Phylogenetic inference with q2-phylogeny¶
Note
This tutorial assumes, you’ve read through the QIIME 2 Overview documentation and have at least worked through some of the other Tutorials.
Inferring phylogenies¶
Several downstream diversity metrics, available within QIIME 2, require that a phylogenetic tree be constructed using the Operational Taxonomic Units (OTUs) or Amplicon Sequence Variants (ASVs) being investigated.
But how do we proceed to construct a phylogeny from our sequence data?
Well, there are two phylogeny-based approaches we can use. Deciding upon which to use is largely dependent on your study questions:
1. A reference-based fragment insertion approach. Which, is likely the ideal choice. Especially, if your reference phylogeny (and associated representative sequences) encompass neighboring relatives of which your sequences can be reliably inserted. Any sequences that do not match well enough to the reference are not inserted. For example, this approach may not work well if your data contain sequences that are not well represented within your reference phylogeny (e.g. missing clades, etc.). For more information, check out these great fragment insertion examples.
2. A de novo approach. Marker genes that can be globally aligned across divergent taxa, are usually amenable to sequence alignment and phylogenetic investigation through this approach. Be mindful of the length of your sequences when constructing a de novo phylogeny, short reads many not have enough phylogenetic information to capture a meaningful phylogeny. This community tutorial will focus on the de novo approaches.
Here, you will learn how to make use of de novo phylogenetic approaches to:
generate a sequence alignment within QIIME 2
mask the alignment if needed
construct a phylogenetic tree
root the phylogenetic tree
If you would like to substitute any of the steps outlined here by making use of tools external to QIIME 2, please see the import, export, and filtering documentation where appropriate.
Sequence Alignment¶
Prior to constructing a phylogeny we must generate a multiple sequence alignment (MSA). When constructing a MSA we are making a statement about the putative homology of the aligned residues (columns of the MSA) by virtue of their sequence similarity.
The number of algorithms to construct a MSA are legion. We will make use of MAFFT (Multiple Alignment using Fast Fourier Transform)) via the q2-alignment plugin. For more information checkout the MAFFT paper.
Let’s start by creating a directory to work in:
mkdir qiime2-phylogeny-tutorial
cd qiime2-phylogeny-tutorial
Next, download the data:
Please select a download option that is most appropriate for your environment:
Download URL: https://data.qiime2.org/2022.11/tutorials/phylogeny/rep-seqs.qza
Save as: rep-seqs.qza
wget \
-O "rep-seqs.qza" \
"https://data.qiime2.org/2022.11/tutorials/phylogeny/rep-seqs.qza"
curl -sL \
"https://data.qiime2.org/2022.11/tutorials/phylogeny/rep-seqs.qza" > \
"rep-seqs.qza"
Run MAFFT
qiime alignment mafft \
--i-sequences rep-seqs.qza \
--o-alignment aligned-rep-seqs.qza
Reducing alignment ambiguity: masking and reference alignments¶
Why mask an alignment?
Masking helps to eliminate alignment columns that are phylogenetically uninformative or misleading before phylogenetic analysis. Much of the time alignment errors can introduce noise and confound phylogenetic inference. It is common practice to mask (remove) these ambiguously aligned regions prior to performing phylogenetic inference. In particular, David Lane’s (1991) chapter 16S/23S rRNA sequencing proposed masking SSU data prior to phylogenetic analysis. However, knowing how to deal with ambiguously aligned regions and when to apply masks largely depends on the marker genes being analyzed and the question being asked of the data.
Note
Keep in mind that this is still an active area of discussion, as highlighted by the following non-exhaustive list of articles: Wu et al. 2012, Ashkenazy et al. 2018, Schloss 2010, Tan et al. 2015, Rajan 2015.
How to mask alignment.
For our purposes, we’ll assume that we have ambiguously aligned columns in the
MAFFT alignment we produced above. The default settings for the
--p-min-conservation of the
alignment mask approximates the
Lane mask filtering of QIIME 1. Keep an eye out for updates to the alignment
plugin.
qiime alignment mask \
--i-alignment aligned-rep-seqs.qza \
--o-masked-alignment masked-aligned-rep-seqs.qza
Reference based alignments
There are several tools that attempt to reduce the amount of ambiguously aligned regions by using curated reference alignments. Traditional, de novo alignment methods mututally align a set of unaligned sequences to create a multiple sequence alignment (MSA) from scratch. Re-running these methods with additional sequences will create MSAs with varying numbers of columns and assignments of bases to each column. These alignments is therefore incompatible with one another and may not be joined through concatenation.
Reference based alignments, on the other hand, are meant to add sequences to an existing alignment. Alignments computed using reference based alignment tools always have widths identical to the reference alignment and maintain the meaning of each column. Therefore, these alignments may be concatenated.
QIIME 2 currently does not wrap any methods for reference-based alignments, but alignments created using these methods can be imported into QIIME 2 as FeatureData[AlignedSequence] artifacts, provided that the alignments are standard FASTA formats. Some examples of tools for reference-based alignment include PyNAST (using NAST), Infernal, and SINA. SILVA Reference
alignments are particularly powerful for rRNA gene sequence data, as knowledge
of secondary structure is incorporated into the curation process, thus
increasing alignment quality.
Note
Alignments constructed using reference based alignment approaches can be masked too, just like the above MAFFT example. Also, the reference alignment approach we are discussing here is distinct from the reference phylogeny approach (i.e. q2-fragment-insertion) we mentioned earlier. That is, we are not inserting our data into an existing tree, but simply trying to create a more robust alignment for making a better de novo phylogeny.
Construct a phylogeny¶
As with MSA algorithms, phylogenetic inference tools are also legion. Fortunately, there are many great resources to learn about phylogentics. Below are just a few introductory resources to get you started:
There are several methods / pipelines available through the q2-phylogeny plugin of :qiime2:. These are based on the following tools:
Methods¶
fasttree¶
FastTree is able to construct phylogenies from large sequence alignments quite rapidly. It does this by using the using a CAT-like rate category approximation, which is also available through RAxML (discussed below). Check out the FastTree online manual for more information.
qiime phylogeny fasttree \
--i-alignment masked-aligned-rep-seqs.qza \
--o-tree fasttree-tree.qza
Tip
For an easy and direct way to view your tree.qza files, upload
them to iTOL. Here, you can interactively view and manipulate your
phylogeny. Even better, while viewing the tree topology in “Normal mode”,
you can drag and drop your associated alignment.qza (the one you used to
build the phylogeny) or a relevent taxonomy.qza file onto the iTOL tree
visualization. This will allow you to directly view the sequence alignment
or taxonomy alongside the phylogeny. 🕶️
raxml¶
Like fasttree, raxml will perform a single phylogentic inference and
return a tree. Note, the default model for raxml is
--p-substitution-model GTRGAMMA. If you’d like to construct a tree using
the CAT model like fasttree, simply replace GTRGAMMA with GTRCAT as
shown below:
qiime phylogeny raxml \
--i-alignment masked-aligned-rep-seqs.qza \
--p-substitution-model GTRCAT \
--o-tree raxml-cat-tree.qza \
--verbose
stdout:
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Sarah Lutteropp (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
Charlie Taylor (UF)
Alignment has 157 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 39.77%
RAxML rapid hill-climbing mode
Using 1 distinct models/data partitions with joint branch length optimization
Executing 1 inferences on the original alignment using 1 distinct randomized MP trees
All free model parameters will be estimated by RAxML
ML estimate of 25 per site rate categories
Likelihood of final tree will be evaluated and optimized under GAMMA
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 157
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
raxmlHPC -m GTRCAT -p 4787 -N 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptxgxppt6 -n q2
Partition: 0 with name: No Name Provided
Base frequencies: 0.243 0.182 0.319 0.256
Inference[0]: Time 0.682235 CAT-based likelihood -1242.537192, best rearrangement setting 5
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -1387.781776 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptxgxppt6/RAxML_result.q2
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -1387.781776 ....
Final GAMMA-based Score of best tree -1387.637559
Program execution info written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptxgxppt6/RAxML_info.q2
Best-scoring ML tree written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptxgxppt6/RAxML_bestTree.q2
Overall execution time: 1.305106 secs or 0.000363 hours or 0.000015 days
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: raxmlHPC -m GTRCAT -p 4787 -N 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptxgxppt6 -n q2
Saved Phylogeny[Unrooted] to: raxml-cat-tree.qza
Perform multiple searches using raxml¶
If you’d like to perform a more thorough search of “tree space” you can
instruct raxml to perform multiple independent searches on the full
alignment by using --p-n-searches 5. Once these 5 independent searches are
completed, only the single best scoring tree will be returned. Note, we are
not bootstrapping here, we’ll do that in a later example. Let’s set
--p-substitution-model GTRCAT. Finally, let’s also manually set a seed via
--p-seed. By setting our seed, we allow other users the ability to
reproduce our phylogeny. That is, anyone using the same sequence alignment and
substitution model, will generate the same tree as long as they set the same
seed value. Although, --p-seed is not a required argument, it is generally
a good idea to set this value.
qiime phylogeny raxml \
--i-alignment masked-aligned-rep-seqs.qza \
--p-substitution-model GTRCAT \
--p-seed 1723 \
--p-n-searches 5 \
--o-tree raxml-cat-searches-tree.qza \
--verbose
stdout:
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Sarah Lutteropp (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
Charlie Taylor (UF)
Alignment has 157 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 39.77%
RAxML rapid hill-climbing mode
Using 1 distinct models/data partitions with joint branch length optimization
Executing 5 inferences on the original alignment using 5 distinct randomized MP trees
All free model parameters will be estimated by RAxML
ML estimate of 25 per site rate categories
Likelihood of final tree will be evaluated and optimized under GAMMA
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 157
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
raxmlHPC -m GTRCAT -p 1723 -N 5 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpt97cqfak -n q2
Partition: 0 with name: No Name Provided
Base frequencies: 0.243 0.182 0.319 0.256
Inference[0]: Time 0.624630 CAT-based likelihood -1238.242991, best rearrangement setting 5
Inference[1]: Time 0.517125 CAT-based likelihood -1249.502284, best rearrangement setting 5
Inference[2]: Time 0.525780 CAT-based likelihood -1242.978035, best rearrangement setting 5
Inference[3]: Time 0.679197 CAT-based likelihood -1243.159855, best rearrangement setting 5
Inference[4]: Time 0.507800 CAT-based likelihood -1261.321621, best rearrangement setting 5
Conducting final model optimizations on all 5 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -1388.324037 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpt97cqfak/RAxML_result.q2.RUN.0
Inference[1] final GAMMA-based Likelihood: -1392.813982 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpt97cqfak/RAxML_result.q2.RUN.1
Inference[2] final GAMMA-based Likelihood: -1388.073642 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpt97cqfak/RAxML_result.q2.RUN.2
Inference[3] final GAMMA-based Likelihood: -1387.945266 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpt97cqfak/RAxML_result.q2.RUN.3
Inference[4] final GAMMA-based Likelihood: -1387.557031 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpt97cqfak/RAxML_result.q2.RUN.4
Starting final GAMMA-based thorough Optimization on tree 4 likelihood -1387.557031 ....
Final GAMMA-based Score of best tree -1387.385075
Program execution info written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpt97cqfak/RAxML_info.q2
Best-scoring ML tree written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpt97cqfak/RAxML_bestTree.q2
Overall execution time: 3.576888 secs or 0.000994 hours or 0.000041 days
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: raxmlHPC -m GTRCAT -p 1723 -N 5 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpt97cqfak -n q2
Saved Phylogeny[Unrooted] to: raxml-cat-searches-tree.qza
raxml-rapid-bootstrap¶
In phylogenetics, it is good practice to check how well the splits /
bipartitions in your phylogeny are supported. Often one is interested in
which clades are robustly separated from other clades in the phylogeny. One
way, of doing this is via bootstrapping (See the Bootstrapping section of the
first introductory link above). In QIIME 2, we’ve provided access to the RAxML
rapid bootstrap feature. The only difference between this command and the
previous are the additional flags --p-bootstrap-replicates and
--p-rapid-bootstrap-seed. It is quite common to perform anywhere from 100 -
1000 bootstrap replicates. The --p-rapid-bootstrap-seed works very much
like the --p-seed argument from above except that it allows anyone to
reproduce the bootstrapping process and the associated supports for your
splits.
As per the RAxML online documentation and the RAxML manual, the rapid bootstrapping command that we will execute below will do the following:
Bootstrap the input alignment 100 times and perform a Maximum Likelihood (ML) search on each.
Find best scoring ML tree through multiple independent searches using the original input alignment. The number of independent searches is determined by the number of bootstrap replicates set in the 1st step. That is, your search becomes more thorough with increasing bootstrap replicates. The ML optimization of RAxML uses every 5th bootstrap tree as the starting tree for an ML search on the original alignment.
Map the bipartitions (bootstrap supports, 1st step) onto the best scoring ML tree (2nd step).
