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/2023.5/tutorials/phylogeny/rep-seqs.qza
Save as: rep-seqs.qza
wget \
-O "rep-seqs.qza" \
"https://data.qiime2.org/2023.5/tutorials/phylogeny/rep-seqs.qza"
curl -sL \
"https://data.qiime2.org/2023.5/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 6668 -N 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpcdb9d360 -n q2
Partition: 0 with name: No Name Provided
Base frequencies: 0.243 0.182 0.319 0.256
Inference[0]: Time 0.755129 CAT-based likelihood -1242.549466, best rearrangement setting 5
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -1387.782172 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpcdb9d360/RAxML_result.q2
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -1387.782172 ....
Final GAMMA-based Score of best tree -1387.637594
Program execution info written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpcdb9d360/RAxML_info.q2
Best-scoring ML tree written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpcdb9d360/RAxML_bestTree.q2
Overall execution time: 1.408973 secs or 0.000391 hours or 0.000016 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 6668 -N 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpcdb9d360 -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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp39wnoeuy -n q2
Partition: 0 with name: No Name Provided
Base frequencies: 0.243 0.182 0.319 0.256
Inference[0]: Time 0.687155 CAT-based likelihood -1238.242991, best rearrangement setting 5
Inference[1]: Time 0.567415 CAT-based likelihood -1249.502284, best rearrangement setting 5
Inference[2]: Time 0.552911 CAT-based likelihood -1242.978035, best rearrangement setting 5
Inference[3]: Time 0.676663 CAT-based likelihood -1243.159855, best rearrangement setting 5
Inference[4]: Time 0.505676 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/tmp39wnoeuy/RAxML_result.q2.RUN.0
Inference[1] final GAMMA-based Likelihood: -1392.813982 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp39wnoeuy/RAxML_result.q2.RUN.1
Inference[2] final GAMMA-based Likelihood: -1388.073642 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp39wnoeuy/RAxML_result.q2.RUN.2
Inference[3] final GAMMA-based Likelihood: -1387.945266 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp39wnoeuy/RAxML_result.q2.RUN.3
Inference[4] final GAMMA-based Likelihood: -1387.557031 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp39wnoeuy/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/tmp39wnoeuy/RAxML_info.q2
Best-scoring ML tree written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp39wnoeuy/RAxML_bestTree.q2
Overall execution time: 3.706928 secs or 0.001030 hours or 0.000043 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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp39wnoeuy -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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl19qkvow -n q2bootstrap
Time for BS model parameter optimization 0.056576
Bootstrap[0]: Time 0.194055 seconds, bootstrap likelihood -1199.758796, best rearrangement setting 12
Bootstrap[1]: Time 0.132028 seconds, bootstrap likelihood -1344.229251, best rearrangement setting 6
Bootstrap[2]: Time 0.120719 seconds, bootstrap likelihood -1295.343000, best rearrangement setting 8
Bootstrap[3]: Time 0.103736 seconds, bootstrap likelihood -1273.768320, best rearrangement setting 8
Bootstrap[4]: Time 0.121239 seconds, bootstrap likelihood -1253.402952, best rearrangement setting 6
Bootstrap[5]: Time 0.130927 seconds, bootstrap likelihood -1260.866113, best rearrangement setting 10
Bootstrap[6]: Time 0.127508 seconds, bootstrap likelihood -1293.636299, best rearrangement setting 14
