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/2023.2/tutorials/phylogeny/rep-seqs.qza
Save as: rep-seqs.qza
wget \
-O "rep-seqs.qza" \
"https://data.qiime2.org/2023.2/tutorials/phylogeny/rep-seqs.qza"
curl -sL \
"https://data.qiime2.org/2023.2/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 7213 -N 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp7cak6z9z -n q2
Partition: 0 with name: No Name Provided
Base frequencies: 0.243 0.182 0.319 0.256
Inference[0]: Time 0.622816 CAT-based likelihood -1241.820508, best rearrangement setting 5
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -1388.324196 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp7cak6z9z/RAxML_result.q2
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -1388.324196 ....
Final GAMMA-based Score of best tree -1387.275934
Program execution info written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp7cak6z9z/RAxML_info.q2
Best-scoring ML tree written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp7cak6z9z/RAxML_bestTree.q2
Overall execution time: 1.267576 secs or 0.000352 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 7213 -N 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp7cak6z9z -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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplws5ec9y -n q2
Partition: 0 with name: No Name Provided
Base frequencies: 0.243 0.182 0.319 0.256
Inference[0]: Time 0.625690 CAT-based likelihood -1238.242991, best rearrangement setting 5
Inference[1]: Time 0.517689 CAT-based likelihood -1249.502284, best rearrangement setting 5
Inference[2]: Time 0.519315 CAT-based likelihood -1242.978035, best rearrangement setting 5
Inference[3]: Time 0.645904 CAT-based likelihood -1243.159855, best rearrangement setting 5
Inference[4]: Time 0.479491 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/tmplws5ec9y/RAxML_result.q2.RUN.0
Inference[1] final GAMMA-based Likelihood: -1392.813982 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplws5ec9y/RAxML_result.q2.RUN.1
Inference[2] final GAMMA-based Likelihood: -1388.073642 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplws5ec9y/RAxML_result.q2.RUN.2
Inference[3] final GAMMA-based Likelihood: -1387.945266 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplws5ec9y/RAxML_result.q2.RUN.3
Inference[4] final GAMMA-based Likelihood: -1387.557031 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplws5ec9y/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/tmplws5ec9y/RAxML_info.q2
Best-scoring ML tree written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplws5ec9y/RAxML_bestTree.q2
Overall execution time: 3.505929 secs or 0.000974 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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplws5ec9y -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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpj2u_vity -n q2bootstrap
Time for BS model parameter optimization 0.053394
Bootstrap[0]: Time 0.179124 seconds, bootstrap likelihood -1199.758796, best rearrangement setting 12
Bootstrap[1]: Time 0.122625 seconds, bootstrap likelihood -1344.229251, best rearrangement setting 6
Bootstrap[2]: Time 0.112755 seconds, bootstrap likelihood -1295.343000, best rearrangement setting 8
Bootstrap[3]: Time 0.097617 seconds, bootstrap likelihood -1273.768320, best rearrangement setting 8
Bootstrap[4]: Time 0.113642 seconds, bootstrap likelihood -1253.402952, best rearrangement setting 6
Bootstrap[5]: Time 0.119544 seconds, bootstrap likelihood -1260.866113, best rearrangement setting 10
Bootstrap[6]: Time 0.116670 seconds, bootstrap likelihood -1293.636299, best rearrangement setting 14
Bootstrap[7]: Time 0.108299 seconds, bootstrap likelihood -1227.178693, best rearrangement setting 6
Bootstrap[8]: Time 0.115202 seconds, bootstrap likelihood -1321.820787, best rearrangement setting 13
Bootstrap[9]: Time 0.125089 seconds, bootstrap likelihood -1147.233446, best rearrangement setting 6
Bootstrap[10]: Time 0.087919 seconds, bootstrap likelihood -1220.766493, best rearrangement setting 13
Bootstrap[11]: Time 0.125959 seconds, bootstrap likelihood -1200.006355, best rearrangement setting 8
Bootstrap[12]: Time 0.135210 seconds, bootstrap likelihood -1346.392834, best rearrangement setting 14
Bootstrap[13]: Time 0.105962 seconds, bootstrap likelihood -1301.111096, best rearrangement setting 14
Bootstrap[14]: Time 0.112084 seconds, bootstrap likelihood -1262.253559, best rearrangement setting 11
Bootstrap[15]: Time 0.119745 seconds, bootstrap likelihood -1215.017551, best rearrangement setting 14
Bootstrap[16]: Time 0.105517 seconds, bootstrap likelihood -1238.832009, best rearrangement setting 7
Bootstrap[17]: Time 0.102633 seconds, bootstrap likelihood -1393.989732, best rearrangement setting 12
Bootstrap[18]: Time 0.102263 seconds, bootstrap likelihood -1173.921002, best rearrangement setting 15
Bootstrap[19]: Time 0.101844 seconds, bootstrap likelihood -1185.726976, best rearrangement setting 11
Bootstrap[20]: Time 0.095009 seconds, bootstrap likelihood -1158.491940, best rearrangement setting 6
Bootstrap[21]: Time 0.091601 seconds, bootstrap likelihood -1154.664272, best rearrangement setting 11
Bootstrap[22]: Time 0.102770 seconds, bootstrap likelihood -1244.159837, best rearrangement setting 10
Bootstrap[23]: Time 0.121056 seconds, bootstrap likelihood -1211.171036, best rearrangement setting 15
Bootstrap[24]: Time 0.103395 seconds, bootstrap likelihood -1261.440677, best rearrangement setting 12
Bootstrap[25]: Time 0.104225 seconds, bootstrap likelihood -1331.836715, best rearrangement setting 15
Bootstrap[26]: Time 0.106413 seconds, bootstrap likelihood -1129.144509, best rearrangement setting 5
Bootstrap[27]: Time 0.130498 seconds, bootstrap likelihood -1226.624056, best rearrangement setting 7
Bootstrap[28]: Time 0.128435 seconds, bootstrap likelihood -1221.046176, best rearrangement setting 12
Bootstrap[29]: Time 0.086563 seconds, bootstrap likelihood -1211.791204, best rearrangement setting 14
Bootstrap[30]: Time 0.108088 seconds, bootstrap likelihood -1389.442380, best rearrangement setting 5
Bootstrap[31]: Time 0.110534 seconds, bootstrap likelihood -1303.638592, best rearrangement setting 12
Bootstrap[32]: Time 0.117676 seconds, bootstrap likelihood -1172.859456, best rearrangement setting 12
Bootstrap[33]: Time 0.103689 seconds, bootstrap likelihood -1244.617135, best rearrangement setting 9
Bootstrap[34]: Time 0.099311 seconds, bootstrap likelihood -1211.871717, best rearrangement setting 15
Bootstrap[35]: Time 0.122700 seconds, bootstrap likelihood -1299.862912, best rearrangement setting 5
Bootstrap[36]: Time 0.095766 seconds, bootstrap likelihood -1141.967505, best rearrangement setting 5
Bootstrap[37]: Time 0.118537 seconds, bootstrap likelihood -1283.923198, best rearrangement setting 12
Bootstrap[38]: Time 0.100050 seconds, bootstrap likelihood -1304.250946, best rearrangement setting 5
Bootstrap[39]: Time 0.091315 seconds, bootstrap likelihood -1407.084376, best rearrangement setting 15
Bootstrap[40]: Time 0.108386 seconds, bootstrap likelihood -1277.946299, best rearrangement setting 13
Bootstrap[41]: Time 0.106808 seconds, bootstrap likelihood -1279.006200, best rearrangement setting 7
Bootstrap[42]: Time 0.098356 seconds, bootstrap likelihood -1160.274606, best rearrangement setting 6
Bootstrap[43]: Time 0.124385 seconds, bootstrap likelihood -1216.079259, best rearrangement setting 14
Bootstrap[44]: Time 0.100075 seconds, bootstrap likelihood -1382.278311, best rearrangement setting 8
Bootstrap[45]: Time 0.112279 seconds, bootstrap likelihood -1099.004439, best rearrangement setting 11
Bootstrap[46]: Time 0.088524 seconds, bootstrap likelihood -1296.527478, best rearrangement setting 8
Bootstrap[47]: Time 0.127867 seconds, bootstrap likelihood -1291.322658, best rearrangement setting 9
Bootstrap[48]: Time 0.085969 seconds, bootstrap likelihood -1161.908080, best rearrangement setting 6
Bootstrap[49]: Time 0.114899 seconds, bootstrap likelihood -1257.348428, best rearrangement setting 13
Bootstrap[50]: Time 0.131340 seconds, bootstrap likelihood -1309.422533, best rearrangement setting 13
Bootstrap[51]: Time 0.096917 seconds, bootstrap likelihood -1197.633097, best rearrangement setting 11
Bootstrap[52]: Time 0.113582 seconds, bootstrap likelihood -1347.123005, best rearrangement setting 8
Bootstrap[53]: Time 0.097969 seconds, bootstrap likelihood -1234.934890, best rearrangement setting 14
Bootstrap[54]: Time 0.108468 seconds, bootstrap likelihood -1227.092434, best rearrangement setting 6
Bootstrap[55]: Time 0.112585 seconds, bootstrap likelihood -1280.635747, best rearrangement setting 7
Bootstrap[56]: Time 0.096670 seconds, bootstrap likelihood -1225.911449, best rearrangement setting 6
Bootstrap[57]: Time 0.092045 seconds, bootstrap likelihood -1236.213347, best rearrangement setting 11
Bootstrap[58]: Time 0.131978 seconds, bootstrap likelihood -1393.245723, best rearrangement setting 14
Bootstrap[59]: Time 0.104433 seconds, bootstrap likelihood -1212.039371, best rearrangement setting 6
Bootstrap[60]: Time 0.092219 seconds, bootstrap likelihood -1248.692011, best rearrangement setting 10
Bootstrap[61]: Time 0.106408 seconds, bootstrap likelihood -1172.820979, best rearrangement setting 13
Bootstrap[62]: Time 0.122527 seconds, bootstrap likelihood -1126.745788, best rearrangement setting 14
Bootstrap[63]: Time 0.096518 seconds, bootstrap likelihood -1267.434444, best rearrangement setting 12
Bootstrap[64]: Time 0.098067 seconds, bootstrap likelihood -1340.680748, best rearrangement setting 5
Bootstrap[65]: Time 0.095061 seconds, bootstrap likelihood -1072.671059, best rearrangement setting 5
Bootstrap[66]: Time 0.119346 seconds, bootstrap likelihood -1234.294838, best rearrangement setting 8
Bootstrap[67]: Time 0.116135 seconds, bootstrap likelihood -1109.249439, best rearrangement setting 15
Bootstrap[68]: Time 0.091674 seconds, bootstrap likelihood -1314.493588, best rearrangement setting 8
Bootstrap[69]: Time 0.098177 seconds, bootstrap likelihood -1173.850035, best rearrangement setting 13
Bootstrap[70]: Time 0.101051 seconds, bootstrap likelihood -1231.066465, best rearrangement setting 10
Bootstrap[71]: Time 0.099261 seconds, bootstrap likelihood -1146.861379, best rearrangement setting 9
Bootstrap[72]: Time 0.085845 seconds, bootstrap likelihood -1148.753369, best rearrangement setting 8
Bootstrap[73]: Time 0.102158 seconds, bootstrap likelihood -1333.374056, best rearrangement setting 9
Bootstrap[74]: Time 0.089028 seconds, bootstrap likelihood -1259.382378, best rearrangement setting 5
Bootstrap[75]: Time 0.096212 seconds, bootstrap likelihood -1319.944496, best rearrangement setting 6
Bootstrap[76]: Time 0.108121 seconds, bootstrap likelihood -1309.042165, best rearrangement setting 14
Bootstrap[77]: Time 0.130930 seconds, bootstrap likelihood -1232.061289, best rearrangement setting 8
Bootstrap[78]: Time 0.109021 seconds, bootstrap likelihood -1261.333984, best rearrangement setting 9
Bootstrap[79]: Time 0.107155 seconds, bootstrap likelihood -1194.644341, best rearrangement setting 13