qiime phylogeny raxml-rapid-bootstrap \
--i-alignment masked-aligned-rep-seqs.qza \
--p-seed 1723 \
--p-rapid-bootstrap-seed 9384 \
--p-bootstrap-replicates 100 \
--p-substitution-model GTRCAT \
--o-tree raxml-cat-bootstrap-tree.qza \
--verbose
stdout:
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Sarah Lutteropp (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
Charlie Taylor (UF)
Alignment has 157 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 39.77%
RAxML rapid bootstrapping and subsequent ML search
Using 1 distinct models/data partitions with joint branch length optimization
Executing 100 rapid bootstrap inferences and thereafter a thorough ML search
All free model parameters will be estimated by RAxML
ML estimate of 25 per site rate categories
Likelihood of final tree will be evaluated and optimized under GAMMA
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 157
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
raxmlHPC -f a -m GTRCAT -p 1723 -x 9384 -N 100 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_kwuz1yb -n q2bootstrap
Time for BS model parameter optimization 0.052752
Bootstrap[0]: Time 0.177800 seconds, bootstrap likelihood -1199.758796, best rearrangement setting 12
Bootstrap[1]: Time 0.122693 seconds, bootstrap likelihood -1344.229251, best rearrangement setting 6
Bootstrap[2]: Time 0.113021 seconds, bootstrap likelihood -1295.343000, best rearrangement setting 8
Bootstrap[3]: Time 0.096906 seconds, bootstrap likelihood -1273.768320, best rearrangement setting 8
Bootstrap[4]: Time 0.113858 seconds, bootstrap likelihood -1253.402952, best rearrangement setting 6
Bootstrap[5]: Time 0.119477 seconds, bootstrap likelihood -1260.866113, best rearrangement setting 10
Bootstrap[6]: Time 0.116693 seconds, bootstrap likelihood -1293.636299, best rearrangement setting 14
Bootstrap[7]: Time 0.106583 seconds, bootstrap likelihood -1227.178693, best rearrangement setting 6
Bootstrap[8]: Time 0.116023 seconds, bootstrap likelihood -1321.820787, best rearrangement setting 13
Bootstrap[9]: Time 0.123995 seconds, bootstrap likelihood -1147.233446, best rearrangement setting 6
Bootstrap[10]: Time 0.087550 seconds, bootstrap likelihood -1220.766493, best rearrangement setting 13
Bootstrap[11]: Time 0.126606 seconds, bootstrap likelihood -1200.006355, best rearrangement setting 8
Bootstrap[12]: Time 0.135856 seconds, bootstrap likelihood -1346.392834, best rearrangement setting 14
Bootstrap[13]: Time 0.112439 seconds, bootstrap likelihood -1301.111096, best rearrangement setting 14
Bootstrap[14]: Time 0.119418 seconds, bootstrap likelihood -1262.253559, best rearrangement setting 11
Bootstrap[15]: Time 0.119437 seconds, bootstrap likelihood -1215.017551, best rearrangement setting 14
Bootstrap[16]: Time 0.112390 seconds, bootstrap likelihood -1238.832009, best rearrangement setting 7
Bootstrap[17]: Time 0.104104 seconds, bootstrap likelihood -1393.989732, best rearrangement setting 12
Bootstrap[18]: Time 0.108394 seconds, bootstrap likelihood -1173.921002, best rearrangement setting 15
Bootstrap[19]: Time 0.113624 seconds, bootstrap likelihood -1185.726976, best rearrangement setting 11
Bootstrap[20]: Time 0.141889 seconds, bootstrap likelihood -1158.491940, best rearrangement setting 6
Bootstrap[21]: Time 0.101156 seconds, bootstrap likelihood -1154.664272, best rearrangement setting 11
Bootstrap[22]: Time 0.110022 seconds, bootstrap likelihood -1244.159837, best rearrangement setting 10
Bootstrap[23]: Time 0.128886 seconds, bootstrap likelihood -1211.171036, best rearrangement setting 15
Bootstrap[24]: Time 0.111348 seconds, bootstrap likelihood -1261.440677, best rearrangement setting 12
Bootstrap[25]: Time 0.111008 seconds, bootstrap likelihood -1331.836715, best rearrangement setting 15
Bootstrap[26]: Time 0.113976 seconds, bootstrap likelihood -1129.144509, best rearrangement setting 5
Bootstrap[27]: Time 0.138939 seconds, bootstrap likelihood -1226.624056, best rearrangement setting 7
Bootstrap[28]: Time 0.125867 seconds, bootstrap likelihood -1221.046176, best rearrangement setting 12
Bootstrap[29]: Time 0.086524 seconds, bootstrap likelihood -1211.791204, best rearrangement setting 14
Bootstrap[30]: Time 0.108149 seconds, bootstrap likelihood -1389.442380, best rearrangement setting 5
Bootstrap[31]: Time 0.110555 seconds, bootstrap likelihood -1303.638592, best rearrangement setting 12
Bootstrap[32]: Time 0.126362 seconds, bootstrap likelihood -1172.859456, best rearrangement setting 12
Bootstrap[33]: Time 0.103655 seconds, bootstrap likelihood -1244.617135, best rearrangement setting 9
Bootstrap[34]: Time 0.099606 seconds, bootstrap likelihood -1211.871717, best rearrangement setting 15
Bootstrap[35]: Time 0.118424 seconds, bootstrap likelihood -1299.862912, best rearrangement setting 5
Bootstrap[36]: Time 0.096077 seconds, bootstrap likelihood -1141.967505, best rearrangement setting 5
Bootstrap[37]: Time 0.123330 seconds, bootstrap likelihood -1283.923198, best rearrangement setting 12
Bootstrap[38]: Time 0.095574 seconds, bootstrap likelihood -1304.250946, best rearrangement setting 5
Bootstrap[39]: Time 0.091579 seconds, bootstrap likelihood -1407.084376, best rearrangement setting 15
Bootstrap[40]: Time 0.108637 seconds, bootstrap likelihood -1277.946299, best rearrangement setting 13
Bootstrap[41]: Time 0.107543 seconds, bootstrap likelihood -1279.006200, best rearrangement setting 7
Bootstrap[42]: Time 0.102190 seconds, bootstrap likelihood -1160.274606, best rearrangement setting 6
Bootstrap[43]: Time 0.124105 seconds, bootstrap likelihood -1216.079259, best rearrangement setting 14
Bootstrap[44]: Time 0.100324 seconds, bootstrap likelihood -1382.278311, best rearrangement setting 8
Bootstrap[45]: Time 0.108733 seconds, bootstrap likelihood -1099.004439, best rearrangement setting 11
Bootstrap[46]: Time 0.088126 seconds, bootstrap likelihood -1296.527478, best rearrangement setting 8
Bootstrap[47]: Time 0.132367 seconds, bootstrap likelihood -1291.322658, best rearrangement setting 9
Bootstrap[48]: Time 0.085572 seconds, bootstrap likelihood -1161.908080, best rearrangement setting 6
Bootstrap[49]: Time 0.118823 seconds, bootstrap likelihood -1257.348428, best rearrangement setting 13
Bootstrap[50]: Time 0.136255 seconds, bootstrap likelihood -1309.422533, best rearrangement setting 13
Bootstrap[51]: Time 0.092691 seconds, bootstrap likelihood -1197.633097, best rearrangement setting 11
Bootstrap[52]: Time 0.109999 seconds, bootstrap likelihood -1347.123005, best rearrangement setting 8
Bootstrap[53]: Time 0.097658 seconds, bootstrap likelihood -1234.934890, best rearrangement setting 14
Bootstrap[54]: Time 0.112010 seconds, bootstrap likelihood -1227.092434, best rearrangement setting 6
Bootstrap[55]: Time 0.120369 seconds, bootstrap likelihood -1280.635747, best rearrangement setting 7
Bootstrap[56]: Time 0.098136 seconds, bootstrap likelihood -1225.911449, best rearrangement setting 6
Bootstrap[57]: Time 0.091508 seconds, bootstrap likelihood -1236.213347, best rearrangement setting 11
Bootstrap[58]: Time 0.131501 seconds, bootstrap likelihood -1393.245723, best rearrangement setting 14
Bootstrap[59]: Time 0.104305 seconds, bootstrap likelihood -1212.039371, best rearrangement setting 6
Bootstrap[60]: Time 0.092823 seconds, bootstrap likelihood -1248.692011, best rearrangement setting 10
Bootstrap[61]: Time 0.107526 seconds, bootstrap likelihood -1172.820979, best rearrangement setting 13
Bootstrap[62]: Time 0.122189 seconds, bootstrap likelihood -1126.745788, best rearrangement setting 14
Bootstrap[63]: Time 0.097147 seconds, bootstrap likelihood -1267.434444, best rearrangement setting 12
Bootstrap[64]: Time 0.093802 seconds, bootstrap likelihood -1340.680748, best rearrangement setting 5
Bootstrap[65]: Time 0.095252 seconds, bootstrap likelihood -1072.671059, best rearrangement setting 5
Bootstrap[66]: Time 0.117957 seconds, bootstrap likelihood -1234.294838, best rearrangement setting 8
Bootstrap[67]: Time 0.112160 seconds, bootstrap likelihood -1109.249439, best rearrangement setting 15
Bootstrap[68]: Time 0.091240 seconds, bootstrap likelihood -1314.493588, best rearrangement setting 8
Bootstrap[69]: Time 0.101430 seconds, bootstrap likelihood -1173.850035, best rearrangement setting 13
Bootstrap[70]: Time 0.101048 seconds, bootstrap likelihood -1231.066465, best rearrangement setting 10
Bootstrap[71]: Time 0.099191 seconds, bootstrap likelihood -1146.861379, best rearrangement setting 9
Bootstrap[72]: Time 0.085972 seconds, bootstrap likelihood -1148.753369, best rearrangement setting 8
Bootstrap[73]: Time 0.099237 seconds, bootstrap likelihood -1333.374056, best rearrangement setting 9
Bootstrap[74]: Time 0.088268 seconds, bootstrap likelihood -1259.382378, best rearrangement setting 5
Bootstrap[75]: Time 0.100185 seconds, bootstrap likelihood -1319.944496, best rearrangement setting 6
Bootstrap[76]: Time 0.108331 seconds, bootstrap likelihood -1309.042165, best rearrangement setting 14
Bootstrap[77]: Time 0.130837 seconds, bootstrap likelihood -1232.061289, best rearrangement setting 8
Bootstrap[78]: Time 0.108573 seconds, bootstrap likelihood -1261.333984, best rearrangement setting 9
Bootstrap[79]: Time 0.111270 seconds, bootstrap likelihood -1194.644341, best rearrangement setting 13
Bootstrap[80]: Time 0.098770 seconds, bootstrap likelihood -1214.037389, best rearrangement setting 9
Bootstrap[81]: Time 0.110637 seconds, bootstrap likelihood -1224.527657, best rearrangement setting 8
Bootstrap[82]: Time 0.126605 seconds, bootstrap likelihood -1241.464826, best rearrangement setting 11
Bootstrap[83]: Time 0.096003 seconds, bootstrap likelihood -1230.730558, best rearrangement setting 6
Bootstrap[84]: Time 0.102703 seconds, bootstrap likelihood -1219.034592, best rearrangement setting 10
Bootstrap[85]: Time 0.109006 seconds, bootstrap likelihood -1280.071994, best rearrangement setting 8
Bootstrap[86]: Time 0.094438 seconds, bootstrap likelihood -1444.747777, best rearrangement setting 9
Bootstrap[87]: Time 0.092781 seconds, bootstrap likelihood -1245.890035, best rearrangement setting 14
Bootstrap[88]: Time 0.107713 seconds, bootstrap likelihood -1287.832766, best rearrangement setting 7
Bootstrap[89]: Time 0.099967 seconds, bootstrap likelihood -1325.245976, best rearrangement setting 5
Bootstrap[90]: Time 0.107884 seconds, bootstrap likelihood -1227.883697, best rearrangement setting 5
Bootstrap[91]: Time 0.108053 seconds, bootstrap likelihood -1273.489392, best rearrangement setting 8
Bootstrap[92]: Time 0.045073 seconds, bootstrap likelihood -1234.725870, best rearrangement setting 7
Bootstrap[93]: Time 0.116150 seconds, bootstrap likelihood -1235.733064, best rearrangement setting 11
Bootstrap[94]: Time 0.096184 seconds, bootstrap likelihood -1204.319488, best rearrangement setting 15
Bootstrap[95]: Time 0.095134 seconds, bootstrap likelihood -1183.328582, best rearrangement setting 11
Bootstrap[96]: Time 0.110306 seconds, bootstrap likelihood -1196.298898, best rearrangement setting 13
Bootstrap[97]: Time 0.115628 seconds, bootstrap likelihood -1339.251746, best rearrangement setting 12
Bootstrap[98]: Time 0.044557 seconds, bootstrap likelihood -1404.363552, best rearrangement setting 7
Bootstrap[99]: Time 0.057857 seconds, bootstrap likelihood -1270.157811, best rearrangement setting 7
Overall Time for 100 Rapid Bootstraps 10.776281 seconds
Average Time per Rapid Bootstrap 0.107763 seconds
Starting ML Search ...
Fast ML optimization finished
Fast ML search Time: 4.173317 seconds
Slow ML Search 0 Likelihood: -1387.994678
Slow ML Search 1 Likelihood: -1387.994678
Slow ML Search 2 Likelihood: -1387.994676
Slow ML Search 3 Likelihood: -1387.994650
Slow ML Search 4 Likelihood: -1387.994685
Slow ML Search 5 Likelihood: -1388.092954
Slow ML Search 6 Likelihood: -1388.182551
Slow ML Search 7 Likelihood: -1388.182563
Slow ML Search 8 Likelihood: -1388.182547
Slow ML Search 9 Likelihood: -1387.994723
Slow ML optimization finished
Slow ML search Time: 2.175799 seconds
Thorough ML search Time: 0.550966 seconds
Final ML Optimization Likelihood: -1387.204993
Model Information:
Model Parameters of Partition 0, Name: No Name Provided, Type of Data: DNA
alpha: 1.227800
Tree-Length: 7.823400
rate A <-> C: 0.332564
rate A <-> G: 2.312784
rate A <-> T: 2.215466
rate C <-> G: 1.243321
rate C <-> T: 3.278770
rate G <-> T: 1.000000
freq pi(A): 0.243216
freq pi(C): 0.181967
freq pi(G): 0.319196
freq pi(T): 0.255621
ML search took 6.906880 secs or 0.001919 hours
Combined Bootstrap and ML search took 17.683474 secs or 0.004912 hours
Drawing Bootstrap Support Values on best-scoring ML tree ...
Found 1 tree in File /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_kwuz1yb/RAxML_bestTree.q2bootstrap
Found 1 tree in File /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_kwuz1yb/RAxML_bestTree.q2bootstrap
Program execution info written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_kwuz1yb/RAxML_info.q2bootstrap
All 100 bootstrapped trees written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_kwuz1yb/RAxML_bootstrap.q2bootstrap
Best-scoring ML tree written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_kwuz1yb/RAxML_bestTree.q2bootstrap
Best-scoring ML tree with support values written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_kwuz1yb/RAxML_bipartitions.q2bootstrap
Best-scoring ML tree with support values as branch labels written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_kwuz1yb/RAxML_bipartitionsBranchLabels.q2bootstrap
Overall execution time for full ML analysis: 17.697314 secs or 0.004916 hours or 0.000205 days
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: raxmlHPC -f a -m GTRCAT -p 1723 -x 9384 -N 100 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_kwuz1yb -n q2bootstrap
Saved Phylogeny[Unrooted] to: raxml-cat-bootstrap-tree.qza
Tip
Optimizing RAxML Run Time.
You may gave noticed that we haven’t added the flag --p-raxml-version to
the RAxML methods. This parameter provides a means to access versions of
RAxML that have optimized vector instructions for various modern x86
processor architectures. Paraphrased from the RAxML manual and help
documentation: Firstly, most recent processors will support SSE3 vector
instructions (i.e. will likely support the faster AVX2 vector instructions).
Secondly, these instructions will substantially accelerate the likelihood
and parsimony computations. In general, SSE3 versions will run approximately
40% faster than the standard version. The AVX2 version will run 10-30%
faster than the SSE3 version. Additionally, keep in mind that using more
cores / threads will not necessarily decrease run time. The RAxML manual
suggests using 1 core per ~500 DNA alignment patterns. Alignment pattern
information is usually visible on screen, when the --verbose option is
used. Additionally, try using a rate category (CAT model; via
--p-substitution-model), which results in equally good trees as the
GAMMA models and is approximately 4 times faster. See the CAT paper. The
CAT approximation is also Ideal for alignments containing 10,000 or more
taxa, and is very much similar the CAT-like model of FastTree2.
iqtree¶
Similar to the raxml and raxml-rapid-bootstrap methods above, we
provide similar functionality for IQ-TREE: iqtree and
iqtree-ultrafast-bootstrap. IQ-TREE is unique compared to the fastree
and raxml options, in that it provides access to 286 models of nucleotide
substitution! IQ-TREE can also determine which of these models best fits your
dataset prior to constructing your tree via its built-in ModelFinder
algorithm. This is the default in QIIME 2, but do not worry, you can set any
one of the 286 models of nucleotide substitution via the
--p-substitution-model flag, e.g. you can set the model as HKY+I+G
instead of the default MFP (a basic short-hand for: “build a phylogeny
after determining the best fit model as determined by ModelFinder”). Keep in
mind the additional computational time required for model testing via
ModelFinder.
