.D.

Postdoctoral Fellow at LBI | IQ | USP
Biologist - CV Lattes: http://lattes.cnpq.br/5170263061293078
Personal site: http://martinsjr.me
Linkedin: http://br.linkedin.com/in/jmartinsjr/en
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LBI - Laboratory of Bioinformatics | http://lbi.iq.usp.br

Instituto de Química - IQ / USP
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Skype: joaquim.martins.jr

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[Bui Quang Minh]

Dear Joachim, 

as it turned out the crash was likely due to -vvv option (verbose mode). This option prints many messages to the screen (or log file) from many threads, which may at some point interfere which each other.

Therefore I recommend NOT to use this option, unless for debugging purpose sometimes.

Cheers, Minh