Bootstrap[7]: Time 0.122254 seconds, bootstrap likelihood -1227.178693, best rearrangement setting 6
Bootstrap[8]: Time 0.126074 seconds, bootstrap likelihood -1321.820787, best rearrangement setting 13
Bootstrap[9]: Time 0.132894 seconds, bootstrap likelihood -1147.233446, best rearrangement setting 6
Bootstrap[10]: Time 0.094927 seconds, bootstrap likelihood -1220.766493, best rearrangement setting 13
Bootstrap[11]: Time 0.137154 seconds, bootstrap likelihood -1200.006355, best rearrangement setting 8
Bootstrap[12]: Time 0.144748 seconds, bootstrap likelihood -1346.392834, best rearrangement setting 14
Bootstrap[13]: Time 0.108005 seconds, bootstrap likelihood -1301.111096, best rearrangement setting 14
Bootstrap[14]: Time 0.120755 seconds, bootstrap likelihood -1262.253559, best rearrangement setting 11
Bootstrap[15]: Time 0.115993 seconds, bootstrap likelihood -1215.017551, best rearrangement setting 14
Bootstrap[16]: Time 0.110834 seconds, bootstrap likelihood -1238.832009, best rearrangement setting 7
Bootstrap[17]: Time 0.099909 seconds, bootstrap likelihood -1393.989732, best rearrangement setting 12
Bootstrap[18]: Time 0.104921 seconds, bootstrap likelihood -1173.921002, best rearrangement setting 15
Bootstrap[19]: Time 0.113186 seconds, bootstrap likelihood -1185.726976, best rearrangement setting 11
Bootstrap[20]: Time 0.100591 seconds, bootstrap likelihood -1158.491940, best rearrangement setting 6
Bootstrap[21]: Time 0.099964 seconds, bootstrap likelihood -1154.664272, best rearrangement setting 11
Bootstrap[22]: Time 0.104703 seconds, bootstrap likelihood -1244.159837, best rearrangement setting 10
Bootstrap[23]: Time 0.128916 seconds, bootstrap likelihood -1211.171036, best rearrangement setting 15
Bootstrap[24]: Time 0.105995 seconds, bootstrap likelihood -1261.440677, best rearrangement setting 12
Bootstrap[25]: Time 0.106250 seconds, bootstrap likelihood -1331.836715, best rearrangement setting 15
Bootstrap[26]: Time 0.110231 seconds, bootstrap likelihood -1129.144509, best rearrangement setting 5
Bootstrap[27]: Time 0.134672 seconds, bootstrap likelihood -1226.624056, best rearrangement setting 7
Bootstrap[28]: Time 0.132092 seconds, bootstrap likelihood -1221.046176, best rearrangement setting 12
Bootstrap[29]: Time 0.087955 seconds, bootstrap likelihood -1211.791204, best rearrangement setting 14
Bootstrap[30]: Time 0.115117 seconds, bootstrap likelihood -1389.442380, best rearrangement setting 5
Bootstrap[31]: Time 0.114189 seconds, bootstrap likelihood -1303.638592, best rearrangement setting 12
Bootstrap[32]: Time 0.126610 seconds, bootstrap likelihood -1172.859456, best rearrangement setting 12
Bootstrap[33]: Time 0.106191 seconds, bootstrap likelihood -1244.617135, best rearrangement setting 9
Bootstrap[34]: Time 0.102332 seconds, bootstrap likelihood -1211.871717, best rearrangement setting 15
Bootstrap[35]: Time 0.122352 seconds, bootstrap likelihood -1299.862912, best rearrangement setting 5
Bootstrap[36]: Time 0.097831 seconds, bootstrap likelihood -1141.967505, best rearrangement setting 5
Bootstrap[37]: Time 0.122057 seconds, bootstrap likelihood -1283.923198, best rearrangement setting 12
Bootstrap[38]: Time 0.098076 seconds, bootstrap likelihood -1304.250946, best rearrangement setting 5
Bootstrap[39]: Time 0.093016 seconds, bootstrap likelihood -1407.084376, best rearrangement setting 15
Bootstrap[40]: Time 0.111601 seconds, bootstrap likelihood -1277.946299, best rearrangement setting 13
Bootstrap[41]: Time 0.110503 seconds, bootstrap likelihood -1279.006200, best rearrangement setting 7
Bootstrap[42]: Time 0.108656 seconds, bootstrap likelihood -1160.274606, best rearrangement setting 6