The simplest way to run the
iqtree command with default
settings and automatic model selection (MFP) is like so:
qiime phylogeny iqtree \
--i-alignment masked-aligned-rep-seqs.qza \
--o-tree iqt-tree.qza \
--verbose
stdout:
IQ-TREE multicore version 2.2.0.3 COVID-edition for Mac OS X 64-bit built Sep 5 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: ghost.mggen.nau.edu (AVX, 16 GB RAM)
Command: iqtree -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpi7orr6zj/q2iqtree -nt 1
Seed: 261007 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Wed Dec 21 19:10:05 2022
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000224113 secs using 83.44% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000552893 secs using 73.07% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 2.00272e-05 secs using 84.88% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 7.51019e-05 secs using 77.23% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.003 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.0267479 secs using 98.9% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1391.311
2. Current log-likelihood: -1389.733
Optimal log-likelihood: -1388.881
Rate parameters: A-C: 0.33789 A-G: 2.29237 A-T: 2.14761 C-G: 1.19040 C-T: 3.28358 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.033
Gamma shape alpha: 1.424
Parameters optimization took 2 rounds (0.014 sec)
Time for fast ML tree search: 0.069 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 484 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1402.497 45 2894.994 2919.637 3046.463
2 GTR+F+I 1401.403 46 2894.806 2920.698 3049.641
3 GTR+F+G4 1387.279 46 2866.558 2892.450 3021.393
4 GTR+F+I+G4 1387.559 47 2869.117 2896.298 3027.318
5 GTR+F+R2 1380.611 47 2855.222 2882.402 3013.423
6 GTR+F+R3 1380.659 49 2859.317 2889.195 3024.250
14 GTR+F+I+I+R2 1380.757 48 2857.513 2886.023 3019.080
15 GTR+F+I+I+R3 1380.696 50 2861.392 2892.681 3029.691
25 SYM+G4 1387.157 43 2860.314 2882.573 3005.051
27 SYM+R2 1382.244 44 2852.489 2875.920 3000.591
36 SYM+I+I+R2 1382.405 45 2854.809 2879.452 3006.278
47 TVM+F+G4 1388.424 45 2866.848 2891.491 3018.317
49 TVM+F+R2 1382.481 46 2856.963 2882.855 3011.798
58 TVM+F+I+I+R2 1382.560 47 2859.119 2886.300 3017.320
69 TVMe+G4 1387.122 42 2858.245 2879.367 2999.616
71 TVMe+R2 1382.298 43 2850.596 2872.854 2995.333
80 TVMe+I+I+R2 1382.453 44 2852.907 2876.339 3001.010
91 TIM3+F+G4 1391.457 44 2870.914 2894.346 3019.017
93 TIM3+F+R2 1384.431 45 2858.861 2883.504 3010.330
102 TIM3+F+I+I+R2 1384.573 46 2861.146 2887.039 3015.981
113 TIM3e+G4 1390.540 41 2863.080 2883.103 3001.085
115 TIM3e+R2 1385.228 42 2854.456 2875.578 2995.827
124 TIM3e+I+I+R2 1385.391 43 2856.782 2879.040 3001.519
135 TIM2+F+G4 1394.180 44 2876.360 2899.792 3024.463
137 TIM2+F+R2 1386.234 45 2862.469 2887.112 3013.938
146 TIM2+F+I+I+R2 1386.377 46 2864.755 2890.647 3019.590
157 TIM2e+G4 1397.742 41 2877.483 2897.507 3015.488
159 TIM2e+R2 1391.117 42 2866.235 2887.357 3007.606
168 TIM2e+I+I+R2 1391.272 43 2868.544 2890.802 3013.281
179 TIM+F+G4 1390.802 44 2869.603 2893.035 3017.706
181 TIM+F+R2 1383.206 45 2856.411 2881.054 3007.880
190 TIM+F+I+I+R2 1383.340 46 2858.680 2884.572 3013.515
201 TIMe+G4 1394.796 41 2871.592 2891.616 3009.597
203 TIMe+R2 1388.300 42 2860.600 2881.723 3001.971
212 TIMe+I+I+R2 1388.456 43 2862.912 2885.171 3007.649
223 TPM3u+F+G4 1392.567 43 2871.134 2893.393 3015.871
225 TPM3u+F+R2 1386.368 44 2860.736 2884.168 3008.839
234 TPM3u+F+I+I+R2 1386.501 45 2863.002 2887.645 3014.471
245 TPM3+G4 1390.540 40 2861.080 2880.039 2995.719
247 TPM3+R2 1385.307 41 2852.614 2872.637 2990.619
256 TPM3+I+I+R2 1385.459 42 2854.917 2876.040 2996.288
267 TPM2u+F+G4 1395.283 43 2876.566 2898.825 3021.303
269 TPM2u+F+R2 1388.114 44 2864.229 2887.661 3012.332
278 TPM2u+F+I+I+R2 1388.249 45 2866.497 2891.140 3017.966
289 TPM2+G4 1397.749 40 2875.499 2894.458 3010.138
291 TPM2+R2 1391.198 41 2864.396 2884.419 3002.401
300 TPM2+I+I+R2 1391.346 42 2866.692 2887.815 3008.063
311 K3Pu+F+G4 1392.050 43 2870.100 2892.359 3014.837
313 K3Pu+F+R2 1385.122 44 2858.245 2881.677 3006.348
322 K3Pu+F+I+I+R2 1385.245 45 2860.491 2885.134 3011.960
333 K3P+G4 1394.786 40 2869.573 2888.532 3004.212
335 K3P+R2 1388.359 41 2858.717 2878.740 2996.722
344 K3P+I+I+R2 1388.531 42 2861.061 2882.184 3002.432
355 TN+F+G4 1394.628 43 2875.256 2897.515 3019.993
357 TN+F+R2 1386.824 44 2861.647 2885.079 3009.750
366 TN+F+I+I+R2 1386.967 45 2863.933 2888.576 3015.402
377 TNe+G4 1397.748 40 2875.497 2894.456 3010.136
379 TNe+R2 1391.134 41 2864.269 2884.292 3002.274
388 TNe+I+I+R2 1391.289 42 2866.578 2887.701 3007.949
399 HKY+F+G4 1395.752 42 2875.504 2896.627 3016.875
401 HKY+F+R2 1388.691 43 2863.382 2885.640 3008.119
410 HKY+F+I+I+R2 1388.820 44 2865.639 2889.071 3013.742
421 K2P+G4 1397.753 39 2873.507 2891.438 3004.780
423 K2P+R2 1391.216 40 2862.433 2881.392 2997.072
432 K2P+I+I+R2 1391.363 41 2864.726 2884.750 3002.731
443 F81+F+G4 1406.478 41 2894.955 2914.979 3032.960
445 F81+F+R2 1400.602 42 2885.203 2906.326 3026.574
454 F81+F+I+I+R2 1400.799 43 2887.598 2909.857 3032.335
465 JC+G4 1408.432 38 2892.865 2909.802 3020.772
467 JC+R2 1403.021 39 2884.041 2901.972 3015.314
476 JC+I+I+R2 1403.194 40 2886.388 2905.348 3021.028
Akaike Information Criterion: TVMe+R2
Corrected Akaike Information Criterion: TPM3+R2
Bayesian Information Criterion: TPM3+R2
Best-fit model: TPM3+R2 chosen according to BIC
All model information printed to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpi7orr6zj/q2iqtree.model.gz
CPU time for ModelFinder: 1.529 seconds (0h:0m:1s)
Wall-clock time for ModelFinder: 1.573 seconds (0h:0m:1s)
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1385.307
Optimal log-likelihood: -1385.304
Rate parameters: A-C: 0.39693 A-G: 1.57493 A-T: 1.00000 C-G: 0.39693 C-T: 1.57493 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.723,0.403) (0.277,2.560)
Parameters optimization took 1 rounds (0.004 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000849009 secs using 96.82% CPU
Computing ML distances took 0.000980 sec (of wall-clock time) 0.000891 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.4121e-05 secs using 88.69% CPU
Constructing RapidNJ tree: done in 0.00013113 secs using 134.2% CPU
Computing RapidNJ tree took 0.000278 sec (of wall-clock time) 0.000308 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.836
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.111 second
Computing log-likelihood of 98 initial trees ... 0.102 seconds
Current best score: -1385.304
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00284696 secs using 99.26% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.303
Optimizing NNI: done in 0.013592 secs using 98.98% CPU
Optimizing NNI: done in 0.014385 secs using 98.56% CPU
Optimizing NNI: done in 0.0141699 secs using 99.32% CPU
Optimizing NNI: done in 0.013526 secs using 98.6% CPU
Optimizing NNI: done in 0.0195889 secs using 98.74% CPU
Optimizing NNI: done in 0.013073 secs using 99.02% CPU
Optimizing NNI: done in 0.01352 secs using 98.31% CPU
Optimizing NNI: done in 0.0148649 secs using 98.36% CPU
Optimizing NNI: done in 0.014097 secs using 98.63% CPU
Iteration 10 / LogL: -1385.338 / Time: 0h:0m:0s
Optimizing NNI: done in 0.014029 secs using 98.81% CPU
Optimizing NNI: done in 0.013206 secs using 99.09% CPU
Optimizing NNI: done in 0.012912 secs using 99.24% CPU
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Optimizing NNI: done in 0.0130279 secs using 98.9% CPU
Optimizing NNI: done in 0.0127461 secs using 99.19% CPU
Optimizing NNI: done in 0.0132172 secs using 99.28% CPU
Optimizing NNI: done in 0.01316 secs using 99.03% CPU
Optimizing NNI: done in 0.0113862 secs using 98.71% CPU
Optimizing NNI: done in 0.0135431 secs using 98.76% CPU
Iteration 20 / LogL: -1385.339 / Time: 0h:0m:0s
Finish initializing candidate tree set (3)
Current best tree score: -1385.303 / CPU time: 0.489
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.014503 secs using 98.66% CPU
Optimizing NNI: done in 0.0297918 secs using 98.55% CPU
Optimizing NNI: done in 0.0200369 secs using 99% CPU
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Optimizing NNI: done in 0.0256569 secs using 98.79% CPU
Optimizing NNI: done in 0.0196528 secs using 99.52% CPU
Iteration 30 / LogL: -1385.707 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.012574 secs using 99.17% CPU
Optimizing NNI: done in 0.0176771 secs using 98.9% CPU
Optimizing NNI: done in 0.0153069 secs using 98.98% CPU
Optimizing NNI: done in 0.021528 secs using 98.71% CPU
Optimizing NNI: done in 0.016993 secs using 99.23% CPU
Optimizing NNI: done in 0.0242 secs using 99% CPU
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Optimizing NNI: done in 0.0265892 secs using 99.05% CPU
Optimizing NNI: done in 0.0125179 secs using 99.34% CPU
Iteration 40 / LogL: -1385.881 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.0134759 secs using 98.81% CPU
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Optimizing NNI: done in 0.018235 secs using 98.74% CPU
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Optimizing NNI: done in 0.0153179 secs using 98.82% CPU
Iteration 50 / LogL: -1385.975 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.01582 secs using 98.74% CPU
Optimizing NNI: done in 0.018393 secs using 98.74% CPU
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Optimizing NNI: done in 0.0145299 secs using 99.17% CPU
Optimizing NNI: done in 0.0148978 secs using 99.3% CPU
Iteration 60 / LogL: -1385.891 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.013443 secs using 99% CPU
Optimizing NNI: done in 0.0231791 secs using 98.95% CPU
Optimizing NNI: done in 0.017554 secs using 99.24% CPU
Optimizing NNI: done in 0.0294929 secs using 98.43% CPU
Optimizing NNI: done in 0.0218899 secs using 98.86% CPU
Optimizing NNI: done in 0.0142782 secs using 98.79% CPU
Optimizing NNI: done in 0.022656 secs using 98.84% CPU
Optimizing NNI: done in 0.00497293 secs using 99.08% CPU
Optimizing NNI: done in 0.016506 secs using 98.97% CPU
Optimizing NNI: done in 0.011802 secs using 99.19% CPU
Iteration 70 / LogL: -1385.304 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0205591 secs using 98.85% CPU
Optimizing NNI: done in 0.0143371 secs using 99.27% CPU
Optimizing NNI: done in 0.0216689 secs using 97.79% CPU
Optimizing NNI: done in 0.0105031 secs using 98.95% CPU
Optimizing NNI: done in 0.0170259 secs using 98.42% CPU
Optimizing NNI: done in 0.0164559 secs using 98.7% CPU
Optimizing NNI: done in 0.015245 secs using 98.83% CPU
Optimizing NNI: done in 0.0215039 secs using 98.36% CPU
Optimizing NNI: done in 0.022331 secs using 98.98% CPU
Optimizing NNI: done in 0.015111 secs using 99.94% CPU
Iteration 80 / LogL: -1394.218 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0123539 secs using 99.95% CPU
Optimizing NNI: done in 0.0138621 secs using 99.93% CPU
Optimizing NNI: done in 0.0141599 secs using 99.94% CPU
Optimizing NNI: done in 0.0150442 secs using 99.95% CPU
Optimizing NNI: done in 0.0109682 secs using 99.94% CPU
Optimizing NNI: done in 0.0143139 secs using 99.94% CPU
Optimizing NNI: done in 0.0152819 secs using 99.95% CPU
Optimizing NNI: done in 0.00992799 secs using 99.95% CPU
Optimizing NNI: done in 0.0124531 secs using 99.94% CPU
Optimizing NNI: done in 0.0210421 secs using 99.95% CPU
Iteration 90 / LogL: -1385.859 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.011955 secs using 99.94% CPU
Optimizing NNI: done in 0.0209742 secs using 99.94% CPU
Optimizing NNI: done in 0.015192 secs using 99.95% CPU
Optimizing NNI: done in 0.017307 secs using 99.95% CPU
Optimizing NNI: done in 0.0111351 secs using 99.95% CPU
Optimizing NNI: done in 0.0173252 secs using 99.95% CPU
Optimizing NNI: done in 0.0124321 secs using 99.95% CPU
Optimizing NNI: done in 0.016021 secs using 99.94% CPU
Optimizing NNI: done in 0.0207522 secs using 99.95% CPU
Optimizing NNI: done in 0.013715 secs using 100% CPU
Iteration 100 / LogL: -1385.306 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0106652 secs using 99.93% CPU
Optimizing NNI: done in 0.0122459 secs using 99.95% CPU
TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:1s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1385.303
Optimal log-likelihood: -1385.303
Rate parameters: A-C: 0.39652 A-G: 1.57285 A-T: 1.00000 C-G: 0.39652 C-T: 1.57285 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.724,0.402) (0.276,2.564)
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1385.303
Total tree length: 6.855
Total number of iterations: 102
CPU time used for tree search: 2.087 sec (0h:0m:2s)
Wall-clock time used for tree search: 1.926 sec (0h:0m:1s)
Total CPU time used: 2.116 sec (0h:0m:2s)
Total wall-clock time used: 1.950 sec (0h:0m:1s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpi7orr6zj/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpi7orr6zj/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpi7orr6zj/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpi7orr6zj/q2iqtree.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpi7orr6zj/q2iqtree.treefile -m "TPM3{0.396517,1.57285}+FQ+R2{0.723516,0.402304,0.276484,2.56408}" --length 214
Date and Time: Wed Dec 21 19:10:08 2022
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpi7orr6zj/q2iqtree -nt 1
Saved Phylogeny[Unrooted] to: iqt-tree.qza
Specifying a substitution model¶
We can also set a substitution model of our choosing. You may have noticed
while watching the onscreen output of the previous command that the best
fitting model selected by ModelFinder is noted. For the sake of argument, let’s
say the best selected model was shown as GTR+F+I+G4. The F is only a
notation to let us know that if a given model supports unequal base
frequencies, then the empirical base frequencies will be used by default.
Using empirical base frequencies (F), rather than estimating them, greatly
reduces computational time. The iqtree plugin will not accept F within
the model notation supplied at the command line, as this will always be implied
automatically for the appropriate model. Also, the iqtree plugin only
accepts G not G4 to be specified within the model notation. The 4
is simply another explicit notation to remind us that four rate categories are
being assumed by default. The notation approach used by the plugin simply helps
to retain simplicity and familiarity when supplying model notations on the
command line. So, in brief, we only have to type GTR+I+G as our input
model:
qiime phylogeny iqtree \
--i-alignment masked-aligned-rep-seqs.qza \
--p-substitution-model 'GTR+I+G' \
--o-tree iqt-gtrig-tree.qza \
--verbose
stdout:
IQ-TREE multicore version 2.2.0.3 COVID-edition for Mac OS X 64-bit built Sep 5 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: ghost.mggen.nau.edu (AVX, 16 GB RAM)
Command: iqtree -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp51h1cwmz/q2iqtree -nt 1
Seed: 573285 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Wed Dec 21 19:10:18 2022
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000216961 secs using 84.81% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000457048 secs using 78.33% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 1.88351e-05 secs using 90.26% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 7.39098e-05 secs using 75.77% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Thoroughly optimizing +I+G parameters from 10 start values...
Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 1.287 / LogL: -1395.194
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.008, 1.376 / LogL: -1395.464
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.009, 1.390 / LogL: -1395.530
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.009, 1.384 / LogL: -1395.523
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.008, 1.375 / LogL: -1395.492
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.009, 1.374 / LogL: -1395.529
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.008, 1.369 / LogL: -1395.476
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.008, 1.365 / LogL: -1395.493
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.008, 1.373 / LogL: -1395.500
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.009, 1.374 / LogL: -1395.511
Optimal pinv,alpha: 0.000, 1.287 / LogL: -1395.194
Parameters optimization took 0.512 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00124383 secs using 97.04% CPU
Computing ML distances took 0.001347 sec (of wall-clock time) 0.001276 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.38826e-05 secs using 90.94% CPU
Constructing RapidNJ tree: done in 9.39369e-05 secs using 150.1% CPU
Computing RapidNJ tree took 0.000217 sec (of wall-clock time) 0.000254 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.836
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.108 second
Computing log-likelihood of 98 initial trees ... 0.131 seconds
Current best score: -1392.836
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.0193992 secs using 98.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.260
Optimizing NNI: done in 0.0269868 secs using 98.99% CPU
Optimizing NNI: done in 0.0143731 secs using 99.07% CPU
Optimizing NNI: done in 0.0148611 secs using 98.77% CPU
Optimizing NNI: done in 0.014185 secs using 99.29% CPU
Optimizing NNI: done in 0.015137 secs using 98.67% CPU
Optimizing NNI: done in 0.0144601 secs using 98.96% CPU
Optimizing NNI: done in 0.0140481 secs using 99.69% CPU
Optimizing NNI: done in 0.0144138 secs using 98.74% CPU
Optimizing NNI: done in 0.014266 secs using 99.12% CPU
Iteration 10 / LogL: -1387.730 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0264869 secs using 98.61% CPU
Optimizing NNI: done in 0.0255589 secs using 99.63% CPU
Optimizing NNI: done in 0.026654 secs using 98.78% CPU
Optimizing NNI: done in 0.0260201 secs using 99.22% CPU
Optimizing NNI: done in 0.0259199 secs using 99.16% CPU
Optimizing NNI: done in 0.0264139 secs using 98.92% CPU
Optimizing NNI: done in 0.0264399 secs using 98.84% CPU
Optimizing NNI: done in 0.0264721 secs using 99.27% CPU
Optimizing NNI: done in 0.0260601 secs using 99.28% CPU
Optimizing NNI: done in 0.0264618 secs using 98.82% CPU
Iteration 20 / LogL: -1387.280 / Time: 0h:0m:1s
Finish initializing candidate tree set (1)
Current best tree score: -1387.260 / CPU time: 0.685
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.020699 secs using 99.08% CPU
Optimizing NNI: done in 0.0190799 secs using 98.93% CPU
Optimizing NNI: done in 0.0688949 secs using 98.92% CPU
Optimizing NNI: done in 0.0332582 secs using 98.97% CPU
Optimizing NNI: done in 0.0331481 secs using 98.69% CPU
Optimizing NNI: done in 0.0274601 secs using 99.26% CPU
Optimizing NNI: done in 0.0310991 secs using 98.98% CPU
Optimizing NNI: done in 0.025357 secs using 99% CPU
Optimizing NNI: done in 0.0246849 secs using 98.97% CPU
Optimizing NNI: done in 0.038347 secs using 98.63% CPU
Iteration 30 / LogL: -1387.401 / Time: 0h:0m:1s (0h:0m:3s left)
Optimizing NNI: done in 0.0365891 secs using 99.06% CPU
Optimizing NNI: done in 0.0378742 secs using 98.37% CPU
Optimizing NNI: done in 0.0454102 secs using 98.55% CPU
Optimizing NNI: done in 0.033551 secs using 98.97% CPU
Optimizing NNI: done in 0.023309 secs using 99.05% CPU
Optimizing NNI: done in 0.020159 secs using 98.44% CPU
Optimizing NNI: done in 0.019711 secs using 99.47% CPU
Optimizing NNI: done in 0.0362921 secs using 98.99% CPU
Optimizing NNI: done in 0.026089 secs using 98.95% CPU
Optimizing NNI: done in 0.0155919 secs using 98.78% CPU
Iteration 40 / LogL: -1387.285 / Time: 0h:0m:1s (0h:0m:2s left)
Optimizing NNI: done in 0.0342271 secs using 98.69% CPU
Optimizing NNI: done in 0.0346389 secs using 98.3% CPU
Optimizing NNI: done in 0.025681 secs using 97.6% CPU
Optimizing NNI: done in 0.051019 secs using 98.45% CPU
Optimizing NNI: done in 0.021888 secs using 99.12% CPU
Optimizing NNI: done in 0.0222442 secs using 98.92% CPU
Optimizing NNI: done in 0.034941 secs using 98.77% CPU
Optimizing NNI: done in 0.02038 secs using 98.12% CPU
Optimizing NNI: done in 0.01741 secs using 98.9% CPU
Optimizing NNI: done in 0.0267589 secs using 99.13% CPU
Iteration 50 / LogL: -1387.381 / Time: 0h:0m:2s (0h:0m:2s left)
Optimizing NNI: done in 0.0188189 secs using 98.88% CPU
Optimizing NNI: done in 0.0217819 secs using 98.3% CPU
Optimizing NNI: done in 0.0364749 secs using 94.74% CPU
Optimizing NNI: done in 0.0254118 secs using 98.93% CPU
Optimizing NNI: done in 0.028791 secs using 99.1% CPU
Optimizing NNI: done in 0.025671 secs using 98.89% CPU
Optimizing NNI: done in 0.0294602 secs using 99.1% CPU
Optimizing NNI: done in 0.0203559 secs using 99.22% CPU
Optimizing NNI: done in 0.0450871 secs using 98.74% CPU
Optimizing NNI: done in 0.012131 secs using 99.18% CPU
Iteration 60 / LogL: -1387.379 / Time: 0h:0m:2s (0h:0m:1s left)
Optimizing NNI: done in 0.0192721 secs using 99.51% CPU
Optimizing NNI: done in 0.0299778 secs using 98.88% CPU
Optimizing NNI: done in 0.0222878 secs using 99.13% CPU
Optimizing NNI: done in 0.0153949 secs using 98.94% CPU
Optimizing NNI: done in 0.0285208 secs using 98.88% CPU
Optimizing NNI: done in 0.037766 secs using 98.82% CPU
Optimizing NNI: done in 0.0294759 secs using 98.95% CPU
Optimizing NNI: done in 0.0146322 secs using 98.37% CPU
Optimizing NNI: done in 0.0246329 secs using 99% CPU
Optimizing NNI: done in 0.0341299 secs using 98.96% CPU
Iteration 70 / LogL: -1387.382 / Time: 0h:0m:2s (0h:0m:1s left)
Optimizing NNI: done in 0.0341921 secs using 99.06% CPU
Optimizing NNI: done in 0.0244648 secs using 99.05% CPU
Optimizing NNI: done in 0.0224729 secs using 98.79% CPU
Optimizing NNI: done in 0.0493729 secs using 98.98% CPU
Optimizing NNI: done in 0.03473 secs using 98.76% CPU
Optimizing NNI: done in 0.0285029 secs using 98.95% CPU
Optimizing NNI: done in 0.031065 secs using 99.2% CPU
Optimizing NNI: done in 0.0512631 secs using 98.89% CPU
Optimizing NNI: done in 0.0308499 secs using 99.02% CPU
Optimizing NNI: done in 0.018234 secs using 98.95% CPU
Iteration 80 / LogL: -1387.500 / Time: 0h:0m:3s (0h:0m:0s left)
Optimizing NNI: done in 0.0230439 secs using 99.01% CPU
Optimizing NNI: done in 0.0366771 secs using 99.29% CPU
Optimizing NNI: done in 0.030189 secs using 98.71% CPU
Optimizing NNI: done in 0.0343542 secs using 98.82% CPU
Optimizing NNI: done in 0.0111558 secs using 98.96% CPU
Optimizing NNI: done in 0.0328109 secs using 98.81% CPU
Optimizing NNI: done in 0.030463 secs using 99.07% CPU
Optimizing NNI: done in 0.0199931 secs using 99.96% CPU
Optimizing NNI: done in 0.0128419 secs using 99.96% CPU
Optimizing NNI: done in 0.0298619 secs using 99.97% CPU
Iteration 90 / LogL: -1387.368 / Time: 0h:0m:3s (0h:0m:0s left)
Optimizing NNI: done in 0.0439639 secs using 99.95% CPU
WARNING: NNI search needs unusual large number of steps (20) to converge!
Optimizing NNI: done in 0.039299 secs using 99.95% CPU
Optimizing NNI: done in 0.0388188 secs using 99.96% CPU
Optimizing NNI: done in 0.0148909 secs using 99.95% CPU
Optimizing NNI: done in 0.017261 secs using 99.96% CPU
Optimizing NNI: done in 0.0425701 secs using 99.96% CPU
Optimizing NNI: done in 0.0347259 secs using 99.95% CPU
Optimizing NNI: done in 0.0462651 secs using 99.82% CPU
Optimizing NNI: done in 0.0417581 secs using 99.97% CPU
Optimizing NNI: done in 0.0309339 secs using 99.96% CPU
Iteration 100 / LogL: -1387.354 / Time: 0h:0m:3s (0h:0m:0s left)
Optimizing NNI: done in 0.027797 secs using 99.96% CPU
Optimizing NNI: done in 0.0373781 secs using 99.79% CPU
TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:3s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.260
Optimal log-likelihood: -1387.255
Rate parameters: A-C: 0.32423 A-G: 2.24117 A-T: 2.12015 C-G: 1.16411 C-T: 3.24849 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.000
Gamma shape alpha: 1.327
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1387.255
Total tree length: 6.712
Total number of iterations: 102
CPU time used for tree search: 3.318 sec (0h:0m:3s)
Wall-clock time used for tree search: 3.298 sec (0h:0m:3s)
Total CPU time used: 3.848 sec (0h:0m:3s)
Total wall-clock time used: 3.833 sec (0h:0m:3s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp51h1cwmz/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp51h1cwmz/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp51h1cwmz/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp51h1cwmz/q2iqtree.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp51h1cwmz/q2iqtree.treefile -m "GTR{0.324234,2.24117,2.12015,1.16411,3.24849}+F{0.243216,0.181967,0.319196,0.255621}+I{3.33554e-07}+G4{1.32696}" --length 214
Date and Time: Wed Dec 21 19:10:22 2022
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp51h1cwmz/q2iqtree -nt 1
Saved Phylogeny[Unrooted] to: iqt-gtrig-tree.qza
Let’s rerun the command above and add the --p-fast option. This option,
only compatible with the iqtree method, resembles the fast search performed
by fasttree. 🏎️ Secondly, let’s also perform multiple tree searches and
keep the best of those trees (as we did earlier with the
raxml --p-n-searches ... command):
qiime phylogeny iqtree \
--i-alignment masked-aligned-rep-seqs.qza \
--p-substitution-model 'GTR+I+G' \
--p-fast \
--p-n-runs 10 \
--o-tree iqt-gtrig-fast-ms-tree.qza \
--verbose
stdout:
IQ-TREE multicore version 2.2.0.3 COVID-edition for Mac OS X 64-bit built Sep 5 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: ghost.mggen.nau.edu (AVX, 16 GB RAM)
Command: iqtree -st DNA --runs 10 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiv_8ye03/q2iqtree -nt 1 -fast
Seed: 156709 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Wed Dec 21 19:10:32 2022
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000256062 secs using 79.67% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000467062 secs using 76.86% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Analyzing sequences: done in 1.88351e-05 secs using 90.26% CPU
Checking for duplicate sequences: done in 7.39098e-05 secs using 75.77% CPU
---> START RUN NUMBER 1 (seed: 156709)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.00 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.50)
1. Initial log-likelihood: -1492.39
2. Current log-likelihood: -1401.89
3. Current log-likelihood: -1396.53
4. Current log-likelihood: -1395.12
5. Current log-likelihood: -1394.39
Optimal log-likelihood: -1393.81
Rate parameters: A-C: 0.27026 A-G: 2.39526 A-T: 2.16931 C-G: 1.24752 C-T: 3.29290 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.415
Parameters optimization took 5 rounds (0.039 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00121808 secs using 98.76% CPU
Computing ML distances took 0.001313 sec (of wall-clock time) 0.001265 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.48363e-05 secs using 114.9% CPU
Constructing RapidNJ tree: done in 9.29832e-05 secs using 151.6% CPU
Computing RapidNJ tree took 0.000218 sec (of wall-clock time) 0.000266 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.793
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0212669 secs using 191% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.213
Optimizing NNI: done in 0.02057 secs using 192.2% CPU
Finish initializing candidate tree set (3)
Current best tree score: -1388.213 / CPU time: 0.051
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.213
2. Current log-likelihood: -1388.014
3. Current log-likelihood: -1387.868
4. Current log-likelihood: -1387.759
5. Current log-likelihood: -1387.676
6. Current log-likelihood: -1387.611
7. Current log-likelihood: -1387.560
Optimal log-likelihood: -1387.519
Rate parameters: A-C: 0.35532 A-G: 2.35213 A-T: 2.13937 C-G: 1.20295 C-T: 3.37020 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.361
Parameters optimization took 7 rounds (0.026 sec)
BEST SCORE FOUND : -1387.519
Total tree length: 6.816
Total number of iterations: 2
CPU time used for tree search: 0.097 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.051 sec (0h:0m:0s)
Total CPU time used: 0.207 sec (0h:0m:0s)
Total wall-clock time used: 0.134 sec (0h:0m:0s)
---> START RUN NUMBER 2 (seed: 157709)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1492.097
2. Current log-likelihood: -1401.816
3. Current log-likelihood: -1396.523
4. Current log-likelihood: -1395.122
5. Current log-likelihood: -1394.389
Optimal log-likelihood: -1393.818
Rate parameters: A-C: 0.27163 A-G: 2.41073 A-T: 2.17144 C-G: 1.24911 C-T: 3.27679 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.416
Parameters optimization took 5 rounds (0.041 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00129604 secs using 192.3% CPU
Computing ML distances took 0.001415 sec (of wall-clock time) 0.002682 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 4.60148e-05 secs using 82.58% CPU
Constructing RapidNJ tree: done in 9.20296e-05 secs using 131.5% CPU
Computing RapidNJ tree took 0.000213 sec (of wall-clock time) 0.000210 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.794
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.020205 secs using 191.8% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.214
Optimizing NNI: done in 0.020211 secs using 192.4% CPU
Finish initializing candidate tree set (3)
Current best tree score: -1388.214 / CPU time: 0.049
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.214
2. Current log-likelihood: -1388.015
3. Current log-likelihood: -1387.868
4. Current log-likelihood: -1387.760
5. Current log-likelihood: -1387.676
6. Current log-likelihood: -1387.611
7. Current log-likelihood: -1387.560
Optimal log-likelihood: -1387.519
Rate parameters: A-C: 0.35522 A-G: 2.35151 A-T: 2.13874 C-G: 1.20261 C-T: 3.36909 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.362
Parameters optimization took 7 rounds (0.026 sec)
BEST SCORE FOUND : -1387.519
Total tree length: 6.815
Total number of iterations: 2
CPU time used for tree search: 0.094 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.049 sec (0h:0m:0s)
Total CPU time used: 0.252 sec (0h:0m:0s)
Total wall-clock time used: 0.133 sec (0h:0m:0s)
---> START RUN NUMBER 3 (seed: 158709)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1493.259
2. Current log-likelihood: -1403.078
3. Current log-likelihood: -1398.354
4. Current log-likelihood: -1396.979
5. Current log-likelihood: -1396.262
Optimal log-likelihood: -1395.753
Rate parameters: A-C: 0.24339 A-G: 2.10097 A-T: 1.98595 C-G: 1.09180 C-T: 2.82193 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.355
Parameters optimization took 5 rounds (0.041 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00141191 secs using 185.8% CPU
Computing ML distances took 0.001493 sec (of wall-clock time) 0.002762 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 6.79493e-05 secs using 88.3% CPU
Constructing RapidNJ tree: done in 0.000130892 secs using 131.4% CPU
Computing RapidNJ tree took 0.000296 sec (of wall-clock time) 0.000308 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.173
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.020499 secs using 191.5% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.961
Optimizing NNI: done in 0.0487859 secs using 191.7% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.961 / CPU time: 0.086
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1387.961
2. Current log-likelihood: -1387.803
3. Current log-likelihood: -1387.684
4. Current log-likelihood: -1387.593
5. Current log-likelihood: -1387.523
6. Current log-likelihood: -1387.468
Optimal log-likelihood: -1387.424
Rate parameters: A-C: 0.33414 A-G: 2.26635 A-T: 2.14117 C-G: 1.17550 C-T: 3.28158 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.353
Parameters optimization took 6 rounds (0.022 sec)
BEST SCORE FOUND : -1387.424
Total tree length: 6.743
Total number of iterations: 2
CPU time used for tree search: 0.166 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.087 sec (0h:0m:0s)
Total CPU time used: 0.318 sec (0h:0m:0s)
Total wall-clock time used: 0.167 sec (0h:0m:0s)
---> START RUN NUMBER 4 (seed: 159709)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1495.571