Bootstrap[80]: Time 0.098712 seconds, bootstrap likelihood -1214.037389, best rearrangement setting 9
Bootstrap[81]: Time 0.106495 seconds, bootstrap likelihood -1224.527657, best rearrangement setting 8
Bootstrap[82]: Time 0.124815 seconds, bootstrap likelihood -1241.464826, best rearrangement setting 11
Bootstrap[83]: Time 0.096129 seconds, bootstrap likelihood -1230.730558, best rearrangement setting 6
Bootstrap[84]: Time 0.110782 seconds, bootstrap likelihood -1219.034592, best rearrangement setting 10
Bootstrap[85]: Time 0.107769 seconds, bootstrap likelihood -1280.071994, best rearrangement setting 8
Bootstrap[86]: Time 0.090461 seconds, bootstrap likelihood -1444.747777, best rearrangement setting 9
Bootstrap[87]: Time 0.092704 seconds, bootstrap likelihood -1245.890035, best rearrangement setting 14
Bootstrap[88]: Time 0.107169 seconds, bootstrap likelihood -1287.832766, best rearrangement setting 7
Bootstrap[89]: Time 0.100058 seconds, bootstrap likelihood -1325.245976, best rearrangement setting 5
Bootstrap[90]: Time 0.112041 seconds, bootstrap likelihood -1227.883697, best rearrangement setting 5
Bootstrap[91]: Time 0.112226 seconds, bootstrap likelihood -1273.489392, best rearrangement setting 8
Bootstrap[92]: Time 0.045621 seconds, bootstrap likelihood -1234.725870, best rearrangement setting 7
Bootstrap[93]: Time 0.117121 seconds, bootstrap likelihood -1235.733064, best rearrangement setting 11
Bootstrap[94]: Time 0.092259 seconds, bootstrap likelihood -1204.319488, best rearrangement setting 15
Bootstrap[95]: Time 0.093455 seconds, bootstrap likelihood -1183.328582, best rearrangement setting 11
Bootstrap[96]: Time 0.106680 seconds, bootstrap likelihood -1196.298898, best rearrangement setting 13
Bootstrap[97]: Time 0.115360 seconds, bootstrap likelihood -1339.251746, best rearrangement setting 12
Bootstrap[98]: Time 0.048037 seconds, bootstrap likelihood -1404.363552, best rearrangement setting 7
Bootstrap[99]: Time 0.058074 seconds, bootstrap likelihood -1270.157811, best rearrangement setting 7
Overall Time for 100 Rapid Bootstraps 10.615300 seconds
Average Time per Rapid Bootstrap 0.106153 seconds
Starting ML Search ...
Fast ML optimization finished
Fast ML search Time: 4.195703 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: 2.124833 seconds
Thorough ML search Time: 0.544509 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 6.869633 secs or 0.001908 hours
Combined Bootstrap and ML search took 17.485121 secs or 0.004857 hours
Drawing Bootstrap Support Values on best-scoring ML tree ...
Found 1 tree in File /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpj2u_vity/RAxML_bestTree.q2bootstrap
Found 1 tree in File /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpj2u_vity/RAxML_bestTree.q2bootstrap
Program execution info written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpj2u_vity/RAxML_info.q2bootstrap
All 100 bootstrapped trees written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpj2u_vity/RAxML_bootstrap.q2bootstrap
Best-scoring ML tree written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpj2u_vity/RAxML_bestTree.q2bootstrap
Best-scoring ML tree with support values written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpj2u_vity/RAxML_bipartitions.q2bootstrap
Best-scoring ML tree with support values as branch labels written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpj2u_vity/RAxML_bipartitionsBranchLabels.q2bootstrap
Overall execution time for full ML analysis: 17.498452 secs or 0.004861 hours or 0.000203 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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpj2u_vity -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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp0vk50h87/q2iqtree -nt 1
Seed: 642161 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Mar 2 14:33:56 2023
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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000221014 secs using 84.16% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000473976 secs using 77.85% 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 84.95% 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)... 0.003 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 0.0306759 secs using 98.78% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1390.629
Optimal log-likelihood: -1389.812
Rate parameters: A-C: 0.31763 A-G: 2.16791 A-T: 2.02305 C-G: 1.12985 C-T: 3.04155 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.035
Gamma shape alpha: 1.407
Parameters optimization took 1 rounds (0.008 sec)
Time for fast ML tree search: 0.076 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 1405.417 45 2900.833 2925.476 3052.302
2 GTR+F+I 1403.836 46 2899.673 2925.565 3054.508
3 GTR+F+G4 1388.332 46 2868.664 2894.556 3023.499
4 GTR+F+I+G4 1388.709 47 2871.418 2898.598 3029.619
5 GTR+F+R2 1382.567 47 2859.134 2886.314 3017.335
6 GTR+F+R3 1382.606 49 2863.212 2893.091 3028.145
14 GTR+F+I+I+R2 1382.709 48 2861.417 2889.926 3022.984
15 GTR+F+I+I+R3 1382.677 50 2865.355 2896.643 3033.654
25 SYM+G4 1388.450 43 2862.899 2885.158 3007.636
27 SYM+R2 1384.040 44 2856.081 2879.513 3004.184
36 SYM+I+I+R2 1384.179 45 2858.358 2883.001 3009.827
47 TVM+F+G4 1389.411 45 2868.823 2893.466 3020.292
49 TVM+F+R2 1384.290 46 2860.581 2886.473 3015.416
58 TVM+F+I+I+R2 1384.288 47 2862.576 2889.756 3020.777
69 TVMe+G4 1388.431 42 2860.861 2881.984 3002.232
71 TVMe+R2 1384.070 43 2854.141 2876.400 2998.878
80 TVMe+I+I+R2 1384.207 44 2856.414 2879.846 3004.517
91 TIM3+F+G4 1392.277 44 2872.555 2895.987 3020.658
93 TIM3+F+R2 1385.911 45 2861.822 2886.465 3013.291
102 TIM3+F+I+I+R2 1386.045 46 2864.090 2889.982 3018.925
113 TIM3e+G4 1391.664 41 2865.328 2885.351 3003.333
115 TIM3e+R2 1386.836 42 2857.673 2878.796 2999.044
124 TIM3e+I+I+R2 1386.991 43 2859.982 2882.241 3004.719
135 TIM2+F+G4 1395.142 44 2878.284 2901.716 3026.387
137 TIM2+F+R2 1388.245 45 2866.489 2891.132 3017.958
146 TIM2+F+I+I+R2 1388.352 46 2868.704 2894.596 3023.539
157 TIM2e+G4 1398.833 41 2879.665 2899.688 3017.670
159 TIM2e+R2 1393.046 42 2870.092 2891.214 3011.463
168 TIM2e+I+I+R2 1393.119 43 2872.238 2894.497 3016.975
179 TIM+F+G4 1391.818 44 2871.637 2895.069 3019.740
181 TIM+F+R2 1385.495 45 2860.989 2885.632 3012.458
190 TIM+F+I+I+R2 1385.586 46 2863.173 2889.065 3018.008
201 TIMe+G4 1396.053 41 2874.107 2894.130 3012.112
203 TIMe+R2 1390.516 42 2865.031 2886.154 3006.402
212 TIMe+I+I+R2 1390.601 43 2867.202 2889.461 3011.939
223 TPM3u+F+G4 1393.267 43 2872.534 2894.793 3017.271
225 TPM3u+F+R2 1387.637 44 2863.275 2886.707 3011.378
234 TPM3u+F+I+I+R2 1387.756 45 2865.513 2890.156 3016.982
245 TPM3+G4 1391.670 40 2863.341 2882.300 2997.980
247 TPM3+R2 1386.891 41 2855.783 2875.806 2993.788
256 TPM3+I+I+R2 1387.026 42 2858.051 2879.174 2999.422
267 TPM2u+F+G4 1396.124 43 2878.248 2900.506 3022.985
269 TPM2u+F+R2 1389.934 44 2867.868 2891.300 3015.971
278 TPM2u+F+I+I+R2 1389.966 45 2869.932 2894.575 3021.401
289 TPM2+G4 1398.849 40 2877.698 2896.657 3012.337
291 TPM2+R2 1393.099 41 2868.197 2888.220 3006.202
300 TPM2+I+I+R2 1393.154 42 2870.308 2891.431 3011.679
311 K3Pu+F+G4 1392.998 43 2871.995 2894.254 3016.732
313 K3Pu+F+R2 1387.256 44 2862.512 2885.943 3010.614
322 K3Pu+F+I+I+R2 1387.276 45 2864.551 2889.194 3016.020
333 K3P+G4 1396.053 40 2872.105 2891.065 3006.744
335 K3P+R2 1390.569 41 2863.137 2883.161 3001.142
344 K3P+I+I+R2 1390.686 42 2865.373 2886.496 3006.744
355 TN+F+G4 1395.494 43 2876.988 2899.247 3021.725
357 TN+F+R2 1388.629 44 2865.258 2888.689 3013.360
366 TN+F+I+I+R2 1388.742 45 2867.483 2892.126 3018.952
377 TNe+G4 1398.835 40 2877.670 2896.630 3012.309
379 TNe+R2 1393.043 41 2868.085 2888.109 3006.091
388 TNe+I+I+R2 1393.116 42 2870.233 2891.356 3011.604
399 HKY+F+G4 1396.493 42 2876.986 2898.109 3018.357
401 HKY+F+R2 1390.329 43 2866.658 2888.917 3011.395
410 HKY+F+I+I+R2 1390.362 44 2868.725 2892.157 3016.828
421 K2P+G4 1398.849 39 2875.699 2893.630 3006.972
423 K2P+R2 1393.099 40 2866.197 2885.157 3000.836
432 K2P+I+I+R2 1393.153 41 2868.306 2888.330 3006.311
443 F81+F+G4 1406.493 41 2894.987 2915.010 3032.992
445 F81+F+R2 1401.182 42 2886.363 2907.486 3027.734
454 F81+F+I+I+R2 1401.268 43 2888.536 2910.795 3033.273
465 JC+G4 1408.772 38 2893.544 2910.481 3021.451
467 JC+R2 1403.900 39 2885.801 2903.732 3017.074
476 JC+I+I+R2 1403.935 40 2887.870 2906.829 3022.509
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/tmp0vk50h87/q2iqtree.model.gz
CPU time for ModelFinder: 1.446 seconds (0h:0m:1s)
Wall-clock time for ModelFinder: 1.491 seconds (0h:0m:1s)
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1386.891
Optimal log-likelihood: -1386.887
Rate parameters: A-C: 0.39145 A-G: 1.51426 A-T: 1.00000 C-G: 0.39145 C-T: 1.51426 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.718,0.396) (0.282,2.538)
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 98.11% CPU
Computing ML distances took 0.000935 sec (of wall-clock time) 0.000893 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.48363e-05 secs using 91.18% CPU
Constructing RapidNJ tree: done in 0.000118971 secs using 145.4% CPU
Computing RapidNJ tree took 0.000273 sec (of wall-clock time) 0.000294 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.863
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.091 second
Computing log-likelihood of 98 initial trees ... 0.087 seconds
Current best score: -1386.887
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00605202 secs using 197.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.310
Optimizing NNI: done in 0.012989 secs using 99.93% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.308
Optimizing NNI: done in 0.012918 secs using 99.97% CPU
Optimizing NNI: done in 0.0126512 secs using 99.91% CPU
Optimizing NNI: done in 0.0118029 secs using 99.93% CPU
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Optimizing NNI: done in 0.011586 secs using 99.95% CPU
Optimizing NNI: done in 0.0116122 secs using 99.94% CPU
Iteration 10 / LogL: -1385.331 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0115159 secs using 99.94% CPU
Optimizing NNI: done in 0.0115991 secs using 99.96% CPU
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Optimizing NNI: done in 0.0115738 secs using 99.95% CPU
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Optimizing NNI: done in 0.011523 secs using 99.96% CPU
Optimizing NNI: done in 0.0114949 secs using 99.95% CPU
Optimizing NNI: done in 0.0117898 secs using 99.95% CPU
Optimizing NNI: done in 0.011858 secs using 99.95% CPU
Optimizing NNI: done in 0.0118248 secs using 99.94% CPU
Iteration 20 / LogL: -1385.341 / Time: 0h:0m:0s
Finish initializing candidate tree set (1)
Current best tree score: -1385.308 / CPU time: 0.425
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0135901 secs using 99.69% CPU
Optimizing NNI: done in 0.0160692 secs using 99.87% CPU
Optimizing NNI: done in 0.00952101 secs using 99.94% CPU
Optimizing NNI: done in 0.0155799 secs using 99.96% CPU
Optimizing NNI: done in 0.0141809 secs using 99.94% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.307
Optimizing NNI: done in 0.0140789 secs using 99.72% CPU
Optimizing NNI: done in 0.016953 secs using 99.86% CPU