Bootstrap[43]: Time 0.131976 seconds, bootstrap likelihood -1216.079259, best rearrangement setting 14
Bootstrap[44]: Time 0.108874 seconds, bootstrap likelihood -1382.278311, best rearrangement setting 8
Bootstrap[45]: Time 0.111613 seconds, bootstrap likelihood -1099.004439, best rearrangement setting 11
Bootstrap[46]: Time 0.096904 seconds, bootstrap likelihood -1296.527478, best rearrangement setting 8
Bootstrap[47]: Time 0.131966 seconds, bootstrap likelihood -1291.322658, best rearrangement setting 9
Bootstrap[48]: Time 0.090672 seconds, bootstrap likelihood -1161.908080, best rearrangement setting 6
Bootstrap[49]: Time 0.121792 seconds, bootstrap likelihood -1257.348428, best rearrangement setting 13
Bootstrap[50]: Time 0.137886 seconds, bootstrap likelihood -1309.422533, best rearrangement setting 13
Bootstrap[51]: Time 0.101962 seconds, bootstrap likelihood -1197.633097, best rearrangement setting 11
Bootstrap[52]: Time 0.115819 seconds, bootstrap likelihood -1347.123005, best rearrangement setting 8
Bootstrap[53]: Time 0.103386 seconds, bootstrap likelihood -1234.934890, best rearrangement setting 14
Bootstrap[54]: Time 0.115443 seconds, bootstrap likelihood -1227.092434, best rearrangement setting 6
Bootstrap[55]: Time 0.119903 seconds, bootstrap likelihood -1280.635747, best rearrangement setting 7
Bootstrap[56]: Time 0.098885 seconds, bootstrap likelihood -1225.911449, best rearrangement setting 6
Bootstrap[57]: Time 0.093505 seconds, bootstrap likelihood -1236.213347, best rearrangement setting 11
Bootstrap[58]: Time 0.136212 seconds, bootstrap likelihood -1393.245723, best rearrangement setting 14
Bootstrap[59]: Time 0.111166 seconds, bootstrap likelihood -1212.039371, best rearrangement setting 6
Bootstrap[60]: Time 0.094707 seconds, bootstrap likelihood -1248.692011, best rearrangement setting 10
Bootstrap[61]: Time 0.113258 seconds, bootstrap likelihood -1172.820979, best rearrangement setting 13
Bootstrap[62]: Time 0.126457 seconds, bootstrap likelihood -1126.745788, best rearrangement setting 14
Bootstrap[63]: Time 0.103841 seconds, bootstrap likelihood -1267.434444, best rearrangement setting 12
Bootstrap[64]: Time 0.096577 seconds, bootstrap likelihood -1340.680748, best rearrangement setting 5
Bootstrap[65]: Time 0.100312 seconds, bootstrap likelihood -1072.671059, best rearrangement setting 5
Bootstrap[66]: Time 0.125874 seconds, bootstrap likelihood -1234.294838, best rearrangement setting 8
Bootstrap[67]: Time 0.120211 seconds, bootstrap likelihood -1109.249439, best rearrangement setting 15
Bootstrap[68]: Time 0.093957 seconds, bootstrap likelihood -1314.493588, best rearrangement setting 8
Bootstrap[69]: Time 0.097466 seconds, bootstrap likelihood -1173.850035, best rearrangement setting 13
Bootstrap[70]: Time 0.103197 seconds, bootstrap likelihood -1231.066465, best rearrangement setting 10
Bootstrap[71]: Time 0.106166 seconds, bootstrap likelihood -1146.861379, best rearrangement setting 9
Bootstrap[72]: Time 0.092670 seconds, bootstrap likelihood -1148.753369, best rearrangement setting 8
Bootstrap[73]: Time 0.104103 seconds, bootstrap likelihood -1333.374056, best rearrangement setting 9
Bootstrap[74]: Time 0.094556 seconds, bootstrap likelihood -1259.382378, best rearrangement setting 5
Bootstrap[75]: Time 0.097477 seconds, bootstrap likelihood -1319.944496, best rearrangement setting 6
Bootstrap[76]: Time 0.111779 seconds, bootstrap likelihood -1309.042165, best rearrangement setting 14
Bootstrap[77]: Time 0.137422 seconds, bootstrap likelihood -1232.061289, best rearrangement setting 8
Bootstrap[78]: Time 0.114677 seconds, bootstrap likelihood -1261.333984, best rearrangement setting 9
