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nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
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Illegal instruction (core dumped) Unable to fit model to data #353

Closed DorothyTamYiLing closed 1 year ago

DorothyTamYiLing commented 2 years ago

Hi,

First of all, thanks for writing Gubbins such an amazing software.

I am trying to run Gubbins in a large dataset alignment (about 3000+ samples, each sample 4800K bp long). I have the following issues and there was also no log file produced. I managed to capture the following printings just before the error occurred:

Gubbins command [Gubbins version v3.2.1]: /home/ubuntu/miniconda3/envs/gubbins/bin/run_gubbins.py --prefix Sflex --starting-tree S-flex.snp-sites.fasta.treefile.mid2.tre mapping-S_flex_2a.masked_rename.aln --filter-percentage 35

error message:

Using 1 distinct models/data partitions with joint branch length optimization

All free model parameters will be estimated by RAxML GAMMA model of rate heterogeneity, 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: 88664 Name: No Name Provided DataType: DNA Substitution Matrix: GTR

RAxML was called as follows:

raxmlHPC-AVX2 -p 7988 -safe -m GTRGAMMA -s mapping-S_flex_2a.masked_rename.aln.snp_sites.aln -n mapping-S_flex_2a.masked_rename.iteration_1_reconstruction -t /home/ubuntu/Dorothy/Shigella_dir/tmpiioyzz7v/mapping-S_flex_2a.masked_rename.iteration_1.tre.rooted -f e -w /home/ubuntu/Dorothy/Shigella_dir/tmpiioyzz7v

Illegal instruction (core dumped) Unable to fit model to data

It would be great if I can know how to solve this problem. Also, because there was not any log file produced, I tried to pipe the standard output of Gubbins into a file using the following command: run_gubbins.py --prefix XX --starting_tree mytree.tre myfasta.fasta > gubbins.log But for some reasons only some of the outputs can be captured using this method.

Many thanks, Dorothy

nickjcroucher commented 2 years ago

It seems as though it is possibly running out of memory when fitting the phylogenetic model to the first alignment - you can try a simpler model for the first iteration (e.g. JC or GTR), a different model fitter (e.g. fasttree), and/or using more memory.

DorothyTamYiLing commented 2 years ago

Hi,

Thanks for the speedy reply, during the weekend! I will have a go and let you know if I have more issue.

Thanks and have a nice weekend.

Best wishes, Dorothy