Optimizing NNI: done in 0.011086 secs using 99.94% CPU
Optimizing NNI: done in 0.013582 secs using 99.94% CPU
Optimizing NNI: done in 0.01632 secs using 99.94% CPU
Iteration 30 / LogL: -1385.379 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.0118489 secs using 99.96% CPU
Optimizing NNI: done in 0.017791 secs using 99.93% CPU
Optimizing NNI: done in 0.01069 secs using 99.94% CPU
Optimizing NNI: done in 0.0192549 secs using 99.94% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.307
Optimizing NNI: done in 0.0210571 secs using 99.75% CPU
Optimizing NNI: done in 0.020108 secs using 99.91% CPU
Optimizing NNI: done in 0.0154989 secs using 99.94% CPU
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Optimizing NNI: done in 0.012043 secs using 99.95% CPU
Optimizing NNI: done in 0.0142651 secs using 99.94% CPU
Iteration 40 / LogL: -1385.708 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.0116959 secs using 99.95% CPU
Optimizing NNI: done in 0.0168109 secs using 99.96% CPU
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Optimizing NNI: done in 0.0159822 secs using 99.96% CPU
Iteration 50 / LogL: -1385.706 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.013207 secs using 99.96% CPU
Optimizing NNI: done in 0.0256581 secs using 99.96% CPU
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Iteration 60 / LogL: -1394.169 / Time: 0h:0m:1s (0h:0m:0s left)
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Iteration 70 / LogL: -1385.628 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.019968 secs using 99.91% CPU
Optimizing NNI: done in 0.0132611 secs using 99.96% CPU
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Optimizing NNI: done in 0.006984 secs using 99.91% CPU
Iteration 80 / LogL: -1385.501 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0123069 secs using 99.96% CPU
Optimizing NNI: done in 0.0173051 secs using 99.94% CPU
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Optimizing NNI: done in 0.0193498 secs using 99.95% CPU
Iteration 90 / LogL: -1385.942 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.01068 secs using 99.93% CPU
Optimizing NNI: done in 0.0114112 secs using 99.93% CPU
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Optimizing NNI: done in 0.0120461 secs using 99.96% CPU
Iteration 100 / LogL: -1385.886 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00999403 secs using 98.53% CPU
Optimizing NNI: done in 0.0136721 secs using 99.94% 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: -1385.307
Optimal log-likelihood: -1385.305
Rate parameters: A-C: 0.39675 A-G: 1.57533 A-T: 1.00000 C-G: 0.39675 C-T: 1.57533 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.722,0.401) (0.278,2.554)
Parameters optimization took 1 rounds (0.003 sec)
BEST SCORE FOUND : -1385.305
Total tree length: 6.873
Total number of iterations: 102
CPU time used for tree search: 1.907 sec (0h:0m:1s)
Wall-clock time used for tree search: 1.727 sec (0h:0m:1s)
Total CPU time used: 1.936 sec (0h:0m:1s)
Total wall-clock time used: 1.751 sec (0h:0m:1s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp0vk50h87/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp0vk50h87/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp0vk50h87/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp0vk50h87/q2iqtree.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp0vk50h87/q2iqtree.treefile -m "TPM3{0.396755,1.57533}+FQ+R2{0.72166,0.400643,0.27834,2.55397}" --length 214
Date and Time: Thu Mar 2 14:33:59 2023
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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp0vk50h87/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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpw5yzxe4s/q2iqtree -nt 1
Seed: 667629 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Mar 2 14:34:09 2023
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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000256062 secs using 81.62% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000480175 secs using 77.47% 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 2.21729e-05 secs using 85.69% 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 7.20024e-05 secs using 76.39% 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, 1.262 / LogL: -1392.811
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.008, 1.354 / LogL: -1393.087
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.009, 1.365 / LogL: -1393.159
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.009, 1.361 / LogL: -1393.149
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.008, 1.359 / LogL: -1393.112
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.009, 1.362 / LogL: -1393.138
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.009, 1.364 / LogL: -1393.160
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.008, 1.358 / LogL: -1393.101
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.008, 1.358 / LogL: -1393.108
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.008, 1.360 / LogL: -1393.118
Optimal pinv,alpha: 0.000, 1.262 / LogL: -1392.811
Parameters optimization took 0.505 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0015471 secs using 94.37% CPU
Computing ML distances took 0.001662 sec (of wall-clock time) 0.001532 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 7.29561e-05 secs using 84.98% CPU
Constructing RapidNJ tree: done in 0.000110865 secs using 140.7% CPU
Computing RapidNJ tree took 0.000272 sec (of wall-clock time) 0.000284 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.724
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.106 second
Computing log-likelihood of 98 initial trees ... 0.132 seconds
Current best score: -1392.724
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.021138 secs using 99.42% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.357
Optimizing NNI: done in 0.0169702 secs using 98.38% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1387.267
Optimizing NNI: done in 0.0148349 secs using 98.41% CPU
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Iteration 10 / LogL: -1387.280 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0276241 secs using 98% CPU
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Iteration 20 / LogL: -1387.280 / Time: 0h:0m:1s
Finish initializing candidate tree set (2)
Current best tree score: -1387.267 / CPU time: 0.708
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.015882 secs using 98.65% CPU
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Optimizing NNI: done in 0.00803399 secs using 99.09% CPU
Optimizing NNI: done in 0.0433309 secs using 98.73% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.265
Iteration 30 / LogL: -1387.265 / Time: 0h:0m:1s (0h:0m:3s left)
Optimizing NNI: done in 0.0276811 secs using 98.9% CPU
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Iteration 40 / LogL: -1387.349 / Time: 0h:0m:1s (0h:0m:2s left)
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BETTER TREE FOUND at iteration 50: -1387.260
Iteration 50 / LogL: -1387.260 / Time: 0h:0m:2s (0h:0m:4s left)
Optimizing NNI: done in 0.0278339 secs using 99.8% CPU
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Iteration 60 / LogL: -1387.349 / Time: 0h:0m:2s (0h:0m:3s left)
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 65: -1387.177
Optimizing NNI: done in 0.0167949 secs using 99.73% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.168
Optimizing NNI: done in 0.026176 secs using 99.74% CPU
Optimizing NNI: done in 0.018501 secs using 99.96% CPU
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Iteration 70 / LogL: -1387.168 / Time: 0h:0m:2s (0h:0m:3s left)
Optimizing NNI: done in 0.0315819 secs using 99.9% CPU
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Iteration 80 / LogL: -1387.400 / Time: 0h:0m:3s (0h:0m:3s left)
Optimizing NNI: done in 0.0254049 secs using 99.13% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.168
Optimizing NNI: done in 0.0460179 secs using 99.79% CPU
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Iteration 90 / LogL: -1387.488 / Time: 0h:0m:3s (0h:0m:2s left)
Optimizing NNI: done in 0.046752 secs using 99.96% CPU
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Iteration 100 / LogL: -1387.383 / Time: 0h:0m:3s (0h:0m:2s left)
Optimizing NNI: done in 0.0254309 secs using 99.96% CPU
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Iteration 110 / LogL: -1387.190 / Time: 0h:0m:4s (0h:0m:2s left)
Optimizing NNI: done in 0.0198419 secs using 99.75% CPU
Optimizing NNI: done in 0.0455379 secs using 99.93% CPU
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Iteration 120 / LogL: -1387.177 / Time: 0h:0m:4s (0h:0m:1s left)
Optimizing NNI: done in 0.018836 secs using 99.96% CPU
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Iteration 130 / LogL: -1387.168 / Time: 0h:0m:4s (0h:0m:1s left)
Optimizing NNI: done in 0.0250089 secs using 99.96% CPU
Optimizing NNI: done in 0.0234351 secs using 99.97% CPU
Optimizing NNI: done in 0.036211 secs using 99.96% CPU
Optimizing NNI: done in 0.0247419 secs using 99.97% CPU
Optimizing NNI: done in 0.015034 secs using 99.95% CPU
Optimizing NNI: done in 0.029619 secs using 99.97% CPU
Optimizing NNI: done in 0.0121431 secs using 99.96% CPU
Optimizing NNI: done in 0.0401671 secs using 99.96% CPU
Optimizing NNI: done in 0.013624 secs using 99.97% CPU
Optimizing NNI: done in 0.0412219 secs using 99.96% CPU
Iteration 140 / LogL: -1387.211 / Time: 0h:0m:4s (0h:0m:0s left)
Optimizing NNI: done in 0.0295231 secs using 99.96% CPU
Optimizing NNI: done in 0.0308831 secs using 99.96% CPU
Optimizing NNI: done in 0.0294318 secs using 99.97% CPU
Optimizing NNI: done in 0.027931 secs using 99.96% CPU
Optimizing NNI: done in 0.023977 secs using 99.96% CPU
Optimizing NNI: done in 0.034765 secs using 99.97% CPU
Optimizing NNI: done in 0.00428605 secs using 99.95% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.168
Optimizing NNI: done in 0.018889 secs using 99.46% CPU
Optimizing NNI: done in 0.0377331 secs using 99.77% CPU
Optimizing NNI: done in 0.0500591 secs using 99.9% CPU
Iteration 150 / LogL: -1387.189 / Time: 0h:0m:5s (0h:0m:0s left)
Optimizing NNI: done in 0.0238528 secs using 99.96% CPU
Optimizing NNI: done in 0.0299902 secs using 99.95% CPU
Optimizing NNI: done in 0.0146902 secs using 99.96% CPU
Optimizing NNI: done in 0.036438 secs using 99.95% CPU
Optimizing NNI: done in 0.0374019 secs using 99.97% CPU
Optimizing NNI: done in 0.0323911 secs using 99.53% CPU
Optimizing NNI: done in 0.026449 secs using 99.97% CPU
Optimizing NNI: done in 0.0165892 secs using 99.97% CPU
Optimizing NNI: done in 0.0390809 secs using 99.88% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.168
Optimizing NNI: done in 0.039396 secs using 99.83% CPU
Iteration 160 / LogL: -1387.168 / Time: 0h:0m:5s (0h:0m:0s left)
Optimizing NNI: done in 0.029084 secs using 99.97% CPU
Optimizing NNI: done in 0.0394139 secs using 99.96% CPU
Optimizing NNI: done in 0.018914 secs using 99.96% CPU
Optimizing NNI: done in 0.0278599 secs using 99.84% CPU
Optimizing NNI: done in 0.0280039 secs using 99.96% CPU
Optimizing NNI: done in 0.0249181 secs using 99.96% CPU
TREE SEARCH COMPLETED AFTER 166 ITERATIONS / Time: 0h:0m:5s