Bootstrap[79]: Time 0.114526 seconds, bootstrap likelihood -1194.644341, best rearrangement setting 13
Bootstrap[80]: Time 0.101761 seconds, bootstrap likelihood -1214.037389, best rearrangement setting 9
Bootstrap[81]: Time 0.113334 seconds, bootstrap likelihood -1224.527657, best rearrangement setting 8
Bootstrap[82]: Time 0.129216 seconds, bootstrap likelihood -1241.464826, best rearrangement setting 11
Bootstrap[83]: Time 0.098020 seconds, bootstrap likelihood -1230.730558, best rearrangement setting 6
Bootstrap[84]: Time 0.105114 seconds, bootstrap likelihood -1219.034592, best rearrangement setting 10
Bootstrap[85]: Time 0.113210 seconds, bootstrap likelihood -1280.071994, best rearrangement setting 8
Bootstrap[86]: Time 0.096899 seconds, bootstrap likelihood -1444.747777, best rearrangement setting 9
Bootstrap[87]: Time 0.102209 seconds, bootstrap likelihood -1245.890035, best rearrangement setting 14
Bootstrap[88]: Time 0.115352 seconds, bootstrap likelihood -1287.832766, best rearrangement setting 7
Bootstrap[89]: Time 0.101550 seconds, bootstrap likelihood -1325.245976, best rearrangement setting 5
Bootstrap[90]: Time 0.116997 seconds, bootstrap likelihood -1227.883697, best rearrangement setting 5
Bootstrap[91]: Time 0.111944 seconds, bootstrap likelihood -1273.489392, best rearrangement setting 8
Bootstrap[92]: Time 0.047855 seconds, bootstrap likelihood -1234.725870, best rearrangement setting 7
Bootstrap[93]: Time 0.122291 seconds, bootstrap likelihood -1235.733064, best rearrangement setting 11
Bootstrap[94]: Time 0.102338 seconds, bootstrap likelihood -1204.319488, best rearrangement setting 15
Bootstrap[95]: Time 0.095701 seconds, bootstrap likelihood -1183.328582, best rearrangement setting 11
Bootstrap[96]: Time 0.110511 seconds, bootstrap likelihood -1196.298898, best rearrangement setting 13
Bootstrap[97]: Time 0.119771 seconds, bootstrap likelihood -1339.251746, best rearrangement setting 12
Bootstrap[98]: Time 0.048371 seconds, bootstrap likelihood -1404.363552, best rearrangement setting 7
Bootstrap[99]: Time 0.061370 seconds, bootstrap likelihood -1270.157811, best rearrangement setting 7
Overall Time for 100 Rapid Bootstraps 11.105609 seconds
Average Time per Rapid Bootstrap 0.111056 seconds
Starting ML Search ...
Fast ML optimization finished
Fast ML search Time: 4.457748 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: 2.240228 seconds
Thorough ML search Time: 0.558754 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 7.260944 secs or 0.002017 hours
Combined Bootstrap and ML search took 18.366755 secs or 0.005102 hours
Drawing Bootstrap Support Values on best-scoring ML tree ...
Found 1 tree in File /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl19qkvow/RAxML_bestTree.q2bootstrap
Found 1 tree in File /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl19qkvow/RAxML_bestTree.q2bootstrap
Program execution info written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl19qkvow/RAxML_info.q2bootstrap
All 100 bootstrapped trees written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl19qkvow/RAxML_bootstrap.q2bootstrap
Best-scoring ML tree written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl19qkvow/RAxML_bestTree.q2bootstrap
Best-scoring ML tree with support values written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl19qkvow/RAxML_bipartitions.q2bootstrap
Best-scoring ML tree with support values as branch labels written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl19qkvow/RAxML_bipartitionsBranchLabels.q2bootstrap