2. Current log-likelihood: -1402.008
3. Current log-likelihood: -1396.794
4. Current log-likelihood: -1395.393
5. Current log-likelihood: -1394.655
Optimal log-likelihood: -1394.081
Rate parameters: A-C: 0.27755 A-G: 2.37595 A-T: 2.10647 C-G: 1.20302 C-T: 3.28732 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.386
Parameters optimization took 5 rounds (0.040 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00127888 secs using 194.5% CPU
Computing ML distances took 0.001369 sec (of wall-clock time) 0.002625 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 6.29425e-05 secs using 73.08% CPU
Constructing RapidNJ tree: done in 0.000100136 secs using 141.8% CPU
Computing RapidNJ tree took 0.000231 sec (of wall-clock time) 0.000247 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.809
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0214698 secs using 191.5% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.217
Optimizing NNI: done in 0.033468 secs using 192% CPU
BETTER TREE FOUND at iteration 2: -1388.188
Finish initializing candidate tree set (4)
Current best tree score: -1388.188 / CPU time: 0.066
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.188
2. Current log-likelihood: -1387.973
3. Current log-likelihood: -1387.830
4. Current log-likelihood: -1387.725
5. Current log-likelihood: -1387.645
6. Current log-likelihood: -1387.584
Optimal log-likelihood: -1387.534
Rate parameters: A-C: 0.36987 A-G: 2.31020 A-T: 2.11745 C-G: 1.22270 C-T: 3.27880 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.006
Gamma shape alpha: 1.332
Parameters optimization took 6 rounds (0.026 sec)
BEST SCORE FOUND : -1387.534
Total tree length: 7.502
Total number of iterations: 2
CPU time used for tree search: 0.126 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.066 sec (0h:0m:0s)
Total CPU time used: 0.283 sec (0h:0m:0s)
Total wall-clock time used: 0.149 sec (0h:0m:0s)
---> START RUN NUMBER 5 (seed: 160709)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1493.550
2. Current log-likelihood: -1403.090
3. Current log-likelihood: -1398.358
4. Current log-likelihood: -1396.975
5. Current log-likelihood: -1396.257
Optimal log-likelihood: -1395.748
Rate parameters: A-C: 0.23785 A-G: 2.06889 A-T: 1.95307 C-G: 1.06292 C-T: 2.77329 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.358
Parameters optimization took 5 rounds (0.041 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00160384 secs using 193.1% CPU
Computing ML distances took 0.001708 sec (of wall-clock time) 0.003275 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 4.79221e-05 secs using 81.38% CPU
Constructing RapidNJ tree: done in 9.17912e-05 secs using 136.2% CPU
Computing RapidNJ tree took 0.000222 sec (of wall-clock time) 0.000215 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.197
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0201702 secs using 192.4% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.961
Optimizing NNI: done in 0.050328 secs using 191.9% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.961 / CPU time: 0.087
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1387.961
2. Current log-likelihood: -1387.803
3. Current log-likelihood: -1387.684
4. Current log-likelihood: -1387.593
5. Current log-likelihood: -1387.523
6. Current log-likelihood: -1387.469
Optimal log-likelihood: -1387.424
Rate parameters: A-C: 0.33442 A-G: 2.26003 A-T: 2.13495 C-G: 1.17227 C-T: 3.27212 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.353
Parameters optimization took 6 rounds (0.022 sec)
BEST SCORE FOUND : -1387.424
Total tree length: 6.742
Total number of iterations: 2
CPU time used for tree search: 0.168 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.088 sec (0h:0m:0s)
Total CPU time used: 0.323 sec (0h:0m:0s)
Total wall-clock time used: 0.170 sec (0h:0m:0s)
---> START RUN NUMBER 6 (seed: 161709)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1493.167
2. Current log-likelihood: -1403.041
3. Current log-likelihood: -1398.313
4. Current log-likelihood: -1396.957
5. Current log-likelihood: -1396.228
Optimal log-likelihood: -1395.709
Rate parameters: A-C: 0.23146 A-G: 2.06957 A-T: 1.96268 C-G: 1.07937 C-T: 2.84174 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.322
Parameters optimization took 5 rounds (0.039 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00130701 secs using 189.6% CPU
Computing ML distances took 0.001392 sec (of wall-clock time) 0.002620 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 5.10216e-05 secs using 82.32% CPU
Constructing RapidNJ tree: done in 8.98838e-05 secs using 146.9% CPU
Computing RapidNJ tree took 0.000222 sec (of wall-clock time) 0.000226 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.184
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.023751 secs using 192.1% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.955
Optimizing NNI: done in 0.0125101 secs using 191.7% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.955 / CPU time: 0.053
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1387.955
2. Current log-likelihood: -1387.798
3. Current log-likelihood: -1387.680
4. Current log-likelihood: -1387.590
5. Current log-likelihood: -1387.521
6. Current log-likelihood: -1387.467
Optimal log-likelihood: -1387.423
Rate parameters: A-C: 0.33566 A-G: 2.27095 A-T: 2.14605 C-G: 1.17829 C-T: 3.29012 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.352
Parameters optimization took 6 rounds (0.022 sec)
BEST SCORE FOUND : -1387.423
Total tree length: 6.744
Total number of iterations: 2
CPU time used for tree search: 0.101 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.053 sec (0h:0m:0s)
Total CPU time used: 0.250 sec (0h:0m:0s)
Total wall-clock time used: 0.131 sec (0h:0m:0s)
---> START RUN NUMBER 7 (seed: 162709)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1491.633
2. Current log-likelihood: -1402.007
3. Current log-likelihood: -1396.792
4. Current log-likelihood: -1395.393
5. Current log-likelihood: -1394.654
Optimal log-likelihood: -1394.081
Rate parameters: A-C: 0.28077 A-G: 2.37447 A-T: 2.10134 C-G: 1.20130 C-T: 3.28121 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.386
Parameters optimization took 5 rounds (0.039 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00129986 secs using 193.1% CPU
Computing ML distances took 0.001382 sec (of wall-clock time) 0.002640 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 4.69685e-05 secs using 80.91% CPU
Constructing RapidNJ tree: done in 9.17912e-05 secs using 126.4% CPU
Computing RapidNJ tree took 0.000200 sec (of wall-clock time) 0.000214 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.810
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.020407 secs using 192.1% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.217
Optimizing NNI: done in 0.033215 secs using 191.5% CPU
BETTER TREE FOUND at iteration 2: -1388.188
Finish initializing candidate tree set (4)
Current best tree score: -1388.188 / CPU time: 0.064
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.188
2. Current log-likelihood: -1387.973
3. Current log-likelihood: -1387.830
4. Current log-likelihood: -1387.725
5. Current log-likelihood: -1387.645
6. Current log-likelihood: -1387.584
Optimal log-likelihood: -1387.534
Rate parameters: A-C: 0.36985 A-G: 2.31003 A-T: 2.11728 C-G: 1.22260 C-T: 3.27851 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.006
Gamma shape alpha: 1.332
Parameters optimization took 6 rounds (0.026 sec)
BEST SCORE FOUND : -1387.534
Total tree length: 7.502
Total number of iterations: 2
CPU time used for tree search: 0.123 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.064 sec (0h:0m:0s)
Total CPU time used: 0.278 sec (0h:0m:0s)
Total wall-clock time used: 0.146 sec (0h:0m:0s)
---> START RUN NUMBER 8 (seed: 163709)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1492.097
2. Current log-likelihood: -1401.816
3. Current log-likelihood: -1396.523
4. Current log-likelihood: -1395.122
5. Current log-likelihood: -1394.389
Optimal log-likelihood: -1393.818
Rate parameters: A-C: 0.27163 A-G: 2.41073 A-T: 2.17144 C-G: 1.24911 C-T: 3.27679 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.416
Parameters optimization took 5 rounds (0.043 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00132704 secs using 188.9% CPU
Computing ML distances took 0.001410 sec (of wall-clock time) 0.002637 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 4.79221e-05 secs using 81.38% CPU
Constructing RapidNJ tree: done in 0.000126123 secs using 121.3% CPU
Computing RapidNJ tree took 0.000255 sec (of wall-clock time) 0.000276 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.794
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0207231 secs using 191.7% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.214
Optimizing NNI: done in 0.020632 secs using 191.7% CPU
Finish initializing candidate tree set (3)
Current best tree score: -1388.214 / CPU time: 0.050
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.214
2. Current log-likelihood: -1388.015
3. Current log-likelihood: -1387.868
4. Current log-likelihood: -1387.760
5. Current log-likelihood: -1387.676
6. Current log-likelihood: -1387.611
7. Current log-likelihood: -1387.560
Optimal log-likelihood: -1387.519
Rate parameters: A-C: 0.35522 A-G: 2.35151 A-T: 2.13874 C-G: 1.20261 C-T: 3.36909 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.362
Parameters optimization took 7 rounds (0.026 sec)
BEST SCORE FOUND : -1387.519
Total tree length: 6.815
Total number of iterations: 2
CPU time used for tree search: 0.096 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.050 sec (0h:0m:0s)
Total CPU time used: 0.259 sec (0h:0m:0s)
Total wall-clock time used: 0.136 sec (0h:0m:0s)
---> START RUN NUMBER 9 (seed: 164709)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1495.571
2. Current log-likelihood: -1402.008
3. Current log-likelihood: -1396.794
4. Current log-likelihood: -1395.393
5. Current log-likelihood: -1394.655
Optimal log-likelihood: -1394.081
Rate parameters: A-C: 0.27755 A-G: 2.37595 A-T: 2.10647 C-G: 1.20301 C-T: 3.28731 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.386
Parameters optimization took 5 rounds (0.039 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00129104 secs using 191.1% CPU
Computing ML distances took 0.001377 sec (of wall-clock time) 0.002598 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 7.00951e-05 secs using 72.76% CPU
Constructing RapidNJ tree: done in 0.000118017 secs using 127.1% CPU
Computing RapidNJ tree took 0.000267 sec (of wall-clock time) 0.000261 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.809
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.020077 secs using 191.6% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.217
Optimizing NNI: done in 0.031868 secs using 192.5% CPU
BETTER TREE FOUND at iteration 2: -1388.188
Finish initializing candidate tree set (4)
Current best tree score: -1388.188 / CPU time: 0.062
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.188
2. Current log-likelihood: -1387.973
3. Current log-likelihood: -1387.830
4. Current log-likelihood: -1387.725
5. Current log-likelihood: -1387.645
6. Current log-likelihood: -1387.584
Optimal log-likelihood: -1387.534
Rate parameters: A-C: 0.36987 A-G: 2.31020 A-T: 2.11745 C-G: 1.22270 C-T: 3.27880 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.006
Gamma shape alpha: 1.332
Parameters optimization took 6 rounds (0.026 sec)
BEST SCORE FOUND : -1387.534
Total tree length: 7.502
Total number of iterations: 2
CPU time used for tree search: 0.120 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.063 sec (0h:0m:0s)
Total CPU time used: 0.276 sec (0h:0m:0s)
Total wall-clock time used: 0.145 sec (0h:0m:0s)
---> START RUN NUMBER 10 (seed: 165709)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1492.097
2. Current log-likelihood: -1401.816
3. Current log-likelihood: -1396.523
4. Current log-likelihood: -1395.122
5. Current log-likelihood: -1394.389
Optimal log-likelihood: -1393.818
Rate parameters: A-C: 0.27163 A-G: 2.41073 A-T: 2.17144 C-G: 1.24911 C-T: 3.27679 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.416
Parameters optimization took 5 rounds (0.042 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00128388 secs using 192.9% CPU
Computing ML distances took 0.001364 sec (of wall-clock time) 0.002596 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 4.81606e-05 secs using 80.98% CPU
Constructing RapidNJ tree: done in 9.10759e-05 secs using 119.7% CPU
Computing RapidNJ tree took 0.000213 sec (of wall-clock time) 0.000195 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.794
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0204771 secs using 191.9% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.214
Optimizing NNI: done in 0.020587 secs using 191.6% CPU
Finish initializing candidate tree set (3)
Current best tree score: -1388.214 / CPU time: 0.050
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.214
2. Current log-likelihood: -1388.015
3. Current log-likelihood: -1387.868
4. Current log-likelihood: -1387.760
5. Current log-likelihood: -1387.676
6. Current log-likelihood: -1387.611
7. Current log-likelihood: -1387.560
Optimal log-likelihood: -1387.519
Rate parameters: A-C: 0.35522 A-G: 2.35151 A-T: 2.13874 C-G: 1.20261 C-T: 3.36909 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.362
Parameters optimization took 7 rounds (0.026 sec)
BEST SCORE FOUND : -1387.519
Total tree length: 6.815
Total number of iterations: 2
CPU time used for tree search: 0.095 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.050 sec (0h:0m:0s)
Total CPU time used: 0.255 sec (0h:0m:0s)
Total wall-clock time used: 0.135 sec (0h:0m:0s)
---> SUMMARIZE RESULTS FROM 10 RUNS
Run 6 gave best log-likelihood: -1387.423
Total CPU time for 10 runs: 2.736 seconds.
Total wall-clock time for 10 runs: 1.469 seconds.
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiv_8ye03/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiv_8ye03/q2iqtree.treefile
Trees from independent runs: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiv_8ye03/q2iqtree.runtrees
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiv_8ye03/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiv_8ye03/q2iqtree.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiv_8ye03/q2iqtree.treefile -m "GTR{0.337156,2.28043,2.14506,1.18328,3.29428}+F{0.243216,0.181967,0.319196,0.255621}+I{0.0160099}+G4{1.38246}" --length 214
Date and Time: Wed Dec 21 19:10:33 2022
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 10 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiv_8ye03/q2iqtree -nt 1 -fast
Saved Phylogeny[Unrooted] to: iqt-gtrig-fast-ms-tree.qza
Single branch tests¶
IQ-TREE provides access to a few single branch testing methods
SH-aLRT via
--p-alrt [INT >= 1000]aBayes via
--p-abayes [TRUE | FALSE]local bootstrap test via
--p-lbp [INT >= 1000]
Single branch tests are commonly used as an alternative to the bootstrapping
approach we’ve discussed above, as they are substantially faster and often
recommended when constructing large phylogenies (e.g. >10,000 taxa). All
three of these methods can be applied simultaneously and viewed within iTOL
as separate bootstrap support values. These values are always in listed in the
following order of alrt / lbp / abayes. We’ll go ahead and apply all of the
branch tests in our next command, while specifying the same substitution model
as above. Feel free to combine this with the --p-fast option. 😉
qiime phylogeny iqtree \
--i-alignment masked-aligned-rep-seqs.qza \
--p-alrt 1000 \
--p-abayes \
--p-lbp 1000 \
--p-substitution-model 'GTR+I+G' \
--o-tree iqt-sbt-tree.qza \
--verbose
stdout:
IQ-TREE multicore version 2.2.0.3 COVID-edition for Mac OS X 64-bit built Sep 5 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: ghost.mggen.nau.edu (AVX, 16 GB RAM)
Command: iqtree -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpx3_xjbco/q2iqtree -nt 1 -alrt 1000 -abayes -lbp 1000
Seed: 387324 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Wed Dec 21 19:10:43 2022
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000231981 secs using 83.2% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000461102 secs using 78.29% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 2.59876e-05 secs using 88.5% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 7.10487e-05 secs using 76% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Thoroughly optimizing +I+G parameters from 10 start values...
Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 1.285 / LogL: -1392.552
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.008, 1.377 / LogL: -1392.829
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.009, 1.392 / LogL: -1392.898
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.009, 1.386 / LogL: -1392.889
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.008, 1.380 / LogL: -1392.852
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.009, 1.385 / LogL: -1392.879
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.007, 1.381 / LogL: -1392.829
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.008, 1.382 / LogL: -1392.844
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.008, 1.385 / LogL: -1392.849
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.008, 1.384 / LogL: -1392.858
Optimal pinv,alpha: 0.000, 1.285 / LogL: -1392.552
Parameters optimization took 0.493 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00130296 secs using 97.78% CPU
Computing ML distances took 0.001432 sec (of wall-clock time) 0.001361 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.48363e-05 secs using 87.53% CPU
Constructing RapidNJ tree: done in 9.20296e-05 secs using 152.1% CPU
Computing RapidNJ tree took 0.000223 sec (of wall-clock time) 0.000243 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.708
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.109 second
Computing log-likelihood of 98 initial trees ... 0.133 seconds
Current best score: -1392.552
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.012928 secs using 98.62% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.258
Optimizing NNI: done in 0.0216098 secs using 99.44% CPU
Optimizing NNI: done in 0.0142038 secs using 99.04% CPU
Optimizing NNI: done in 0.0142848 secs using 99.09% CPU
Optimizing NNI: done in 0.0145421 secs using 98.78% CPU
Optimizing NNI: done in 0.0144131 secs using 98.97% CPU
Optimizing NNI: done in 0.0144498 secs using 99.04% CPU
Optimizing NNI: done in 0.0263011 secs using 98.96% CPU
Optimizing NNI: done in 0.0278041 secs using 98.25% CPU
Optimizing NNI: done in 0.026782 secs using 98.85% CPU
Iteration 10 / LogL: -1387.279 / Time: 0h:0m:0s
Optimizing NNI: done in 0.026495 secs using 99.07% CPU
Optimizing NNI: done in 0.026603 secs using 99.14% CPU
Optimizing NNI: done in 0.0264981 secs using 99.17% CPU
Optimizing NNI: done in 0.026814 secs using 98.53% CPU
Optimizing NNI: done in 0.0262771 secs using 99.17% CPU
Optimizing NNI: done in 0.0259631 secs using 99.15% CPU
Optimizing NNI: done in 0.0264471 secs using 98.75% CPU
Optimizing NNI: done in 0.0277469 secs using 98.06% CPU
Optimizing NNI: done in 0.026958 secs using 98.82% CPU
Optimizing NNI: done in 0.026134 secs using 99.15% CPU
Iteration 20 / LogL: -1387.279 / Time: 0h:0m:1s
Finish initializing candidate tree set (2)
Current best tree score: -1387.258 / CPU time: 0.717
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0468829 secs using 98.78% CPU
Optimizing NNI: done in 0.020052 secs using 98.62% CPU
Optimizing NNI: done in 0.014879 secs using 98.77% CPU
Optimizing NNI: done in 0.0323348 secs using 98.74% CPU
Optimizing NNI: done in 0.0242541 secs using 98.7% CPU
Optimizing NNI: done in 0.037302 secs using 98.55% CPU
Optimizing NNI: done in 0.0278091 secs using 99.09% CPU
Optimizing NNI: done in 0.045341 secs using 98.98% CPU
Optimizing NNI: done in 0.0348492 secs using 99.01% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.257
Optimizing NNI: done in 0.028878 secs using 99.02% CPU
Iteration 30 / LogL: -1387.648 / Time: 0h:0m:1s (0h:0m:3s left)
Optimizing NNI: done in 0.0258901 secs using 98.97% CPU
Optimizing NNI: done in 0.0269511 secs using 98.75% CPU
Optimizing NNI: done in 0.0304101 secs using 98.4% CPU
Optimizing NNI: done in 0.03754 secs using 99.08% CPU
Optimizing NNI: done in 0.0410469 secs using 99.04% CPU
Optimizing NNI: done in 0.0276439 secs using 99.01% CPU
Optimizing NNI: done in 0.0322771 secs using 98.74% CPU
Optimizing NNI: done in 0.0225291 secs using 99.04% CPU
Optimizing NNI: done in 0.029856 secs using 99.09% CPU
Optimizing NNI: done in 0.0378909 secs using 99.12% CPU
Iteration 40 / LogL: -1387.352 / Time: 0h:0m:1s (0h:0m:2s left)
Optimizing NNI: done in 0.0177629 secs using 98.21% CPU
Optimizing NNI: done in 0.04755 secs using 99.07% CPU
Optimizing NNI: done in 0.020016 secs using 98.8% CPU
Optimizing NNI: done in 0.0391841 secs using 98.92% CPU
Optimizing NNI: done in 0.027298 secs using 98.97% CPU
Optimizing NNI: done in 0.0277131 secs using 99.18% CPU
Optimizing NNI: done in 0.0277779 secs using 99.18% CPU
Optimizing NNI: done in 0.0332351 secs using 98.58% CPU
Optimizing NNI: done in 0.0274451 secs using 98.79% CPU
Optimizing NNI: done in 0.0695369 secs using 98.89% CPU
Iteration 50 / LogL: -1387.431 / Time: 0h:0m:2s (0h:0m:2s left)
Optimizing NNI: done in 0.0318041 secs using 98.69% CPU
Optimizing NNI: done in 0.0278411 secs using 99.08% CPU
Optimizing NNI: done in 0.033685 secs using 98.97% CPU
Optimizing NNI: done in 0.0325611 secs using 98.86% CPU
Optimizing NNI: done in 0.0228798 secs using 96.86% CPU
Optimizing NNI: done in 0.021359 secs using 99.23% CPU
Optimizing NNI: done in 0.026082 secs using 98.95% CPU
Optimizing NNI: done in 0.0193949 secs using 98.3% CPU
Optimizing NNI: done in 0.0406749 secs using 98.76% CPU
Optimizing NNI: done in 0.046237 secs using 98.44% CPU
Iteration 60 / LogL: -1387.350 / Time: 0h:0m:2s (0h:0m:1s left)
Optimizing NNI: done in 0.0308242 secs using 98.71% CPU
Optimizing NNI: done in 0.0282762 secs using 98.61% CPU
Optimizing NNI: done in 0.0531969 secs using 98.79% CPU
Optimizing NNI: done in 0.0215909 secs using 99.05% CPU
Optimizing NNI: done in 0.0354509 secs using 98.85% CPU
Optimizing NNI: done in 0.02844 secs using 99.01% CPU
Optimizing NNI: done in 0.0516558 secs using 98.73% CPU
Optimizing NNI: done in 0.0479739 secs using 98.87% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 68: -1387.169
Optimizing NNI: done in 0.0551591 secs using 98.82% CPU
Optimizing NNI: done in 0.0199511 secs using 98.43% CPU
Iteration 70 / LogL: -1387.446 / Time: 0h:0m:2s (0h:0m:4s left)
Optimizing NNI: done in 0.0487809 secs using 98.92% CPU
Optimizing NNI: done in 0.057683 secs using 98.86% CPU
Optimizing NNI: done in 0.0321488 secs using 98.76% CPU
Optimizing NNI: done in 0.069562 secs using 98.96% CPU
Optimizing NNI: done in 0.0319169 secs using 99.25% CPU
Optimizing NNI: done in 0.026679 secs using 99.86% CPU
Optimizing NNI: done in 0.025842 secs using 99.85% CPU
Optimizing NNI: done in 0.02933 secs using 99.96% CPU
Optimizing NNI: done in 0.029635 secs using 99.86% CPU
Optimizing NNI: done in 0.018878 secs using 99.96% CPU
Iteration 80 / LogL: -1387.337 / Time: 0h:0m:3s (0h:0m:3s left)
Optimizing NNI: done in 0.032444 secs using 99.74% CPU
Optimizing NNI: done in 0.040951 secs using 99.97% CPU
Optimizing NNI: done in 0.02773 secs using 99.97% CPU
Optimizing NNI: done in 0.0228052 secs using 99.97% CPU
Optimizing NNI: done in 0.023221 secs using 99.97% CPU
Optimizing NNI: done in 0.0137529 secs using 99.95% CPU
Optimizing NNI: done in 0.0249798 secs using 99.96% CPU
Optimizing NNI: done in 0.0277941 secs using 99.84% CPU
Optimizing NNI: done in 0.0415249 secs using 99.8% CPU
Optimizing NNI: done in 0.0371151 secs using 99.93% CPU
Iteration 90 / LogL: -1387.337 / Time: 0h:0m:3s (0h:0m:3s left)
Optimizing NNI: done in 0.0496681 secs using 99.84% CPU
Optimizing NNI: done in 0.032577 secs using 99.96% CPU
Optimizing NNI: done in 0.033638 secs using 99.81% CPU
Optimizing NNI: done in 0.0322471 secs using 99.79% CPU
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UPDATE BEST LOG-LIKELIHOOD: -1387.169
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Iteration 100 / LogL: -1397.858 / Time: 0h:0m:3s (0h:0m:2s left)
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UPDATE BEST LOG-LIKELIHOOD: -1387.169
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Iteration 110 / LogL: -1387.397 / Time: 0h:0m:4s (0h:0m:2s left)
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Iteration 120 / LogL: -1387.337 / Time: 0h:0m:4s (0h:0m:1s left)
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Iteration 130 / LogL: -1387.170 / Time: 0h:0m:4s (0h:0m:1s left)
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UPDATE BEST LOG-LIKELIHOOD: -1387.169
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Iteration 140 / LogL: -1387.359 / Time: 0h:0m:5s (0h:0m:1s left)
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BETTER TREE FOUND at iteration 144: -1387.169
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Iteration 150 / LogL: -1387.169 / Time: 0h:0m:5s (0h:0m:3s left)
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Iteration 160 / LogL: -1387.191 / Time: 0h:0m:5s (0h:0m:2s left)
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UPDATE BEST LOG-LIKELIHOOD: -1387.169
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Iteration 170 / LogL: -1387.204 / Time: 0h:0m:5s (0h:0m:2s left)
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
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Iteration 180 / LogL: -1387.169 / Time: 0h:0m:6s (0h:0m:2s left)
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Iteration 190 / LogL: -1387.169 / Time: 0h:0m:6s (0h:0m:1s left)
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Iteration 200 / LogL: -1387.175 / Time: 0h:0m:6s (0h:0m:1s left)
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Iteration 210 / LogL: -1387.314 / Time: 0h:0m:6s (0h:0m:1s left)
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Iteration 220 / LogL: -1387.169 / Time: 0h:0m:7s (0h:0m:0s left)
Optimizing NNI: done in 0.018419 secs using 99.96% CPU
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Iteration 230 / LogL: -1387.169 / Time: 0h:0m:7s (0h:0m:0s left)
Optimizing NNI: done in 0.0362599 secs using 99.96% CPU
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Iteration 240 / LogL: -1387.169 / Time: 0h:0m:7s (0h:0m:0s left)
Optimizing NNI: done in 0.027554 secs using 99.97% CPU
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Optimizing NNI: done in 0.020411 secs using 99.97% CPU
TREE SEARCH COMPLETED AFTER 245 ITERATIONS / Time: 0h:0m:7s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.168
Optimal log-likelihood: -1387.167
Rate parameters: A-C: 0.34679 A-G: 2.32660 A-T: 2.14696 C-G: 1.23684 C-T: 3.22330 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.000
Gamma shape alpha: 1.286
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1387.167
Testing tree branches by SH-like aLRT with 1000 replicates...
Testing tree branches by local-BP test with 1000 replicates...
Testing tree branches by aBayes parametric test...
0.067 sec.
Total tree length: 7.597
Total number of iterations: 245
CPU time used for tree search: 7.457 sec (0h:0m:7s)
Wall-clock time used for tree search: 7.323 sec (0h:0m:7s)
Total CPU time used: 8.035 sec (0h:0m:8s)
Total wall-clock time used: 7.905 sec (0h:0m:7s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpx3_xjbco/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpx3_xjbco/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpx3_xjbco/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpx3_xjbco/q2iqtree.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpx3_xjbco/q2iqtree.treefile -m "GTR{0.346793,2.3266,2.14696,1.23684,3.2233}+F{0.243216,0.181967,0.319196,0.255621}+I{2.86927e-07}+G4{1.2863}" --length 214
Date and Time: Wed Dec 21 19:10:51 2022
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpx3_xjbco/q2iqtree -nt 1 -alrt 1000 -abayes -lbp 1000
Saved Phylogeny[Unrooted] to: iqt-sbt-tree.qza
Tip
IQ-TREE search settings.
There are quite a few adjustable parameters available for iqtree that
can be modified improve searches through “tree space” and prevent the search
algorithms from getting stuck in local optima. One particular best
practice to aid in this regard, is to adjust the following parameters:
--p-perturb-nni-strength and --p-stop-iter (each respectively maps
to the -pers and -nstop flags of iqtree ). In brief, the larger
the value for NNI (nearest-neighbor interchange) perturbation, the larger
the jumps in “tree space”. This value should be set high enough to allow the
search algorithm to avoid being trapped in local optima, but not to high
that the search is haphazardly jumping around “tree space”. That is, like
Goldilocks and the three 🐻s you need to find a setting that is “just
right”, or at least within a set of reasonable bounds. One way of assessing
this, is to do a few short trial runs using the --verbose flag. If you
see that the likelihood values are jumping around to much, then lowering the
value for --p-perturb-nni-strength may be warranted. As for the stopping
criteria, i.e. --p-stop-iter, the higher this value, the more thorough
your search in “tree space”. Be aware, increasing this value may also
increase the run time. That is, the search will continue until it has
sampled a number of trees, say 100 (default), without finding a better
scoring tree. If a better tree is found, then the counter resets, and the
search continues. These two parameters deserve special consideration when a
given data set contains many short sequences, quite common for microbiome
survey data. We can modify our original command to include these extra
parameters with the recommended modifications for short sequences, i.e. a
lower value for perturbation strength (shorter reads do not contain as much
phylogenetic information, thus we should limit how far we jump around in
“tree space”) and a larger number of stop iterations. See the IQ-TREE
command reference for more details about default parameter settings.
Finally, we’ll let iqtree perform the model testing, and automatically
determine the optimal number of CPU cores to use.