--------------------------------------------------------------------
| 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: 0.34928 A-G: 2.33362 A-T: 2.15522 C-G: 1.24158 C-T: 3.23718 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: 1.285
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1387.167
Total tree length: 7.602
Total number of iterations: 166
CPU time used for tree search: 5.132 sec (0h:0m:5s)
Wall-clock time used for tree search: 5.089 sec (0h:0m:5s)
Total CPU time used: 5.655 sec (0h:0m:5s)
Total wall-clock time used: 5.617 sec (0h:0m:5s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpw5yzxe4s/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpw5yzxe4s/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpw5yzxe4s/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpw5yzxe4s/q2iqtree.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpw5yzxe4s/q2iqtree.treefile -m "GTR{0.349284,2.33362,2.15522,1.24158,3.23718}+F{0.243216,0.181967,0.319196,0.255621}+I{2.88757e-07}+G4{1.28499}" --length 214
Date and Time: Thu Mar 2 14:34:15 2023
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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpw5yzxe4s/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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpqkm9kovz/q2iqtree -nt 1 -fast
Seed: 17834 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Mar 2 14:34:25 2023
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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000272989 secs using 75.46% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000484943 secs using 76.3% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Analyzing sequences: done in 1.81198e-05 secs using 88.3% CPU
Checking for duplicate sequences: done in 6.8903e-05 secs using 76.92% CPU
---> START RUN NUMBER 1 (seed: 17834)
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: -1491.63
2. Current log-likelihood: -1402.01
3. Current log-likelihood: -1396.79
4. Current log-likelihood: -1395.39
5. Current log-likelihood: -1394.65
Optimal log-likelihood: -1394.08
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 0.00138903 secs using 96.9% CPU
Computing ML distances took 0.001484 sec (of wall-clock time) 0.001411 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.50747e-05 secs using 90.79% CPU
Constructing RapidNJ tree: done in 0.000149965 secs using 142% CPU
Computing RapidNJ tree took 0.000297 sec (of wall-clock time) 0.000352 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 0.020844 secs using 192% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.217
Optimizing NNI: done in 0.033273 secs using 191.6% CPU
BETTER TREE FOUND at iteration 2: -1388.188
Finish initializing candidate tree set (4)
Current best tree score: -1388.188 / CPU time: 0.065
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: 2.31002 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: 0.124 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.065 sec (0h:0m:0s)
Total CPU time used: 0.235 sec (0h:0m:0s)
Total wall-clock time used: 0.149 sec (0h:0m:0s)
---> START RUN NUMBER 2 (seed: 18834)
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 0.00133181 secs using 187.8% CPU
Computing ML distances took 0.001417 sec (of wall-clock time) 0.002636 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 7.29561e-05 secs using 68.53% CPU
Constructing RapidNJ tree: done in 0.000138044 secs using 150% CPU
Computing RapidNJ tree took 0.000314 sec (of wall-clock time) 0.000327 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 0.0208061 secs using 191.3% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.217
Optimizing NNI: done in 0.0337348 secs using 190.7% CPU
BETTER TREE FOUND at iteration 2: -1388.188
Finish initializing candidate tree set (4)
Current best tree score: -1388.188 / CPU time: 0.065
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: 0.124 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.065 sec (0h:0m:0s)
Total CPU time used: 0.281 sec (0h:0m:0s)
Total wall-clock time used: 0.149 sec (0h:0m:0s)
---> START RUN NUMBER 3 (seed: 19834)
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: -1492.389
2. Current log-likelihood: -1401.890
3. Current log-likelihood: -1396.534
4. Current log-likelihood: -1395.117
5. Current log-likelihood: -1394.389
Optimal log-likelihood: -1393.814
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 (0.040 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00131798 secs using 186.8% CPU
Computing ML distances took 0.001405 sec (of wall-clock time) 0.002601 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 4.69685e-05 secs using 83.03% CPU
Constructing RapidNJ tree: done in 0.000108957 secs using 115.6% CPU
Computing RapidNJ tree took 0.000231 sec (of wall-clock time) 0.000218 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 0.0206349 secs using 191.5% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.213
Optimizing NNI: done in 0.0206361 secs using 191.4% CPU
Finish initializing candidate tree set (3)
Current best tree score: -1388.213 / 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: -1388.213
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: 0.095 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.050 sec (0h:0m:0s)
Total CPU time used: 0.253 sec (0h:0m:0s)
Total wall-clock time used: 0.134 sec (0h:0m:0s)
---> START RUN NUMBER 4 (seed: 20834)
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: -1496.015
2. Current log-likelihood: -1403.630
3. Current log-likelihood: -1398.533
4. Current log-likelihood: -1397.077
5. Current log-likelihood: -1396.256
6. Current log-likelihood: -1395.746
Optimal log-likelihood: -1395.367
Rate parameters: A-C: 0.23661 A-G: 2.05004 A-T: 1.94884 C-G: 1.06761 C-T: 2.81214 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.021
Gamma shape alpha: 1.337
Parameters optimization took 6 rounds (0.042 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00146914 secs using 191.7% CPU
Computing ML distances took 0.001586 sec (of wall-clock time) 0.003014 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 6.50883e-05 secs using 79.89% CPU
Constructing RapidNJ tree: done in 0.000104189 secs using 126.7% CPU
Computing RapidNJ tree took 0.000267 sec (of wall-clock time) 0.000255 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.724
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.020736 secs using 190.8% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.981
Optimizing NNI: done in 0.0281549 secs using 191.6% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.981 / CPU time: 0.061
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: -1387.981
2. Current log-likelihood: -1387.812
3. Current log-likelihood: -1387.686
4. Current log-likelihood: -1387.592
5. Current log-likelihood: -1387.521
6. Current log-likelihood: -1387.466
Optimal log-likelihood: -1387.423
Rate parameters: A-C: 0.32761 A-G: 2.25268 A-T: 2.12562 C-G: 1.16855 C-T: 3.25523 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: 1.358
Parameters optimization took 6 rounds (0.024 sec)
BEST SCORE FOUND : -1387.423
Total tree length: 6.701
Total number of iterations: 2
CPU time used for tree search: 0.117 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.061 sec (0h:0m:0s)
Total CPU time used: 0.275 sec (0h:0m:0s)
Total wall-clock time used: 0.145 sec (0h:0m:0s)
---> START RUN NUMBER 5 (seed: 21834)
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: -1492.491
2. Current log-likelihood: -1404.606
3. Current log-likelihood: -1399.220
4. Current log-likelihood: -1397.821
5. Current log-likelihood: -1397.063
Optimal log-likelihood: -1396.484
Rate parameters: A-C: 0.24153 A-G: 2.03298 A-T: 1.94373 C-G: 1.02159 C-T: 2.79340 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: 1.438
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 0.00127578 secs using 192.9% CPU
Computing ML distances took 0.001359 sec (of wall-clock time) 0.002596 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 9.10759e-05 secs using 125.2% CPU
Computing RapidNJ tree took 0.000202 sec (of wall-clock time) 0.000207 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.204
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.020267 secs using 192.2% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.198
Optimizing NNI: done in 0.0304232 secs using 191.2% CPU
UPDATE BEST LOG-LIKELIHOOD: -1388.190
Finish initializing candidate tree set (3)
Current best tree score: -1388.190 / CPU time: 0.061
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: -1388.190
2. Current log-likelihood: -1387.968
3. Current log-likelihood: -1387.808
4. Current log-likelihood: -1387.688
5. Current log-likelihood: -1387.597
6. Current log-likelihood: -1387.526
7. Current log-likelihood: -1387.471
Optimal log-likelihood: -1387.426
Rate parameters: A-C: 0.33201 A-G: 2.23761 A-T: 2.11213 C-G: 1.16005 C-T: 3.23466 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: 1.356
Parameters optimization took 7 rounds (0.027 sec)
BEST SCORE FOUND : -1387.426
Total tree length: 6.737
Total number of iterations: 2
CPU time used for tree search: 0.117 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.061 sec (0h:0m:0s)
Total CPU time used: 0.275 sec (0h:0m:0s)
Total wall-clock time used: 0.145 sec (0h:0m:0s)
---> START RUN NUMBER 6 (seed: 22834)
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: 2.06956 A-T: 1.96268 C-G: 1.07937 C-T: 2.84175 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 0.0016861 secs using 194.1% CPU
Computing ML distances took 0.001815 sec (of wall-clock time) 0.003481 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 4.60148e-05 secs using 82.58% CPU
Constructing RapidNJ tree: done in 0.000125885 secs using 81.82% CPU
Computing RapidNJ tree took 0.000249 sec (of wall-clock time) 0.000196 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 0.022681 secs using 191.9% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.955
Optimizing NNI: done in 0.0122979 secs using 192% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.955 / CPU time: 0.052
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 (0.023 sec)
BEST SCORE FOUND : -1387.423
Total tree length: 6.744
Total number of iterations: 2
CPU time used for tree search: 0.100 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.052 sec (0h:0m:0s)
Total CPU time used: 0.250 sec (0h:0m:0s)
Total wall-clock time used: 0.132 sec (0h:0m:0s)
---> START RUN NUMBER 7 (seed: 23834)
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 (0.040 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00127196 secs using 192.8% CPU
Computing ML distances took 0.001362 sec (of wall-clock time) 0.002591 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 4.81606e-05 secs using 83.06% CPU
Constructing RapidNJ tree: done in 9.01222e-05 secs using 122.1% CPU
Computing RapidNJ tree took 0.000205 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 0.0206981 secs using 191.2% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.214
Optimizing NNI: done in 0.020545 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: 0.095 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.050 sec (0h:0m:0s)