Overall execution time for full ML analysis: 18.376695 secs or 0.005105 hours or 0.000213 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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl19qkvow -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 2.2.2.3 COVID-edition for Mac OS X 64-bit built May 16 2023
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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_3p9smci/q2iqtree -nt 1
Seed: 723441 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Tue May 30 15:52:19 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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000590086 secs using 32.2% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000525951 secs using 75.86% 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 7.82013e-05 secs using 75.45% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.002 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 0.0321519 secs using 97.6% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1390.939
2. Current log-likelihood: -1389.577
Optimal log-likelihood: -1388.784
Rate parameters: A-C: 0.37208 A-G: 2.39696 A-T: 2.17455 C-G: 1.26016 C-T: 3.36375 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.034
Gamma shape alpha: 1.405
Parameters optimization took 2 rounds (0.012 sec)
Time for fast ML tree search: 0.074 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 1402.602 45 2895.204 2919.847 3046.673
2 GTR+F+I 1401.121 46 2894.242 2920.134 3049.077
3 GTR+F+G4 1387.358 46 2866.716 2892.608 3021.551
4 GTR+F+I+G4 1387.724 47 2869.448 2896.628 3027.648
5 GTR+F+R2 1382.364 47 2858.729 2885.910 3016.930
6 GTR+F+R3 1382.420 49 2862.840 2892.718 3027.773
14 GTR+F+I+R2 1382.418 48 2860.837 2889.346 3022.403
15 GTR+F+I+R3 1382.449 50 2864.899 2896.187 3033.197
25 SYM+G4 1387.134 43 2860.269 2882.528 3005.006
27 SYM+R2 1383.095 44 2854.189 2877.621 3002.292
36 SYM+I+R2 1383.227 45 2856.454 2881.097 3007.923
47 TVM+F+G4 1388.357 45 2866.713 2891.356 3018.182
49 TVM+F+R2 1383.789 46 2859.578 2885.470 3014.413
58 TVM+F+I+R2 1383.812 47 2861.625 2888.805 3019.826
69 TVMe+G4 1387.122 42 2858.245 2879.368 2999.616
71 TVMe+R2 1383.080 43 2852.159 2874.418 2996.896
80 TVMe+I+R2 1383.224 44 2854.449 2877.881 3002.552
91 TIM3+F+G4 1391.377 44 2870.754 2894.186 3018.857
93 TIM3+F+R2 1385.912 45 2861.825 2886.468 3013.294
102 TIM3+F+I+R2 1386.041 46 2864.082 2889.975 3018.917
113 TIM3e+G4 1390.358 41 2862.715 2882.738 3000.720
115 TIM3e+R2 1385.918 42 2855.836 2876.959 2997.207
124 TIM3e+I+R2 1386.073 43 2858.145 2880.404 3002.882
135 TIM2+F+G4 1393.635 44 2875.270 2898.702 3023.373
137 TIM2+F+R2 1387.681 45 2865.362 2890.005 3016.831
146 TIM2+F+I+R2 1387.782 46 2867.564 2893.456 3022.399
157 TIM2e+G4 1396.795 41 2875.589 2895.613 3013.594
159 TIM2e+R2 1391.574 42 2867.148 2888.270 3008.519
168 TIM2e+I+R2 1391.651 43 2869.302 2891.561 3014.039
179 TIM+F+G4 1390.363 44 2868.726 2892.158 3016.829
181 TIM+F+R2 1384.933 45 2859.866 2884.509 3011.335
190 TIM+F+I+R2 1385.016 46 2862.032 2887.925 3016.867
201 TIMe+G4 1394.002 41 2870.005 2890.028 3008.010
203 TIMe+R2 1389.000 42 2862.000 2883.123 3003.371
212 TIMe+I+R2 1389.095 43 2864.190 2886.449 3008.927
223 TPM3u+F+G4 1392.306 43 2870.611 2892.870 3015.348
225 TPM3u+F+R2 1387.329 44 2862.659 2886.091 3010.762
234 TPM3u+F+I+R2 1387.462 45 2864.923 2889.566 3016.392
245 TPM3+G4 1390.374 40 2860.748 2879.708 2995.387
247 TPM3+R2 1385.925 41 2853.851 2873.874 2991.856
256 TPM3+I+R2 1386.070 42 2856.140 2877.263 2997.511
267 TPM2u+F+G4 1394.533 43 2875.067 2897.325 3019.804
269 TPM2u+F+R2 1389.057 44 2866.113 2889.545 3014.216
278 TPM2u+F+I+R2 1389.101 45 2868.201 2892.844 3019.670
289 TPM2+G4 1396.823 40 2873.646 2892.605 3008.285
291 TPM2+R2 1391.578 41 2865.155 2885.178 3003.160
300 TPM2+I+R2 1391.649 42 2867.297 2888.420 3008.668