qiime phylogeny iqtree \
--i-alignment masked-aligned-rep-seqs.qza \
--p-perturb-nni-strength 0.2 \
--p-stop-iter 200 \
--p-n-cores 1 \
--o-tree iqt-nnisi-fast-tree.qza \
--verbose
stdout:
IQ-TREE multicore version 2.2.0.3 COVID-edition for Mac OS X 64-bit built Sep 5 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: ghost.mggen.nau.edu (AVX, 16 GB RAM)
Command: iqtree -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpckcd7c3g/q2iqtree -nt 1 -nstop 200 -pers 0.200000
Seed: 107350 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Wed Dec 21 19:11:01 2022
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000250101 secs using 85.97% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000509024 secs using 74.26% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 2.19345e-05 secs using 82.06% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 7.08103e-05 secs using 74.85% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.0190251 secs using 98.86% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1389.711
Optimal log-likelihood: -1388.843
Rate parameters: A-C: 0.36734 A-G: 2.36723 A-T: 2.14911 C-G: 1.23876 C-T: 3.32308 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.034
Gamma shape alpha: 1.420
Parameters optimization took 1 rounds (0.009 sec)
Time for fast ML tree search: 0.057 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 484 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1402.573 45 2895.147 2919.790 3046.616
2 GTR+F+I 1401.119 46 2894.238 2920.130 3049.072
3 GTR+F+G4 1387.362 46 2866.724 2892.616 3021.559
4 GTR+F+I+G4 1387.729 47 2869.458 2896.638 3027.658
5 GTR+F+R2 1382.368 47 2858.736 2885.917 3016.937
6 GTR+F+R3 1382.422 49 2862.845 2892.723 3027.778
14 GTR+F+I+I+R2 1382.420 48 2860.840 2889.349 3022.406
15 GTR+F+I+I+R3 1382.451 50 2864.902 2896.191 3033.201
25 SYM+G4 1387.133 43 2860.266 2882.525 3005.003
27 SYM+R2 1383.095 44 2854.190 2877.621 3002.292
36 SYM+I+I+R2 1383.227 45 2856.454 2881.097 3007.923
47 TVM+F+G4 1388.357 45 2866.713 2891.356 3018.182
49 TVM+F+R2 1383.790 46 2859.580 2885.472 3014.415
58 TVM+F+I+I+R2 1383.813 47 2861.626 2888.806 3019.826
69 TVMe+G4 1387.121 42 2858.243 2879.366 2999.614
71 TVMe+R2 1383.080 43 2852.159 2874.418 2996.896
80 TVMe+I+I+R2 1383.224 44 2854.449 2877.881 3002.552
91 TIM3+F+G4 1391.377 44 2870.754 2894.186 3018.857
93 TIM3+F+R2 1385.913 45 2861.826 2886.469 3013.295
102 TIM3+F+I+I+R2 1386.042 46 2864.083 2889.976 3018.918
113 TIM3e+G4 1390.357 41 2862.713 2882.736 3000.718
115 TIM3e+R2 1385.918 42 2855.835 2876.958 2997.206
124 TIM3e+I+I+R2 1386.072 43 2858.145 2880.404 3002.882
135 TIM2+F+G4 1393.635 44 2875.271 2898.703 3023.374
137 TIM2+F+R2 1387.682 45 2865.363 2890.006 3016.832
146 TIM2+F+I+I+R2 1387.782 46 2867.565 2893.457 3022.400
157 TIM2e+G4 1396.794 41 2875.588 2895.611 3013.593
159 TIM2e+R2 1391.573 42 2867.147 2888.270 3008.518
168 TIM2e+I+I+R2 1391.651 43 2869.302 2891.561 3014.039
179 TIM+F+G4 1390.364 44 2868.727 2892.159 3016.830
181 TIM+F+R2 1384.935 45 2859.870 2884.512 3011.339
190 TIM+F+I+I+R2 1385.017 46 2862.035 2887.927 3016.870
201 TIMe+G4 1394.002 41 2870.004 2890.027 3008.009
203 TIMe+R2 1389.000 42 2862.001 2883.123 3003.372
212 TIMe+I+I+R2 1389.095 43 2864.190 2886.449 3008.927
223 TPM3u+F+G4 1392.305 43 2870.611 2892.870 3015.348
225 TPM3u+F+R2 1387.330 44 2862.659 2886.091 3010.762
234 TPM3u+F+I+I+R2 1387.462 45 2864.924 2889.567 3016.393
245 TPM3+G4 1390.373 40 2860.746 2879.706 2995.385
247 TPM3+R2 1385.925 41 2853.850 2873.873 2991.855
256 TPM3+I+I+R2 1386.070 42 2856.140 2877.263 2997.511
267 TPM2u+F+G4 1394.533 43 2875.067 2897.326 3019.804
269 TPM2u+F+R2 1389.057 44 2866.114 2889.546 3014.217
278 TPM2u+F+I+I+R2 1389.101 45 2868.202 2892.845 3019.671
289 TPM2+G4 1396.823 40 2873.645 2892.605 3008.284
291 TPM2+R2 1391.577 41 2865.155 2885.178 3003.160
300 TPM2+I+I+R2 1391.649 42 2867.297 2888.420 3008.668
311 K3Pu+F+G4 1391.381 43 2868.762 2891.021 3013.499
313 K3Pu+F+R2 1386.372 44 2860.743 2884.175 3008.846
322 K3Pu+F+I+I+R2 1386.425 45 2862.851 2887.494 3014.320
333 K3P+G4 1394.015 40 2868.030 2886.989 3002.669
335 K3P+R2 1389.002 41 2860.005 2880.028 2998.010
344 K3P+I+I+R2 1389.099 42 2862.198 2883.320 3003.569
355 TN+F+G4 1394.039 43 2874.077 2896.336 3018.814
357 TN+F+R2 1388.242 44 2864.484 2887.916 3012.587
366 TN+F+I+I+R2 1388.289 45 2866.579 2891.221 3018.048
377 TNe+G4 1396.791 40 2873.581 2892.541 3008.220
379 TNe+R2 1391.586 41 2865.171 2885.195 3003.176
388 TNe+I+I+R2 1391.666 42 2867.332 2888.454 3008.703
399 HKY+F+G4 1394.951 42 2873.902 2895.024 3015.273
401 HKY+F+R2 1389.609 43 2865.218 2887.477 3009.955
410 HKY+F+I+I+R2 1389.664 44 2867.327 2890.759 3015.430
421 K2P+G4 1396.824 39 2871.648 2889.579 3002.921
423 K2P+R2 1391.594 40 2863.189 2882.148 2997.828
432 K2P+I+I+R2 1391.664 41 2865.327 2885.351 3003.332
443 F81+F+G4 1405.743 41 2893.487 2913.510 3031.492
445 F81+F+R2 1400.806 42 2885.613 2906.736 3026.984
454 F81+F+I+I+R2 1400.909 43 2887.818 2910.077 3032.555
465 JC+G4 1407.650 38 2891.300 2908.237 3019.207
467 JC+R2 1402.858 39 2883.716 2901.648 3014.990
476 JC+I+I+R2 1402.926 40 2885.852 2904.812 3020.491
Akaike Information Criterion: TVMe+R2
Corrected Akaike Information Criterion: TPM3+R2
Bayesian Information Criterion: TPM3+R2
Best-fit model: TPM3+R2 chosen according to BIC
All model information printed to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpckcd7c3g/q2iqtree.model.gz
CPU time for ModelFinder: 1.402 seconds (0h:0m:1s)
Wall-clock time for ModelFinder: 1.424 seconds (0h:0m:1s)
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1385.925
Optimal log-likelihood: -1385.924
Rate parameters: A-C: 0.40868 A-G: 1.56207 A-T: 1.00000 C-G: 0.40868 C-T: 1.56207 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.716,0.409) (0.284,2.491)
Parameters optimization took 1 rounds (0.004 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000856876 secs using 96.28% CPU
Computing ML distances took 0.000937 sec (of wall-clock time) 0.000883 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.4121e-05 secs using 77.6% CPU
Constructing RapidNJ tree: done in 9.17912e-05 secs using 114.4% CPU
Computing RapidNJ tree took 0.000220 sec (of wall-clock time) 0.000191 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.820
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.103 second
Computing log-likelihood of 98 initial trees ... 0.100 seconds
Current best score: -1385.924
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00479102 secs using 99% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.880
Optimizing NNI: done in 0.0134859 secs using 98.71% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1385.311
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Iteration 10 / LogL: -1385.344 / Time: 0h:0m:0s
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Iteration 20 / LogL: -1385.343 / Time: 0h:0m:0s
Finish initializing candidate tree set (2)
Current best tree score: -1385.311 / CPU time: 0.475
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
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Optimizing NNI: done in 0.010483 secs using 98.62% CPU
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UPDATE BEST LOG-LIKELIHOOD: -1385.310
Iteration 30 / LogL: -1385.310 / Time: 0h:0m:0s (0h:0m:3s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.310
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Iteration 60 / LogL: -1385.310 / Time: 0h:0m:0s (0h:0m:2s left)
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Iteration 90 / LogL: -1385.312 / Time: 0h:0m:1s (0h:0m:1s left)
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Iteration 100 / LogL: -1385.507 / Time: 0h:0m:1s (0h:0m:1s left)
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BETTER TREE FOUND at iteration 107: -1385.310
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UPDATE BEST LOG-LIKELIHOOD: -1385.310
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UPDATE BEST LOG-LIKELIHOOD: -1385.310
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UPDATE BEST LOG-LIKELIHOOD: -1385.310
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Iteration 240 / LogL: -1385.310 / Time: 0h:0m:2s (0h:0m:0s left)
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Iteration 250 / LogL: -1385.310 / Time: 0h:0m:3s (0h:0m:0s left)
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Iteration 260 / LogL: -1385.311 / Time: 0h:0m:3s (0h:0m:0s left)
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Iteration 300 / LogL: -1385.310 / Time: 0h:0m:3s (0h:0m:0s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.310
Optimizing NNI: done in 0.00970006 secs using 99.93% CPU
TREE SEARCH COMPLETED AFTER 308 ITERATIONS / Time: 0h:0m:3s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1385.310
Optimal log-likelihood: -1385.306
Rate parameters: A-C: 0.39450 A-G: 1.56675 A-T: 1.00000 C-G: 0.39450 C-T: 1.56675 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.721,0.402) (0.279,2.542)
Parameters optimization took 1 rounds (0.005 sec)
BEST SCORE FOUND : -1385.306
Total tree length: 6.847
Total number of iterations: 308
CPU time used for tree search: 3.859 sec (0h:0m:3s)
Wall-clock time used for tree search: 3.710 sec (0h:0m:3s)
Total CPU time used: 3.890 sec (0h:0m:3s)
Total wall-clock time used: 3.736 sec (0h:0m:3s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpckcd7c3g/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpckcd7c3g/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpckcd7c3g/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpckcd7c3g/q2iqtree.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpckcd7c3g/q2iqtree.treefile -m "TPM3{0.394497,1.56675}+FQ+R2{0.720585,0.401955,0.279415,2.5423}" --length 214
Date and Time: Wed Dec 21 19:11:06 2022
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpckcd7c3g/q2iqtree -nt 1 -nstop 200 -pers 0.200000
Saved Phylogeny[Unrooted] to: iqt-nnisi-fast-tree.qza
iqtree-ultrafast-bootstrap¶
As per our discussion in the raxml-rapid-bootstrap section above, we can
also use IQ-TREE to evaluate how well our splits / bipartitions are supported
within our phylogeny via the ultrafast bootstrap algorithm. Below, we’ll
apply the plugin’s
ultrafast bootstrap command:
automatic model selection (MFP), perform 1000 bootstrap replicates
(minimum required), set the same generally suggested parameters for
constructing a phylogeny from short sequences, and automatically determine the
optimal number of CPU cores to use:
qiime phylogeny iqtree-ultrafast-bootstrap \
--i-alignment masked-aligned-rep-seqs.qza \
--p-perturb-nni-strength 0.2 \
--p-stop-iter 200 \
--p-n-cores 1 \
--o-tree iqt-nnisi-bootstrap-tree.qza \
--verbose
stdout:
IQ-TREE multicore version 2.2.0.3 COVID-edition for Mac OS X 64-bit built Sep 5 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: ghost.mggen.nau.edu (AVX, 16 GB RAM)
Command: iqtree -bb 1000 -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxcp702f0/q2iqtreeufboot -nt 1 -nstop 200 -pers 0.200000
Seed: 956160 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Wed Dec 21 19:11:15 2022
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000264883 secs using 79.66% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000491858 secs using 75.43% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 2.90871e-05 secs using 75.63% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 7.41482e-05 secs using 76.87% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.0348301 secs using 98.72% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1389.605
Optimal log-likelihood: -1388.793
Rate parameters: A-C: 0.37543 A-G: 2.37167 A-T: 2.15335 C-G: 1.24272 C-T: 3.32366 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.034
Gamma shape alpha: 1.400
Parameters optimization took 1 rounds (0.006 sec)
Time for fast ML tree search: 0.070 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 484 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1402.600 45 2895.200 2919.843 3046.669
2 GTR+F+I 1401.121 46 2894.242 2920.135 3049.077
3 GTR+F+G4 1387.358 46 2866.716 2892.609 3021.551
4 GTR+F+I+G4 1387.726 47 2869.452 2896.633 3027.653
5 GTR+F+R2 1382.364 47 2858.729 2885.910 3016.930
6 GTR+F+R3 1382.420 49 2862.841 2892.719 3027.773
14 GTR+F+I+I+R2 1382.418 48 2860.837 2889.346 3022.403
15 GTR+F+I+I+R3 1382.449 50 2864.898 2896.187 3033.197
25 SYM+G4 1387.134 43 2860.269 2882.528 3005.006
27 SYM+R2 1383.095 44 2854.189 2877.621 3002.292
36 SYM+I+I+R2 1383.227 45 2856.454 2881.097 3007.923
47 TVM+F+G4 1388.357 45 2866.713 2891.356 3018.182
49 TVM+F+R2 1383.789 46 2859.578 2885.470 3014.413
58 TVM+F+I+I+R2 1383.812 47 2861.625 2888.805 3019.826
69 TVMe+G4 1387.122 42 2858.245 2879.368 2999.616
71 TVMe+R2 1383.079 43 2852.159 2874.418 2996.896
80 TVMe+I+I+R2 1383.224 44 2854.449 2877.881 3002.552
91 TIM3+F+G4 1391.377 44 2870.754 2894.186 3018.857
93 TIM3+F+R2 1385.912 45 2861.825 2886.468 3013.294
102 TIM3+F+I+I+R2 1386.041 46 2864.082 2889.975 3018.917
113 TIM3e+G4 1390.358 41 2862.715 2882.738 3000.720
115 TIM3e+R2 1385.918 42 2855.836 2876.959 2997.207
124 TIM3e+I+I+R2 1386.073 43 2858.145 2880.404 3002.882
135 TIM2+F+G4 1393.635 44 2875.270 2898.702 3023.373
137 TIM2+F+R2 1387.681 45 2865.362 2890.005 3016.831
146 TIM2+F+I+I+R2 1387.782 46 2867.564 2893.456 3022.399
157 TIM2e+G4 1396.795 41 2875.589 2895.613 3013.594
159 TIM2e+R2 1391.574 42 2867.148 2888.270 3008.519
168 TIM2e+I+I+R2 1391.651 43 2869.302 2891.561 3014.039
179 TIM+F+G4 1390.363 44 2868.726 2892.158 3016.829
181 TIM+F+R2 1384.933 45 2859.866 2884.509 3011.335
190 TIM+F+I+I+R2 1385.016 46 2862.032 2887.925 3016.867
201 TIMe+G4 1394.002 41 2870.005 2890.028 3008.010
203 TIMe+R2 1389.000 42 2862.000 2883.123 3003.371
212 TIMe+I+I+R2 1389.095 43 2864.190 2886.449 3008.927
223 TPM3u+F+G4 1392.306 43 2870.611 2892.870 3015.348
225 TPM3u+F+R2 1387.329 44 2862.659 2886.091 3010.762
234 TPM3u+F+I+I+R2 1387.462 45 2864.923 2889.566 3016.392
245 TPM3+G4 1390.374 40 2860.748 2879.708 2995.387
247 TPM3+R2 1385.925 41 2853.851 2873.874 2991.856
256 TPM3+I+I+R2 1386.070 42 2856.140 2877.263 2997.511
267 TPM2u+F+G4 1394.533 43 2875.067 2897.325 3019.804
269 TPM2u+F+R2 1389.057 44 2866.113 2889.545 3014.216
278 TPM2u+F+I+I+R2 1389.101 45 2868.201 2892.844 3019.670
289 TPM2+G4 1396.823 40 2873.646 2892.605 3008.285
291 TPM2+R2 1391.578 41 2865.155 2885.178 3003.160
300 TPM2+I+I+R2 1391.649 42 2867.297 2888.420 3008.668
311 K3Pu+F+G4 1391.381 43 2868.762 2891.021 3013.499
313 K3Pu+F+R2 1386.371 44 2860.742 2884.174 3008.845
322 K3Pu+F+I+I+R2 1386.425 45 2862.850 2887.493 3014.319
333 K3P+G4 1394.015 40 2868.030 2886.989 3002.669
335 K3P+R2 1389.002 41 2860.004 2880.028 2998.009
344 K3P+I+I+R2 1389.099 42 2862.197 2883.320 3003.568
355 TN+F+G4 1394.038 43 2874.077 2896.336 3018.814
357 TN+F+R2 1388.241 44 2864.483 2887.915 3012.586
366 TN+F+I+I+R2 1388.289 45 2866.578 2891.221 3018.047
377 TNe+G4 1396.791 40 2873.582 2892.542 3008.221
379 TNe+R2 1391.586 41 2865.172 2885.195 3003.177
388 TNe+I+I+R2 1391.666 42 2867.332 2888.454 3008.703
399 HKY+F+G4 1394.951 42 2873.902 2895.024 3015.273
401 HKY+F+R2 1389.609 43 2865.217 2887.476 3009.954
410 HKY+F+I+I+R2 1389.663 44 2867.327 2890.759 3015.430
421 K2P+G4 1396.825 39 2871.649 2889.580 3002.922
423 K2P+R2 1391.594 40 2863.189 2882.148 2997.828
432 K2P+I+I+R2 1391.664 41 2865.327 2885.351 3003.332
443 F81+F+G4 1405.743 41 2893.486 2913.509 3031.491
445 F81+F+R2 1400.805 42 2885.611 2906.733 3026.982
454 F81+F+I+I+R2 1400.908 43 2887.816 2910.075 3032.553
465 JC+G4 1407.650 38 2891.299 2908.236 3019.206
467 JC+R2 1402.858 39 2883.715 2901.646 3014.988
476 JC+I+I+R2 1402.926 40 2885.851 2904.811 3020.490
Akaike Information Criterion: TVMe+R2
Corrected Akaike Information Criterion: TPM3+R2
Bayesian Information Criterion: TPM3+R2
Best-fit model: TPM3+R2 chosen according to BIC
All model information printed to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxcp702f0/q2iqtreeufboot.model.gz
CPU time for ModelFinder: 1.420 seconds (0h:0m:1s)
Wall-clock time for ModelFinder: 1.441 seconds (0h:0m:1s)
Generating 1000 samples for ultrafast bootstrap (seed: 956160)...