Total CPU time used: 0.253 sec (0h:0m:0s)
Total wall-clock time used: 0.134 sec (0h:0m:0s)
---> START RUN NUMBER 8 (seed: 24834)
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 0.00128412 secs using 193.3% CPU
Computing ML distances took 0.001365 sec (of wall-clock time) 0.002606 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 9.29832e-05 secs using 131.2% CPU
Computing RapidNJ tree took 0.000204 sec (of wall-clock time) 0.000217 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 0.020303 secs using 192.1% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.217
Optimizing NNI: done in 0.0320539 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: 0.063
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: 0.122 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.064 sec (0h:0m:0s)
Total CPU time used: 0.279 sec (0h:0m:0s)
Total wall-clock time used: 0.147 sec (0h:0m:0s)
---> START RUN NUMBER 9 (seed: 25834)
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 (0.040 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00126505 secs using 193.7% CPU
Computing ML distances took 0.001348 sec (of wall-clock time) 0.002586 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.00679e-05 secs using 81.89% CPU
Constructing RapidNJ tree: done in 9.29832e-05 secs using 132.3% CPU
Computing RapidNJ tree took 0.000222 sec (of wall-clock time) 0.000226 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 0.020395 secs using 191.8% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.217
Optimizing NNI: done in 0.033216 secs using 191.9% 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: 0.36987 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: 0.123 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.064 sec (0h:0m:0s)
Total CPU time used: 0.280 sec (0h:0m:0s)
Total wall-clock time used: 0.147 sec (0h:0m:0s)
---> START RUN NUMBER 10 (seed: 26834)
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: 1.98596 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 0.0013001 secs using 188.8% CPU
Computing ML distances took 0.001390 sec (of wall-clock time) 0.002589 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 4.50611e-05 secs using 82.11% CPU
Constructing RapidNJ tree: done in 8.98838e-05 secs using 123.5% CPU
Computing RapidNJ tree took 0.000198 sec (of wall-clock time) 0.000206 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 0.0206151 secs using 192.4% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.961
Optimizing NNI: done in 0.0506899 secs using 191.8% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.961 / CPU time: 0.089
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 (0.023 sec)
BEST SCORE FOUND : -1387.424
Total tree length: 6.743
Total number of iterations: 2
CPU time used for tree search: 0.170 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.089 sec (0h:0m:0s)
Total CPU time used: 0.322 sec (0h:0m:0s)
Total wall-clock time used: 0.169 sec (0h:0m:0s)
---> SUMMARIZE RESULTS FROM 10 RUNS
Run 4 gave best log-likelihood: -1387.423
Total CPU time for 10 runs: 2.738 seconds.
Total wall-clock time for 10 runs: 1.473 seconds.
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpqkm9kovz/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpqkm9kovz/q2iqtree.treefile
Trees from independent runs: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpqkm9kovz/q2iqtree.runtrees
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpqkm9kovz/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpqkm9kovz/q2iqtree.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpqkm9kovz/q2iqtree.treefile -m "GTR{0.323508,2.25836,2.12824,1.16565,3.23834}+F{0.243216,0.181967,0.319196,0.255621}+I{0.0163392}+G4{1.37314}" --length 214
Date and Time: Thu Mar 2 14:34:26 2023
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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpqkm9kovz/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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp2sjrvszo/q2iqtree -nt 1 -alrt 1000 -abayes -lbp 1000
Seed: 303949 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Mar 2 14:34:36 2023
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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000218153 secs using 83.89% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000458956 secs using 78% 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 79.89% 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 6.98566e-05 secs using 75.87% 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, 1.261 / LogL: -1392.812
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.008, 1.354 / LogL: -1393.088
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.009, 1.366 / LogL: -1393.159
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.009, 1.362 / LogL: -1393.150
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.008, 1.357 / LogL: -1393.112
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.009, 1.361 / LogL: -1393.138
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.009, 1.364 / LogL: -1393.160
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.008, 1.358 / LogL: -1393.102
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.008, 1.359 / LogL: -1393.108
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.008, 1.361 / LogL: -1393.119
Optimal pinv,alpha: 0.000, 1.261 / LogL: -1392.812
Parameters optimization took 0.505 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00125098 secs using 97.84% CPU
Computing ML distances took 0.001365 sec (of wall-clock time) 0.001303 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.31673e-05 secs using 79% CPU
Constructing RapidNJ tree: done in 9.08375e-05 secs using 137.6% CPU
Computing RapidNJ tree took 0.000209 sec (of wall-clock time) 0.000224 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.727
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.107 second
Computing log-likelihood of 98 initial trees ... 0.131 seconds
Current best score: -1392.727
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.021138 secs using 98.94% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.357
Optimizing NNI: done in 0.0162389 secs using 99.24% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1387.266
Optimizing NNI: done in 0.0119371 secs using 98.47% CPU
Optimizing NNI: done in 0.0126679 secs using 98.44% CPU
Optimizing NNI: done in 0.0142648 secs using 98.82% CPU
Optimizing NNI: done in 0.014322 secs using 99.13% CPU
Optimizing NNI: done in 0.0161331 secs using 97.97% CPU
Optimizing NNI: done in 0.0144069 secs using 98.92% CPU
Optimizing NNI: done in 0.0144169 secs using 98.95% CPU
Optimizing NNI: done in 0.0147729 secs using 98.65% CPU
Iteration 10 / LogL: -1387.735 / Time: 0h:0m:0s
Optimizing NNI: done in 0.013984 secs using 99.35% CPU
Optimizing NNI: done in 0.0144751 secs using 98.87% CPU
Optimizing NNI: done in 0.0263841 secs using 98.87% CPU
Optimizing NNI: done in 0.0265789 secs using 98.8% CPU
Optimizing NNI: done in 0.0263951 secs using 98.98% CPU
Optimizing NNI: done in 0.026489 secs using 98.46% CPU
Optimizing NNI: done in 0.026212 secs using 98.82% CPU
Optimizing NNI: done in 0.026454 secs using 99.14% CPU
Optimizing NNI: done in 0.0272949 secs using 98.43% CPU
Optimizing NNI: done in 0.0260968 secs using 98.8% CPU
Iteration 20 / LogL: -1387.280 / Time: 0h:0m:1s
Finish initializing candidate tree set (2)
Current best tree score: -1387.266 / CPU time: 0.652
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
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Iteration 30 / LogL: -1396.675 / Time: 0h:0m:1s (0h:0m:3s left)
Optimizing NNI: done in 0.028899 secs using 99.2% CPU
Optimizing NNI: done in 0.051291 secs using 99.86% CPU
Optimizing NNI: done in 0.01685 secs using 99.97% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.264
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Iteration 40 / LogL: -1387.353 / Time: 0h:0m:1s (0h:0m:2s left)
Optimizing NNI: done in 0.0303578 secs using 99.96% CPU
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Iteration 50 / LogL: -1387.349 / Time: 0h:0m:2s (0h:0m:2s left)
Optimizing NNI: done in 0.0402479 secs using 99.96% CPU
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Iteration 60 / LogL: -1387.381 / Time: 0h:0m:2s (0h:0m:1s left)
Optimizing NNI: done in 0.0315781 secs using 99.92% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 69: -1387.169
Optimizing NNI: done in 0.049691 secs using 99.69% CPU
Iteration 70 / LogL: -1387.340 / Time: 0h:0m:2s (0h:0m:3s left)
Optimizing NNI: done in 0.0181549 secs using 99.93% CPU
Optimizing NNI: done in 0.014971 secs using 99.96% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.169
Optimizing NNI: done in 0.0396161 secs using 99.85% CPU
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Iteration 80 / LogL: -1387.532 / Time: 0h:0m:3s (0h:0m:3s left)
Optimizing NNI: done in 0.0379989 secs using 99.96% CPU
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UPDATE BEST LOG-LIKELIHOOD: -1387.169
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Iteration 90 / LogL: -1387.336 / Time: 0h:0m:3s (0h:0m:2s left)
Optimizing NNI: done in 0.0330172 secs using 99.96% CPU
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WARNING: NNI search needs unusual large number of steps (20) to converge!
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Iteration 100 / LogL: -1387.211 / Time: 0h:0m:3s (0h:0m:2s left)
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Iteration 110 / LogL: -1406.093 / Time: 0h:0m:3s (0h:0m:2s left)
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Iteration 120 / LogL: -1387.335 / Time: 0h:0m:4s (0h:0m:1s left)
Optimizing NNI: done in 0.0395648 secs using 99.96% CPU
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Iteration 130 / LogL: -1396.400 / Time: 0h:0m:4s (0h:0m:1s left)
Optimizing NNI: done in 0.019664 secs using 99.95% CPU
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Iteration 140 / LogL: -1387.169 / Time: 0h:0m:4s (0h:0m:0s left)
Optimizing NNI: done in 0.0205631 secs using 99.97% CPU
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
Iteration 150 / LogL: -1387.168 / Time: 0h:0m:5s (0h:0m:0s left)
Optimizing NNI: done in 0.0485251 secs using 99.76% CPU
Optimizing NNI: done in 0.040694 secs using 99.85% CPU
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
Optimizing NNI: done in 0.040307 secs using 99.84% CPU
Optimizing NNI: done in 0.0167701 secs using 99.96% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.168
Iteration 160 / LogL: -1387.168 / Time: 0h:0m:5s (0h:0m:0s left)
Optimizing NNI: done in 0.0180449 secs using 99.72% CPU
Optimizing NNI: done in 0.0184031 secs using 99.89% CPU
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Optimizing NNI: done in 0.0294309 secs using 99.96% CPU
Iteration 170 / LogL: -1387.179 / Time: 0h:0m:5s (0h:0m:-1s left)
TREE SEARCH COMPLETED AFTER 170 ITERATIONS / Time: 0h:0m:5s
--------------------------------------------------------------------
| 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: 0.34775 A-G: 2.33305 A-T: 2.15352 C-G: 1.24055 C-T: 3.23394 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: 1.284
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...