311 K3Pu+F+G4 1391.381 43 2868.762 2891.021 3013.499
313 K3Pu+F+R2 1386.371 44 2860.742 2884.174 3008.845
322 K3Pu+F+I+R2 1386.425 45 2862.850 2887.493 3014.319
333 K3P+G4 1394.015 40 2868.030 2886.989 3002.669
335 K3P+R2 1389.002 41 2860.004 2880.028 2998.009
344 K3P+I+R2 1389.099 42 2862.197 2883.320 3003.568
355 TN+F+G4 1394.038 43 2874.077 2896.336 3018.814
357 TN+F+R2 1388.241 44 2864.483 2887.915 3012.586
366 TN+F+I+R2 1388.289 45 2866.578 2891.221 3018.047
377 TNe+G4 1396.791 40 2873.582 2892.542 3008.221
379 TNe+R2 1391.586 41 2865.172 2885.195 3003.177
388 TNe+I+R2 1391.666 42 2867.332 2888.454 3008.703
399 HKY+F+G4 1394.951 42 2873.902 2895.024 3015.273
401 HKY+F+R2 1389.609 43 2865.217 2887.476 3009.954
410 HKY+F+I+R2 1389.663 44 2867.327 2890.759 3015.430
421 K2P+G4 1396.825 39 2871.649 2889.580 3002.922
423 K2P+R2 1391.594 40 2863.189 2882.148 2997.828
432 K2P+I+R2 1391.664 41 2865.327 2885.351 3003.332
443 F81+F+G4 1405.743 41 2893.486 2913.509 3031.491
445 F81+F+R2 1400.805 42 2885.611 2906.733 3026.982
454 F81+F+I+R2 1400.908 43 2887.816 2910.075 3032.553
465 JC+G4 1407.650 38 2891.299 2908.236 3019.206
467 JC+R2 1402.858 39 2883.715 2901.646 3014.988
476 JC+I+R2 1402.926 40 2885.851 2904.811 3020.490
Akaike Information Criterion: TVMe+R2
Corrected Akaike Information Criterion: TPM3+R2
Bayesian Information Criterion: TPM3+R2
Best-fit model: TPM3+R2 chosen according to BIC
All model information printed to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_3p9smci/q2iqtree.model.gz
CPU time for ModelFinder: 1.465 seconds (0h:0m:1s)
Wall-clock time for ModelFinder: 1.514 seconds (0h:0m:1s)
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1385.925
Optimal log-likelihood: -1385.924
Rate parameters: A-C: 0.40868 A-G: 1.56206 A-T: 1.00000 C-G: 0.40868 C-T: 1.56206 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.716,0.409) (0.284,2.490)
Parameters optimization took 1 rounds (0.004 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00105906 secs using 95.93% CPU
Computing ML distances took 0.001152 sec (of wall-clock time) 0.001081 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 7.79629e-05 secs using 120.6% CPU
Constructing RapidNJ tree: done in 0.000157118 secs using 147% CPU
Computing RapidNJ tree took 0.000344 sec (of wall-clock time) 0.000439 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.820
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.111 second
Computing log-likelihood of 98 initial trees ... 0.089 seconds
Current best score: -1385.924
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00461197 secs using 99.94% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.880
Optimizing NNI: done in 0.0140898 secs using 99.75% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1385.311
Optimizing NNI: done in 0.014611 secs using 99.79% CPU
Optimizing NNI: done in 0.013335 secs using 99.67% CPU
Optimizing NNI: done in 0.0131788 secs using 99.69% CPU
Optimizing NNI: done in 0.0126891 secs using 99.9% CPU
Optimizing NNI: done in 0.0129139 secs using 99.94% CPU
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Optimizing NNI: done in 0.0135 secs using 99.27% CPU
Optimizing NNI: done in 0.0137889 secs using 99.75% CPU
Iteration 10 / LogL: -1385.344 / Time: 0h:0m:0s
Optimizing NNI: done in 0.013695 secs using 99.82% CPU
Optimizing NNI: done in 0.0125389 secs using 99.62% CPU
Optimizing NNI: done in 0.012166 secs using 99.9% CPU
Optimizing NNI: done in 0.012327 secs using 99.51% CPU
Optimizing NNI: done in 0.012419 secs using 99.9% CPU
Optimizing NNI: done in 0.01244 secs using 99.95% CPU
Optimizing NNI: done in 0.0126619 secs using 99.95% CPU
Optimizing NNI: done in 0.0125439 secs using 99.94% CPU