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1385.925
Optimal log-likelihood: -1385.924
Rate parameters: A-C: 0.40868 A-G: 1.56206 A-T: 1.00000 C-G: 0.40868 C-T: 1.56206 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.716,0.409) (0.284,2.490)
Parameters optimization took 1 rounds (0.005 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000873089 secs using 96.1% CPU
Computing ML distances took 0.000968 sec (of wall-clock time) 0.000905 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.4121e-05 secs using 88.69% CPU
Constructing RapidNJ tree: done in 9.20296e-05 secs using 150% CPU
Computing RapidNJ tree took 0.000214 sec (of wall-clock time) 0.000243 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.820
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.106 second
Computing log-likelihood of 98 initial trees ... 0.100 seconds
Current best score: -1385.924
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00939703 secs using 97.96% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.880
Optimizing NNI: done in 0.023685 secs using 98.75% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1385.311
Optimizing NNI: done in 0.025053 secs using 98.99% CPU
BETTER TREE FOUND at iteration 3: -1385.309
Optimizing NNI: done in 0.0241978 secs using 98.94% CPU
Optimizing NNI: done in 0.0245099 secs using 97.95% CPU
Optimizing NNI: done in 0.0223899 secs using 98.83% CPU
Optimizing NNI: done in 0.022475 secs using 98.89% CPU
Optimizing NNI: done in 0.022347 secs using 98.91% CPU
Optimizing NNI: done in 0.022469 secs using 98.63% CPU
Optimizing NNI: done in 0.022459 secs using 98.8% CPU
Iteration 10 / LogL: -1385.344 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0241599 secs using 98.8% CPU
Optimizing NNI: done in 0.0234849 secs using 99.17% CPU
Optimizing NNI: done in 0.0241129 secs using 98.73% CPU
Optimizing NNI: done in 0.0225971 secs using 98.68% CPU
Optimizing NNI: done in 0.0223551 secs using 98.64% CPU
Optimizing NNI: done in 0.021934 secs using 99.15% CPU
Optimizing NNI: done in 0.0219641 secs using 99.18% CPU
Optimizing NNI: done in 0.0223711 secs using 98.79% CPU
Optimizing NNI: done in 0.021692 secs using 99.18% CPU
Optimizing NNI: done in 0.021867 secs using 99.05% CPU
Iteration 20 / LogL: -1385.343 / Time: 0h:0m:0s
Finish initializing candidate tree set (3)
Current best tree score: -1385.309 / CPU time: 0.674
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.010803 secs using 99.01% CPU
Optimizing NNI: done in 0.0155399 secs using 98.98% CPU
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Iteration 30 / LogL: -1385.895 / Time: 0h:0m:1s (0h:0m:6s left)
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Iteration 40 / LogL: -1390.247 / Time: 0h:0m:1s (0h:0m:5s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.309
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Optimizing NNI: done in 0.0156071 secs using 98.62% CPU
Iteration 50 / LogL: -1385.641 / Time: 0h:0m:1s (0h:0m:4s left)
Log-likelihood cutoff on original alignment: -1418.996
Optimizing NNI: done in 0.0164821 secs using 98.24% CPU
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Iteration 60 / LogL: -1385.549 / Time: 0h:0m:1s (0h:0m:4s left)
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Iteration 70 / LogL: -1385.310 / Time: 0h:0m:2s (0h:0m:3s left)
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Iteration 80 / LogL: -1385.312 / Time: 0h:0m:2s (0h:0m:3s left)
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Iteration 90 / LogL: -1385.556 / Time: 0h:0m:2s (0h:0m:3s left)
Optimizing NNI: done in 0.0134668 secs using 99.95% CPU
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Iteration 100 / LogL: -1385.311 / Time: 0h:0m:2s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -1417.213
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.997
Optimizing NNI: done in 0.0127139 secs using 99.94% CPU
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Iteration 110 / LogL: -1385.530 / Time: 0h:0m:2s (0h:0m:2s left)
Optimizing NNI: done in 0.0117009 secs using 99.97% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.309
Optimizing NNI: done in 0.0122411 secs using 99.63% CPU
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Iteration 120 / LogL: -1385.636 / Time: 0h:0m:3s (0h:0m:2s left)
Optimizing NNI: done in 0.018116 secs using 99.68% CPU
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UPDATE BEST LOG-LIKELIHOOD: -1385.309
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Iteration 130 / LogL: -1385.570 / Time: 0h:0m:3s (0h:0m:1s left)
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Iteration 140 / LogL: -1385.314 / Time: 0h:0m:3s (0h:0m:1s left)
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Iteration 150 / LogL: -1385.309 / Time: 0h:0m:3s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -1417.213
Optimizing NNI: done in 0.00981784 secs using 99.93% CPU
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Iteration 160 / LogL: -1385.322 / Time: 0h:0m:3s (0h:0m:1s left)
Optimizing NNI: done in 0.0145228 secs using 99.96% CPU
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UPDATE BEST LOG-LIKELIHOOD: -1385.309
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Iteration 170 / LogL: -1385.310 / Time: 0h:0m:4s (0h:0m:0s left)
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Iteration 180 / LogL: -1385.507 / Time: 0h:0m:4s (0h:0m:0s left)
Optimizing NNI: done in 0.0180171 secs using 99.95% CPU
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Iteration 190 / LogL: -1385.309 / Time: 0h:0m:4s (0h:0m:0s left)
Optimizing NNI: done in 0.00551605 secs using 99.94% CPU
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Iteration 200 / LogL: -1385.310 / Time: 0h:0m:4s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -1417.625
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.994
Optimizing NNI: done in 0.012383 secs using 99.94% CPU
Optimizing NNI: done in 0.0240059 secs using 99.96% CPU
Optimizing NNI: done in 0.018254 secs using 99.79% CPU
Optimizing NNI: done in 0.0157881 secs using 99.93% CPU
TREE SEARCH COMPLETED AFTER 204 ITERATIONS / Time: 0h:0m:4s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1385.309
Optimal log-likelihood: -1385.305
Rate parameters: A-C: 0.39447 A-G: 1.56669 A-T: 1.00000 C-G: 0.39447 C-T: 1.56669 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.721,0.402) (0.279,2.542)
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1385.305
Creating bootstrap support values...
Split supports printed to NEXUS file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxcp702f0/q2iqtreeufboot.splits.nex
Total tree length: 6.847
Total number of iterations: 204
CPU time used for tree search: 4.896 sec (0h:0m:4s)
Wall-clock time used for tree search: 4.886 sec (0h:0m:4s)
Total CPU time used: 5.010 sec (0h:0m:5s)
Total wall-clock time used: 4.999 sec (0h:0m:4s)
Computing bootstrap consensus tree...
Reading input file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxcp702f0/q2iqtreeufboot.splits.nex...
20 taxa and 153 splits.
Consensus tree written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxcp702f0/q2iqtreeufboot.contree
Reading input trees file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxcp702f0/q2iqtreeufboot.contree
Log-likelihood of consensus tree: -1385.306
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxcp702f0/q2iqtreeufboot.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxcp702f0/q2iqtreeufboot.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxcp702f0/q2iqtreeufboot.mldist
Ultrafast bootstrap approximation results written to:
Split support values: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxcp702f0/q2iqtreeufboot.splits.nex
Consensus tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxcp702f0/q2iqtreeufboot.contree
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxcp702f0/q2iqtreeufboot.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxcp702f0/q2iqtreeufboot.treefile -m "TPM3{0.394473,1.56669}+FQ+R2{0.720555,0.401953,0.279445,2.54207}" --length 214
Date and Time: Wed Dec 21 19:11:22 2022
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -bb 1000 -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxcp702f0/q2iqtreeufboot -nt 1 -nstop 200 -pers 0.200000
Saved Phylogeny[Unrooted] to: iqt-nnisi-bootstrap-tree.qza
Perform single branch tests alongside ufboot¶
We can also apply single branch test methods concurrently with ultrafast bootstrapping. The support values will always be represented in the following order: alrt / lbp / abayes / ufboot. Again, these values can be seen as separately listed bootstrap values in iTOL. We’ll also specify a model as we did earlier.
qiime phylogeny iqtree-ultrafast-bootstrap \
--i-alignment masked-aligned-rep-seqs.qza \
--p-perturb-nni-strength 0.2 \
--p-stop-iter 200 \
--p-n-cores 1 \
--p-alrt 1000 \
--p-abayes \
--p-lbp 1000 \
--p-substitution-model 'GTR+I+G' \
--o-tree iqt-nnisi-bootstrap-sbt-gtrig-tree.qza \
--verbose
stdout:
IQ-TREE multicore version 2.2.0.3 COVID-edition for Mac OS X 64-bit built Sep 5 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: ghost.mggen.nau.edu (AVX, 16 GB RAM)
Command: iqtree -bb 1000 -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptoah5gdk/q2iqtreeufboot -nt 1 -alrt 1000 -abayes -lbp 1000 -nstop 200 -pers 0.200000
Seed: 146896 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Wed Dec 21 19:11:32 2022
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000217199 secs using 84.25% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000458956 secs using 78.44% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 1.90735e-05 secs using 83.89% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 7.39098e-05 secs using 77.12% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
Generating 1000 samples for ultrafast bootstrap (seed: 146896)...
NOTE: 1 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Thoroughly optimizing +I+G parameters from 10 start values...
Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 1.245 / LogL: -1394.426
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.008, 1.308 / LogL: -1394.715
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.009, 1.319 / LogL: -1394.789
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.009, 1.316 / LogL: -1394.785
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.008, 1.311 / LogL: -1394.749
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.009, 1.314 / LogL: -1394.777
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.008, 1.309 / LogL: -1394.722
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.008, 1.310 / LogL: -1394.735
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.008, 1.312 / LogL: -1394.747
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.009, 1.313 / LogL: -1394.756
Optimal pinv,alpha: 0.000, 1.245 / LogL: -1394.426
Parameters optimization took 0.490 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00126481 secs using 97.88% CPU
Computing ML distances took 0.001366 sec (of wall-clock time) 0.001308 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.48363e-05 secs using 89.36% CPU
Constructing RapidNJ tree: done in 9.01222e-05 secs using 154.2% CPU
Computing RapidNJ tree took 0.000241 sec (of wall-clock time) 0.000267 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.974
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| INITIALIZING CANDIDATE TREE SET |
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Generating 98 parsimony trees... 0.105 second
Computing log-likelihood of 98 initial trees ... 0.132 seconds
Current best score: -1392.974
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.0291929 secs using 98.77% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.274
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Iteration 10 / LogL: -1387.731 / Time: 0h:0m:1s
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Iteration 20 / LogL: -1387.285 / Time: 0h:0m:1s
Finish initializing candidate tree set (2)
Current best tree score: -1387.274 / CPU time: 0.897
Number of iterations: 20
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| OPTIMIZING CANDIDATE TREE SET |
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Iteration 30 / LogL: -1387.358 / Time: 0h:0m:1s (0h:0m:10s left)
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BETTER TREE FOUND at iteration 38: -1387.266
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Iteration 40 / LogL: -1387.300 / Time: 0h:0m:2s (0h:0m:10s left)
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Iteration 50 / LogL: -1387.356 / Time: 0h:0m:2s (0h:0m:8s left)
Log-likelihood cutoff on original alignment: -1414.443
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UPDATE BEST LOG-LIKELIHOOD: -1387.259
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Iteration 100 / LogL: -1387.358 / Time: 0h:0m:4s (0h:0m:5s left)
Log-likelihood cutoff on original alignment: -1414.928
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.994
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Iteration 110 / LogL: -1387.357 / Time: 0h:0m:4s (0h:0m:5s left)
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BETTER TREE FOUND at iteration 112: -1387.259
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UPDATE BEST LOG-LIKELIHOOD: -1387.259
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UPDATE BEST LOG-LIKELIHOOD: -1387.259
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Iteration 150 / LogL: -1387.276 / Time: 0h:0m:5s (0h:0m:6s left)
Log-likelihood cutoff on original alignment: -1415.310
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UPDATE BEST LOG-LIKELIHOOD: -1387.259
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UPDATE BEST LOG-LIKELIHOOD: -1387.259
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Iteration 200 / LogL: -1387.357 / Time: 0h:0m:7s (0h:0m:3s left)
Log-likelihood cutoff on original alignment: -1415.310
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.996
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UPDATE BEST LOG-LIKELIHOOD: -1387.259
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Iteration 250 / LogL: -1387.261 / Time: 0h:0m:8s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -1415.310
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UPDATE BEST LOG-LIKELIHOOD: -1387.259
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Iteration 280 / LogL: -1387.288 / Time: 0h:0m:9s (0h:0m:1s left)
Optimizing NNI: done in 0.0103672 secs using 99.95% CPU
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Iteration 290 / LogL: -1387.308 / Time: 0h:0m:9s (0h:0m:0s left)
Optimizing NNI: done in 0.0120602 secs using 99.96% CPU
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Iteration 300 / LogL: -1387.314 / Time: 0h:0m:10s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -1415.310
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.996
Optimizing NNI: done in 0.016058 secs using 99.96% CPU
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Iteration 310 / LogL: -1387.550 / Time: 0h:0m:10s (0h:0m:3s left)
Optimizing NNI: done in 0.0229299 secs using 99.97% CPU
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TREE SEARCH COMPLETED AFTER 313 ITERATIONS / Time: 0h:0m:10s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.259
Optimal log-likelihood: -1387.255
Rate parameters: A-C: 0.32476 A-G: 2.22309 A-T: 2.10421 C-G: 1.15455 C-T: 3.22830 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.000
Gamma shape alpha: 1.322
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1387.255
Testing tree branches by SH-like aLRT with 1000 replicates...
Testing tree branches by local-BP test with 1000 replicates...
Testing tree branches by aBayes parametric test...
0.059 sec.
Creating bootstrap support values...
Split supports printed to NEXUS file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptoah5gdk/q2iqtreeufboot.splits.nex
Total tree length: 6.730
Total number of iterations: 313
CPU time used for tree search: 10.056 sec (0h:0m:10s)
Wall-clock time used for tree search: 9.939 sec (0h:0m:9s)
Total CPU time used: 10.705 sec (0h:0m:10s)
Total wall-clock time used: 10.595 sec (0h:0m:10s)
Computing bootstrap consensus tree...
Reading input file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptoah5gdk/q2iqtreeufboot.splits.nex...
20 taxa and 184 splits.
Consensus tree written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptoah5gdk/q2iqtreeufboot.contree
Reading input trees file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptoah5gdk/q2iqtreeufboot.contree
Log-likelihood of consensus tree: -1387.256
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptoah5gdk/q2iqtreeufboot.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptoah5gdk/q2iqtreeufboot.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptoah5gdk/q2iqtreeufboot.mldist
Ultrafast bootstrap approximation results written to:
Split support values: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptoah5gdk/q2iqtreeufboot.splits.nex
Consensus tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptoah5gdk/q2iqtreeufboot.contree
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptoah5gdk/q2iqtreeufboot.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptoah5gdk/q2iqtreeufboot.treefile -m "GTR{0.324755,2.22309,2.10421,1.15455,3.2283}+F{0.243216,0.181967,0.319196,0.255621}+I{3.25587e-07}+G4{1.32202}" --length 214
Date and Time: Wed Dec 21 19:11:42 2022
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -bb 1000 -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/edb27ebe-b918-4abb-9236-f52b22b3e93b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmptoah5gdk/q2iqtreeufboot -nt 1 -alrt 1000 -abayes -lbp 1000 -nstop 200 -pers 0.200000
Saved Phylogeny[Unrooted] to: iqt-nnisi-bootstrap-sbt-gtrig-tree.qza
Tip
If there is a need to reduce the impact of potential model
violations that occur during a UFBoot search, and / or would simply
like to be more rigorous, we can add the --p-bnni option to any of the
iqtree-ultrafast-bootstrap commands above.
Root the phylogeny¶
In order to make proper use of diversity metrics such as UniFrac, the phylogeny must be rooted. Typically an outgroup is chosen when rooting a tree. In general, phylogenetic inference tools using Maximum Likelihood often return an unrooted tree by default.
QIIME 2 provides a way to
mid-point root our
phylogeny. Other rooting options may be available in the future. For now, we’ll
root our bootstrap tree from iqtree-ultrafast-bootstrap like so:
qiime phylogeny midpoint-root \
--i-tree iqt-nnisi-bootstrap-sbt-gtrig-tree.qza \
--o-rooted-tree iqt-nnisi-bootstrap-sbt-gtrig-tree-rooted.qza
Tip
iTOL viewing Reminder. We can view our tree and its associated alignment via iTOL. All you need to do is upload the iqt-nnisi-bootstrap-sbt-gtrig-tree-rooted.qza tree file. Display the tree in Normal mode. Then drag and drop the masked-aligned-rep-seqs.qza file onto the visualization. Now you can view the phylogeny alongside the alignment.
Pipelines¶
Here we will outline the use of the phylogeny pipeline align-to-tree-mafft-fasttree
One advantage of pipelines is that they combine ordered sets of commonly used commands, into one condensed simple command. To keep these “convenience” pipelines easy to use, it is quite common to only expose a few options to the user. That is, most of the commands executed via pipelines are often configured to use default option settings. However, options that are deemed important enough for the user to consider setting, are made available. The options exposed via a given pipeline will largely depend upon what it is doing. Pipelines are also a great way for new users to get started, as it helps to lay a foundation of good practices in setting up standard operating procedures.
Rather than run one or more of the following QIIME 2 commands listed below:
qiime alignment mafft ...qiime alignment mask ...qiime phylogeny fasttree ...qiime phylogeny midpoint-root ...
We can make use of the pipeline align-to-tree-mafft-fasttree to automate the above four steps in one go. Here is the description taken from the pipeline help doc:
This pipeline will start by creating a sequence alignment using MAFFT, after which any alignment columns that are phylogenetically uninformative or ambiguously aligned will be removed (masked). The resulting masked alignment will be used to infer a phylogenetic tree and then subsequently rooted at its midpoint. Output files from each step of the pipeline will be saved. This includes both the unmasked and masked MAFFT alignment from q2-alignment methods, and both the rooted and unrooted phylogenies from q2-phylogeny methods.
This can all be accomplished by simply running the following:
qiime phylogeny align-to-tree-mafft-fasttree \
--i-sequences rep-seqs.qza \
--output-dir mafft-fasttree-output
Output artifacts:
Congratulations! You now know how to construct a phylogeny in QIIME 2!