0.056 sec.
Total tree length: 7.605
Total number of iterations: 170
CPU time used for tree search: 5.202 sec (0h:0m:5s)
Wall-clock time used for tree search: 5.048 sec (0h:0m:5s)
Total CPU time used: 5.781 sec (0h:0m:5s)
Total wall-clock time used: 5.630 sec (0h:0m:5s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp2sjrvszo/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp2sjrvszo/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp2sjrvszo/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp2sjrvszo/q2iqtree.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp2sjrvszo/q2iqtree.treefile -m "GTR{0.347752,2.33305,2.15352,1.24055,3.23394}+F{0.243216,0.181967,0.319196,0.255621}+I{2.89198e-07}+G4{1.28449}" --length 214
Date and Time: Thu Mar 2 14:34:41 2023
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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp2sjrvszo/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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpft4zsklp/q2iqtree -nt 1 -nstop 200 -pers 0.200000
Seed: 723446 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Mar 2 14:34:51 2023
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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000232935 secs using 81.57% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000494957 secs using 76.98% 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 86.62% 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
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.0262461 secs using 98.14% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1391.281
2. Current log-likelihood: -1389.723
Optimal log-likelihood: -1388.882
Rate parameters: A-C: 0.33813 A-G: 2.30739 A-T: 2.15805 C-G: 1.19220 C-T: 3.30147 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: 1.423
Parameters optimization took 2 rounds (0.014 sec)
Time for fast ML tree search: 0.064 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 1387.278 46 2866.557 2892.449 3021.392
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 3013.422
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 1387.155 43 2860.310 2882.568 3005.047
27 SYM+R2 1382.244 44 2852.489 2875.921 3000.592
36 SYM+I+I+R2 1382.405 45 2854.809 2879.452 3006.278
47 TVM+F+G4 1388.425 45 2866.850 2891.493 3018.319
49 TVM+F+R2 1382.482 46 2856.965 2882.857 3011.799
58 TVM+F+I+I+R2 1382.560 47 2859.119 2886.300 3017.320
69 TVMe+G4 1387.122 42 2858.244 2879.367 2999.615
71 TVMe+R2 1382.298 43 2850.596 2872.855 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/tmpft4zsklp/q2iqtree.model.gz
CPU time for ModelFinder: 1.532 seconds (0h:0m:1s)
Wall-clock time for ModelFinder: 1.555 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: 1.57495 A-T: 1.00000 C-G: 0.39693 C-T: 1.57495 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 (0.003 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000797033 secs using 97.86% CPU
Computing ML distances took 0.000886 sec (of wall-clock time) 0.000847 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 9.98974e-05 secs using 158.2% CPU
Computing RapidNJ tree took 0.000244 sec (of wall-clock time) 0.000265 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.836
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.090 second
Computing log-likelihood of 98 initial trees ... 0.086 seconds
Current best score: -1385.304
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.002774 secs using 197.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.303
Optimizing NNI: done in 0.0125618 secs using 197.1% CPU
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Iteration 10 / LogL: -1385.342 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0124009 secs using 99.96% CPU
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Iteration 20 / LogL: -1385.330 / Time: 0h:0m:0s
Finish initializing candidate tree set (1)
Current best tree score: -1385.303 / CPU time: 0.431
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0193419 secs using 99.54% CPU
Optimizing NNI: done in 0.0140131 secs using 99.92% CPU
Optimizing NNI: done in 0.00487709 secs using 99.98% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.303
Optimizing NNI: done in 0.011812 secs using 99.51% CPU
Optimizing NNI: done in 0.012619 secs using 99.87% CPU
Optimizing NNI: done in 0.0045228 secs using 99.92% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.303
Optimizing NNI: done in 0.0121381 secs using 99.54% CPU
Optimizing NNI: done in 0.00774002 secs using 99.82% CPU
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Iteration 30 / LogL: -1385.326 / Time: 0h:0m:0s (0h:0m:3s left)
Optimizing NNI: done in 0.00632286 secs using 99.94% CPU
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Iteration 40 / LogL: -1385.653 / Time: 0h:0m:0s (0h:0m:2s left)
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Iteration 50 / LogL: -1385.306 / Time: 0h:0m:0s (0h:0m:2s left)
Optimizing NNI: done in 0.00929999 secs using 99.96% CPU
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Iteration 60 / LogL: -1385.859 / Time: 0h:0m:0s (0h:0m:2s left)
Optimizing NNI: done in 0.00988197 secs using 99.94% CPU
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Iteration 70 / LogL: -1385.952 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.010402 secs using 99.94% CPU
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Iteration 80 / LogL: -1385.306 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.00517821 secs using 99.98% CPU
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Iteration 90 / LogL: -1385.304 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.010287 secs using 99.94% CPU
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Iteration 100 / LogL: -1385.877 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.0102391 secs using 99.46% CPU
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Iteration 110 / LogL: -1385.313 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.00939703 secs using 99.94% CPU
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Iteration 120 / LogL: -1385.644 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.00544405 secs using 99.93% CPU
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Iteration 130 / LogL: -1385.644 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0124011 secs using 99.96% CPU
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Iteration 140 / LogL: -1388.428 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00935602 secs using 99.92% CPU
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Optimizing NNI: done in 0.00453496 secs using 99.91% CPU
Iteration 150 / LogL: -1395.962 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0056541 secs using 99.95% CPU
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Iteration 160 / LogL: -1385.340 / Time: 0h:0m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.0118272 secs using 99.95% CPU
Optimizing NNI: done in 0.0123942 secs using 99.93% CPU
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Optimizing NNI: done in 0.0113809 secs using 99.95% CPU
Optimizing NNI: done in 0.00433111 secs using 99.95% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.303
Optimizing NNI: done in 0.0142729 secs using 99.41% CPU
Optimizing NNI: done in 0.0140309 secs using 99.85% CPU
Optimizing NNI: done in 0.00502801 secs using 99.92% CPU
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Iteration 170 / LogL: -1385.644 / Time: 0h:0m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.0119159 secs using 99.93% CPU
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Iteration 180 / LogL: -1385.608 / Time: 0h:0m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.0135171 secs using 99.93% CPU
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Iteration 190 / LogL: -1385.674 / Time: 0h:0m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.0130081 secs using 99.94% CPU
Optimizing NNI: done in 0.00679612 secs using 99.95% CPU
Optimizing NNI: done in 0.00563884 secs using 99.93% CPU
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Optimizing NNI: done in 0.00858688 secs using 99.94% CPU
Optimizing NNI: done in 0.00951195 secs using 99.97% CPU
Iteration 200 / LogL: -1385.792 / Time: 0h:0m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.0137732 secs using 99.94% CPU
Optimizing NNI: done in 0.010185 secs using 99.95% CPU
TREE SEARCH COMPLETED AFTER 202 ITERATIONS / Time: 0h:0m:2s
--------------------------------------------------------------------
| 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: 0.39653 A-G: 1.57282 A-T: 1.00000 C-G: 0.39653 C-T: 1.57282 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.723,0.402) (0.277,2.564)
Parameters optimization took 1 rounds (0.003 sec)
BEST SCORE FOUND : -1385.303
Total tree length: 6.855
Total number of iterations: 202
CPU time used for tree search: 2.650 sec (0h:0m:2s)
Wall-clock time used for tree search: 2.468 sec (0h:0m:2s)
Total CPU time used: 2.676 sec (0h:0m:2s)
Total wall-clock time used: 2.490 sec (0h:0m:2s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpft4zsklp/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpft4zsklp/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpft4zsklp/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpft4zsklp/q2iqtree.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpft4zsklp/q2iqtree.treefile -m "TPM3{0.396533,1.57282}+FQ+R2{0.723446,0.402243,0.276554,2.56369}" --length 214
Date and Time: Thu Mar 2 14:34:55 2023
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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpft4zsklp/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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpbkhehawd/q2iqtreeufboot -nt 1 -nstop 200 -pers 0.200000
Seed: 491276 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Mar 2 14:35:05 2023
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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000222206 secs using 82.81% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000513792 secs using 73.96% 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 7.10487e-05 secs using 76% 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 0.0247221 secs using 98.63% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1396.575
2. Current log-likelihood: -1395.213
Optimal log-likelihood: -1394.464
Rate parameters: A-C: 0.21819 A-G: 2.03593 A-T: 1.93394 C-G: 1.05109 C-T: 2.56337 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: 1.322
Parameters optimization took 2 rounds (0.014 sec)
Time for fast ML tree search: 0.061 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 1411.054 45 2912.108 2936.751 3063.577
2 GTR+F+I 1409.135 46 2910.270 2936.162 3065.105
3 GTR+F+G4 1392.992 46 2877.983 2903.876 3032.818
4 GTR+F+I+G4 1393.280 47 2880.561 2907.741 3038.762
5 GTR+F+R2 1387.712 47 2869.423 2896.604 3027.624
6 GTR+F+R3 1387.747 49 2873.494 2903.372 3038.427
14 GTR+F+I+I+R2 1387.798 48 2871.597 2900.106 3033.164
15 GTR+F+I+I+R3 1387.816 50 2875.631 2906.920 3043.930
25 SYM+G4 1393.506 43 2873.012 2895.271 3017.749
27 SYM+R2 1389.901 44 2867.802 2891.234 3015.905
36 SYM+I+I+R2 1390.056 45 2870.112 2894.755 3021.581
47 TVM+F+G4 1393.474 45 2876.947 2901.590 3028.416
49 TVM+F+R2 1388.475 46 2868.950 2894.842 3023.785
58 TVM+F+I+I+R2 1388.497 47 2870.994 2898.175 3029.195
69 TVMe+G4 1393.632 42 2871.264 2892.387 3012.635
71 TVMe+R2 1389.912 43 2865.824 2888.083 3010.561
80 TVMe+I+I+R2 1390.032 44 2868.063 2891.495 3016.166
91 TIM3+F+G4 1396.957 44 2881.914 2905.346 3030.017
93 TIM3+F+R2 1391.441 45 2872.881 2897.524 3024.350
102 TIM3+F+I+I+R2 1391.573 46 2875.146 2901.038 3029.981
113 TIM3e+G4 1397.005 41 2876.010 2896.033 3014.015
115 TIM3e+R2 1393.195 42 2870.390 2891.513 3011.761
124 TIM3e+I+I+R2 1393.369 43 2872.737 2894.996 3017.474
135 TIM2+F+G4 1401.480 44 2890.961 2914.393 3039.064
137 TIM2+F+R2 1395.762 45 2881.524 2906.167 3032.993
146 TIM2+F+I+I+R2 1395.853 46 2883.706 2909.598 3038.540
157 TIM2e+G4 1406.407 41 2894.815 2914.838 3032.820
159 TIM2e+R2 1402.269 42 2888.539 2909.662 3029.910
168 TIM2e+I+I+R2 1402.374 43 2890.749 2913.007 3035.486
179 TIM+F+G4 1397.972 44 2883.943 2907.375 3032.046
181 TIM+F+R2 1392.182 45 2874.365 2899.008 3025.834
190 TIM+F+I+I+R2 1392.255 46 2876.511 2902.403 3031.346
201 TIMe+G4 1403.787 41 2889.575 2909.598 3027.580
203 TIMe+R2 1399.417 42 2882.835 2903.958 3024.206
212 TIMe+I+I+R2 1399.551 43 2885.102 2907.361 3029.839
223 TPM3u+F+G4 1397.423 43 2880.846 2903.105 3025.583
225 TPM3u+F+R2 1392.257 44 2872.514 2895.946 3020.617
234 TPM3u+F+I+I+R2 1392.403 45 2874.805 2899.448 3026.274
245 TPM3+G4 1397.145 40 2874.290 2893.250 3008.929
247 TPM3+R2 1393.233 41 2868.465 2888.489 3006.471
256 TPM3+I+I+R2 1393.402 42 2870.804 2891.927 3012.175
267 TPM2u+F+G4 1401.931 43 2889.862 2912.120 3034.599
269 TPM2u+F+R2 1396.514 44 2881.029 2904.461 3029.132
278 TPM2u+F+I+I+R2 1396.609 45 2883.218 2907.861 3034.687
289 TPM2+G4 1406.566 40 2893.132 2912.092 3027.771
291 TPM2+R2 1402.312 41 2886.624 2906.647 3024.629
300 TPM2+I+I+R2 1402.426 42 2888.852 2909.975 3030.223
311 K3Pu+F+G4 1398.551 43 2883.101 2905.360 3027.838
313 K3Pu+F+R2 1393.054 44 2874.109 2897.541 3022.212
322 K3Pu+F+I+I+R2 1393.149 45 2876.299 2900.942 3027.768
333 K3P+G4 1403.892 40 2887.785 2906.744 3022.424
335 K3P+R2 1399.422 41 2880.844 2900.867 3018.849
344 K3P+I+I+R2 1399.575 42 2883.151 2904.274 3024.522
355 TN+F+G4 1401.586 43 2889.173 2911.432 3033.910
357 TN+F+R2 1395.969 44 2879.938 2903.370 3028.041
366 TN+F+I+I+R2 1396.066 45 2882.132 2906.775 3033.601
377 TNe+G4 1406.460 40 2892.919 2911.879 3027.558
379 TNe+R2 1402.304 41 2886.608 2906.631 3024.613
388 TNe+I+I+R2 1402.407 42 2888.814 2909.937 3030.185
399 HKY+F+G4 1402.059 42 2888.117 2909.240 3029.488
401 HKY+F+R2 1396.722 43 2879.445 2901.704 3024.182
410 HKY+F+I+I+R2 1396.828 44 2881.656 2905.088 3029.759
421 K2P+G4 1406.634 39 2891.268 2909.199 3022.541
423 K2P+R2 1402.339 40 2884.677 2903.637 3019.316
432 K2P+I+I+R2 1402.460 41 2886.919 2906.943 3024.924
443 F81+F+G4 1410.287 41 2902.575 2922.598 3040.580
445 F81+F+R2 1405.897 42 2895.793 2916.916 3037.164
454 F81+F+I+I+R2 1405.928 43 2897.857 2920.116 3042.594
465 JC+G4 1414.943 38 2905.887 2922.824 3033.794
467 JC+R2 1411.518 39 2901.035 2918.966 3032.308
476 JC+I+I+R2 1411.519 40 2903.039 2921.998 3037.678
Akaike Information Criterion: TVMe+R2
Corrected Akaike Information Criterion: TVMe+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/tmpbkhehawd/q2iqtreeufboot.model.gz
CPU time for ModelFinder: 1.436 seconds (0h:0m:1s)
Wall-clock time for ModelFinder: 1.457 seconds (0h:0m:1s)
Generating 1000 samples for ultrafast bootstrap (seed: 491276)...
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1393.233
Optimal log-likelihood: -1393.222
Rate parameters: A-C: 0.30881 A-G: 1.35555 A-T: 1.00000 C-G: 0.30881 C-T: 1.35555 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.687,0.341) (0.313,2.448)
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 0.000901937 secs using 98.34% CPU
Computing ML distances took 0.000991 sec (of wall-clock time) 0.000950 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 5.6982e-05 secs using 85.99% CPU
Constructing RapidNJ tree: done in 9.10759e-05 secs using 153.7% CPU
Computing RapidNJ tree took 0.000218 sec (of wall-clock time) 0.000243 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.436
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.105 second
Computing log-likelihood of 98 initial trees ... 0.088 seconds
Current best score: -1393.222
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00840211 secs using 99.71% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1392.059
Optimizing NNI: done in 0.023921 secs using 99.95% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1385.324
Optimizing NNI: done in 0.022557 secs using 99.96% CPU
BETTER TREE FOUND at iteration 3: -1385.321
Optimizing NNI: done in 0.034265 secs using 99.96% CPU
Optimizing NNI: done in 0.0209651 secs using 99.96% CPU
Optimizing NNI: done in 0.0210249 secs using 99.97% CPU
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Optimizing NNI: done in 0.0237319 secs using 99.96% CPU
Optimizing NNI: done in 0.0196741 secs using 99.97% CPU
Optimizing NNI: done in 0.0211191 secs using 99.96% CPU
Iteration 10 / LogL: -1385.326 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0180609 secs using 99.96% CPU
Optimizing NNI: done in 0.018122 secs using 99.97% CPU
Optimizing NNI: done in 0.0194528 secs using 99.96% CPU
Optimizing NNI: done in 0.0216851 secs using 99.8% CPU
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Optimizing NNI: done in 0.0193989 secs using 99.96% CPU
Optimizing NNI: done in 0.019568 secs using 99.94% CPU
Iteration 20 / LogL: -1385.346 / Time: 0h:0m:0s
Finish initializing candidate tree set (4)
Current best tree score: -1385.321 / CPU time: 0.639
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.00964499 secs using 99.68% CPU
Optimizing NNI: done in 0.018712 secs using 99.9% CPU
Optimizing NNI: done in 0.0196152 secs using 99.95% CPU
Optimizing NNI: done in 0.014133 secs using 99.96% CPU
Optimizing NNI: done in 0.0183492 secs using 99.96% CPU
Optimizing NNI: done in 0.0191259 secs using 99.96% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.320
Optimizing NNI: done in 0.0206389 secs using 99.75% CPU
Optimizing NNI: done in 0.020159 secs using 99.93% CPU
Optimizing NNI: done in 0.016995 secs using 99.95% CPU
Optimizing NNI: done in 0.020612 secs using 99.96% CPU
Iteration 30 / LogL: -1385.334 / Time: 0h:0m:0s (0h:0m:5s left)
Optimizing NNI: done in 0.0194049 secs using 99.95% CPU
Optimizing NNI: done in 0.0130761 secs using 99.95% CPU
Optimizing NNI: done in 0.015784 secs using 99.97% CPU
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Optimizing NNI: done in 0.013592 secs using 99.94% CPU
Optimizing NNI: done in 0.00815296 secs using 99.88% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.320
Iteration 40 / LogL: -1385.320 / Time: 0h:0m:1s (0h:0m:4s left)
Optimizing NNI: done in 0.0210612 secs using 99.83% CPU
Optimizing NNI: done in 0.023572 secs using 99.93% CPU
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Optimizing NNI: done in 0.022362 secs using 99.95% CPU
Optimizing NNI: done in 0.00796294 secs using 99.95% CPU
BETTER TREE FOUND at iteration 49: -1385.320
Optimizing NNI: done in 0.0244632 secs using 99.75% CPU
Iteration 50 / LogL: -1385.730 / Time: 0h:0m:1s (0h:0m:5s left)
Log-likelihood cutoff on original alignment: -1418.936
Optimizing NNI: done in 0.0200779 secs using 99.88% CPU
Optimizing NNI: done in 0.016778 secs using 99.94% CPU
Optimizing NNI: done in 0.018945 secs using 99.96% CPU
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Optimizing NNI: done in 0.00996399 secs using 99.96% CPU
Optimizing NNI: done in 0.0132661 secs using 99.95% CPU
Iteration 60 / LogL: -1385.542 / Time: 0h:0m:1s (0h:0m:5s left)
Optimizing NNI: done in 0.00687408 secs using 99.94% CPU
Optimizing NNI: done in 0.0128582 secs using 99.95% CPU
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Optimizing NNI: done in 0.0107539 secs using 99.96% CPU
Optimizing NNI: done in 0.0250902 secs using 99.96% CPU
Iteration 70 / LogL: -1385.321 / Time: 0h:0m:1s (0h:0m:4s left)
Optimizing NNI: done in 0.0189581 secs using 99.97% CPU
Optimizing NNI: done in 0.0149369 secs using 99.97% CPU
Optimizing NNI: done in 0.0179071 secs using 99.96% CPU
Optimizing NNI: done in 0.011457 secs using 99.96% CPU
Optimizing NNI: done in 0.018856 secs using 99.96% CPU
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Optimizing NNI: done in 0.0154269 secs using 99.96% CPU
Optimizing NNI: done in 0.00497389 secs using 99.94% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.320
Optimizing NNI: done in 0.024338 secs using 99.76% CPU
Optimizing NNI: done in 0.01438 secs using 99.94% CPU
Iteration 80 / LogL: -1385.323 / Time: 0h:0m:1s (0h:0m:4s left)
Optimizing NNI: done in 0.0170898 secs using 99.95% CPU
Optimizing NNI: done in 0.0140359 secs using 99.95% CPU
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Optimizing NNI: done in 0.0195918 secs using 99.96% CPU
Optimizing NNI: done in 0.030848 secs using 99.96% CPU
Iteration 90 / LogL: -1385.322 / Time: 0h:0m:2s (0h:0m:3s left)
Optimizing NNI: done in 0.0127239 secs using 99.96% CPU
Optimizing NNI: done in 0.00994587 secs using 99.93% CPU
Optimizing NNI: done in 0.0133059 secs using 99.96% CPU
Optimizing NNI: done in 0.0218961 secs using 99.94% CPU
Optimizing NNI: done in 0.0158749 secs using 99.96% CPU
Optimizing NNI: done in 0.00848198 secs using 99.96% CPU
Optimizing NNI: done in 0.0115211 secs using 99.96% CPU
Optimizing NNI: done in 0.0115891 secs using 99.96% CPU
Optimizing NNI: done in 0.0151341 secs using 99.96% CPU
Optimizing NNI: done in 0.0175331 secs using 99.95% CPU
Iteration 100 / LogL: -1385.543 / Time: 0h:0m:2s (0h:0m:3s left)
Log-likelihood cutoff on original alignment: -1419.391
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.998
Optimizing NNI: done in 0.00852704 secs using 99.94% CPU
Optimizing NNI: done in 0.0181439 secs using 99.96% CPU
Optimizing NNI: done in 0.017082 secs using 99.96% CPU
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Optimizing NNI: done in 0.0159161 secs using 99.95% CPU
Optimizing NNI: done in 0.00496888 secs using 99.94% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.320
Optimizing NNI: done in 0.0223079 secs using 99.74% CPU
Optimizing NNI: done in 0.0168881 secs using 99.95% CPU
Optimizing NNI: done in 0.00726295 secs using 99.93% CPU
Optimizing NNI: done in 0.017947 secs using 99.96% CPU
Iteration 110 / LogL: -1385.323 / Time: 0h:0m:2s (0h:0m:3s left)
Optimizing NNI: done in 0.0145571 secs using 99.91% CPU
Optimizing NNI: done in 0.020628 secs using 99.96% CPU
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Optimizing NNI: done in 0.00869012 secs using 99.94% CPU
Optimizing NNI: done in 0.005054 secs using 99.98% CPU
Iteration 120 / LogL: -1391.760 / Time: 0h:0m:2s (0h:0m:3s left)
Optimizing NNI: done in 0.00814509 secs using 99.96% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.320
Optimizing NNI: done in 0.0175309 secs using 99.73% CPU
Optimizing NNI: done in 0.0160351 secs using 99.94% CPU
Optimizing NNI: done in 0.00998187 secs using 99.95% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.320
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Iteration 130 / LogL: -1385.321 / Time: 0h:0m:3s (0h:0m:2s left)
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Iteration 140 / LogL: -1385.727 / Time: 0h:0m:3s (0h:0m:2s left)
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Optimizing NNI: done in 0.00653696 secs using 99.94% CPU
Iteration 150 / LogL: -1395.492 / Time: 0h:0m:3s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -1419.391
Optimizing NNI: done in 0.0171351 secs using 99.95% CPU
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Iteration 160 / LogL: -1385.322 / Time: 0h:0m:3s (0h:0m:2s left)
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Iteration 170 / LogL: -1385.327 / Time: 0h:0m:3s (0h:0m:1s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.320
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Iteration 180 / LogL: -1385.320 / Time: 0h:0m:4s (0h:0m:1s left)
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Iteration 190 / LogL: -1385.562 / Time: 0h:0m:4s (0h:0m:1s left)
Optimizing NNI: done in 0.0133691 secs using 99.95% CPU
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Iteration 200 / LogL: -1385.324 / Time: 0h:0m:4s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -1419.391
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.999
Optimizing NNI: done in 0.0181291 secs using 99.96% CPU
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Iteration 210 / LogL: -1385.320 / Time: 0h:0m:4s (0h:0m:2s left)
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Iteration 220 / LogL: -1385.321 / Time: 0h:0m:5s (0h:0m:1s left)
Optimizing NNI: done in 0.00763202 secs using 99.96% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.320
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Iteration 230 / LogL: -1385.323 / Time: 0h:0m:5s (0h:0m:1s left)
Optimizing NNI: done in 0.0202658 secs using 99.96% CPU
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Iteration 240 / LogL: -1385.321 / Time: 0h:0m:5s (0h:0m:1s left)
Optimizing NNI: done in 0.0199831 secs using 99.95% CPU
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Iteration 250 / LogL: -1385.322 / Time: 0h:0m:5s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -1419.391
TREE SEARCH COMPLETED AFTER 250 ITERATIONS / Time: 0h:0m:5s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1385.320
Optimal log-likelihood: -1385.310
Rate parameters: A-C: 0.39425 A-G: 1.57282 A-T: 1.00000 C-G: 0.39425 C-T: 1.57282 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.717,0.394) (0.283,2.535)
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1385.310
Creating bootstrap support values...
Split supports printed to NEXUS file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpbkhehawd/q2iqtreeufboot.splits.nex
Total tree length: 6.954
Total number of iterations: 250
CPU time used for tree search: 5.876 sec (0h:0m:5s)
Wall-clock time used for tree search: 5.722 sec (0h:0m:5s)
Total CPU time used: 5.983 sec (0h:0m:5s)
Total wall-clock time used: 5.928 sec (0h:0m:5s)
Computing bootstrap consensus tree...
Reading input file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpbkhehawd/q2iqtreeufboot.splits.nex...
20 taxa and 168 splits.
Consensus tree written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpbkhehawd/q2iqtreeufboot.contree
Reading input trees file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpbkhehawd/q2iqtreeufboot.contree
Log-likelihood of consensus tree: -1385.310
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpbkhehawd/q2iqtreeufboot.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpbkhehawd/q2iqtreeufboot.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpbkhehawd/q2iqtreeufboot.mldist
Ultrafast bootstrap approximation results written to:
Split support values: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpbkhehawd/q2iqtreeufboot.splits.nex
Consensus tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpbkhehawd/q2iqtreeufboot.contree
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpbkhehawd/q2iqtreeufboot.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpbkhehawd/q2iqtreeufboot.treefile -m "TPM3{0.394248,1.57282}+FQ+R2{0.716992,0.39424,0.283008,2.53468}" --length 214
Date and Time: Thu Mar 2 14:35:12 2023
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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpbkhehawd/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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplgguo09a/q2iqtreeufboot -nt 1 -alrt 1000 -abayes -lbp 1000 -nstop 200 -pers 0.200000
Seed: 626855 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Mar 2 14:35:22 2023
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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000218153 secs using 84.34% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000486851 secs using 78.26% 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 1.88351e-05 secs using 84.95% 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 78.47% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
Generating 1000 samples for ultrafast bootstrap (seed: 626855)...
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, 1.287 / 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 0.516 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00129318 secs using 96.82% CPU
Computing ML distances took 0.001388 sec (of wall-clock time) 0.001318 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.38826e-05 secs using 77.95% CPU
Constructing RapidNJ tree: done in 9.08375e-05 secs using 136.5% CPU
Computing RapidNJ tree took 0.000217 sec (of wall-clock time) 0.000219 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.836
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.102 second
Computing log-likelihood of 97 initial trees ... 0.127 seconds
Current best score: -1392.836
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.0291119 secs using 98.56% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.260
Optimizing NNI: done in 0.0395641 secs using 98.97% CPU
Optimizing NNI: done in 0.021359 secs using 98.81% CPU
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Iteration 10 / LogL: -1387.280 / Time: 0h:0m:1s
Optimizing NNI: done in 0.038671 secs using 99.03% CPU
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Optimizing NNI: done in 0.0294659 secs using 99.3% CPU
Iteration 20 / LogL: -1387.265 / Time: 0h:0m:1s
Finish initializing candidate tree set (1)
Current best tree score: -1387.260 / CPU time: 0.891
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0232201 secs using 98.94% CPU
Optimizing NNI: done in 0.0232899 secs using 98.69% CPU
Optimizing NNI: done in 0.0166061 secs using 98.52% CPU
Optimizing NNI: done in 0.00877213 secs using 98.58% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.258
Optimizing NNI: done in 0.0163779 secs using 99.37% CPU
Optimizing NNI: done in 0.018811 secs using 98.94% CPU
Optimizing NNI: done in 0.00704098 secs using 99.97% CPU
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Optimizing NNI: done in 0.0227821 secs using 99.97% CPU
Optimizing NNI: done in 0.0427999 secs using 99.97% CPU
Iteration 30 / LogL: -1387.353 / Time: 0h:0m:1s (0h:0m:9s left)
Optimizing NNI: done in 0.027566 secs using 99.96% CPU
Optimizing NNI: done in 0.0307531 secs using 99.96% CPU
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Optimizing NNI: done in 0.0092268 secs using 99.97% CPU
Optimizing NNI: done in 0.0255311 secs using 99.95% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.257
Optimizing NNI: done in 0.00841117 secs using 99.95% CPU
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Iteration 50 / LogL: -1387.356 / Time: 0h:0m:2s (0h:0m:6s left)
Log-likelihood cutoff on original alignment: -1412.731
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BETTER TREE FOUND at iteration 78: -1387.255
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Iteration 100 / LogL: -1387.352 / Time: 0h:0m:3s (0h:0m:6s left)
Log-likelihood cutoff on original alignment: -1412.731
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.998
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UPDATE BEST LOG-LIKELIHOOD: -1387.254
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Iteration 200 / LogL: -1387.378 / Time: 0h:0m:6s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -1412.731
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.998
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UPDATE BEST LOG-LIKELIHOOD: -1387.254
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Iteration 250 / LogL: -1387.291 / Time: 0h:0m:7s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -1412.731
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Iteration 270 / LogL: -1387.536 / Time: 0h:0m:8s (0h:0m:0s left)
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TREE SEARCH COMPLETED AFTER 279 ITERATIONS / Time: 0h:0m:8s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.254
Optimal log-likelihood: -1387.253
Rate parameters: A-C: 0.32481 A-G: 2.24166 A-T: 2.12055 C-G: 1.16277 C-T: 3.24963 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 : -1387.253
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...
0.055 sec.
Creating bootstrap support values...
Split supports printed to NEXUS file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplgguo09a/q2iqtreeufboot.splits.nex
Total tree length: 6.712
Total number of iterations: 279
CPU time used for tree search: 8.271 sec (0h:0m:8s)
Wall-clock time used for tree search: 8.129 sec (0h:0m:8s)
Total CPU time used: 8.942 sec (0h:0m:8s)
Total wall-clock time used: 8.809 sec (0h:0m:8s)
Computing bootstrap consensus tree...
Reading input file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplgguo09a/q2iqtreeufboot.splits.nex...
20 taxa and 158 splits.
Consensus tree written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplgguo09a/q2iqtreeufboot.contree
Reading input trees file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplgguo09a/q2iqtreeufboot.contree
Log-likelihood of consensus tree: -1387.254
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplgguo09a/q2iqtreeufboot.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplgguo09a/q2iqtreeufboot.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplgguo09a/q2iqtreeufboot.mldist
Ultrafast bootstrap approximation results written to:
Split support values: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplgguo09a/q2iqtreeufboot.splits.nex
Consensus tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplgguo09a/q2iqtreeufboot.contree
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplgguo09a/q2iqtreeufboot.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplgguo09a/q2iqtreeufboot.treefile -m "GTR{0.324814,2.24166,2.12055,1.16277,3.24963}+F{0.243216,0.181967,0.319196,0.255621}+I{3.33622e-07}+G4{1.32712}" --length 214
Date and Time: Thu Mar 2 14:35:31 2023
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/ffb9868c-08f0-49f7-b06f-04d6ae97052b/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmplgguo09a/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!