Optimizing NNI: done in 0.012455 secs using 99.94% CPU
Optimizing NNI: done in 0.0125411 secs using 99.82% CPU
Iteration 20 / LogL: -1385.343 / Time: 0h:0m:0s
Finish initializing candidate tree set (2)
Current best tree score: -1385.311 / CPU time: 0.469
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0133851 secs using 99.65% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.311
Optimizing NNI: done in 0.021307 secs using 99.75% CPU
Optimizing NNI: done in 0.018312 secs using 99.95% CPU
Optimizing NNI: done in 0.013207 secs using 99.95% CPU
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Optimizing NNI: done in 0.017076 secs using 99.87% CPU
Optimizing NNI: done in 0.020529 secs using 99.91% CPU
Iteration 30 / LogL: -1385.928 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.0286088 secs using 99.94% CPU
Optimizing NNI: done in 0.0237181 secs using 99.93% CPU
Optimizing NNI: done in 0.0164268 secs using 99.78% CPU
Optimizing NNI: done in 0.018683 secs using 99.9% CPU
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Optimizing NNI: done in 0.00774288 secs using 99.96% CPU
Iteration 40 / LogL: -1385.928 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.0120099 secs using 99.68% CPU
Optimizing NNI: done in 0.0173111 secs using 99.77% CPU
Optimizing NNI: done in 0.0136659 secs using 99.91% CPU
Optimizing NNI: done in 0.023108 secs using 99.95% CPU
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Optimizing NNI: done in 0.019701 secs using 99.87% CPU
Optimizing NNI: done in 0.0163569 secs using 99.92% CPU
Iteration 50 / LogL: -1385.324 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.0207882 secs using 99.95% CPU
Optimizing NNI: done in 0.0142689 secs using 99.96% CPU
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Optimizing NNI: done in 0.0141392 secs using 99.92% CPU
Iteration 60 / LogL: -1385.508 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.013541 secs using 99.96% CPU
Optimizing NNI: done in 0.0126882 secs using 99.64% CPU
Optimizing NNI: done in 0.0225751 secs using 99.91% CPU
Optimizing NNI: done in 0.0161641 secs using 99.81% CPU
Optimizing NNI: done in 0.012471 secs using 99.91% CPU
Optimizing NNI: done in 0.0191419 secs using 98.33% CPU
Optimizing NNI: done in 0.00804615 secs using 99.92% CPU
Optimizing NNI: done in 0.019882 secs using 99.85% CPU
Optimizing NNI: done in 0.0136969 secs using 99.67% CPU
Optimizing NNI: done in 0.017267 secs using 99.72% CPU
Iteration 70 / LogL: -1393.509 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0111301 secs using 99.52% CPU
Optimizing NNI: done in 0.0124171 secs using 99.85% CPU
Optimizing NNI: done in 0.0128889 secs using 99.95% CPU
Optimizing NNI: done in 0.016084 secs using 99.94% CPU
Optimizing NNI: done in 0.0185809 secs using 99.95% CPU
Optimizing NNI: done in 0.0132849 secs using 99.96% CPU
Optimizing NNI: done in 0.0197079 secs using 99.95% CPU
Optimizing NNI: done in 0.01245 secs using 99.96% CPU
Optimizing NNI: done in 0.0136199 secs using 99.83% CPU
Optimizing NNI: done in 0.0163679 secs using 99.94% CPU
Iteration 80 / LogL: -1386.127 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0163929 secs using 99.62% CPU
Optimizing NNI: done in 0.010855 secs using 99.8% CPU
Optimizing NNI: done in 0.0154791 secs using 99.95% CPU
Optimizing NNI: done in 0.0140259 secs using 99.94% CPU
Optimizing NNI: done in 0.0117421 secs using 99.95% CPU
Optimizing NNI: done in 0.0149808 secs using 99.84% CPU
Optimizing NNI: done in 0.0105839 secs using 99.89% CPU
Optimizing NNI: done in 0.0213671 secs using 99.81% CPU
Optimizing NNI: done in 0.015708 secs using 99.91% CPU
Optimizing NNI: done in 0.024354 secs using 99.94% CPU
Iteration 90 / LogL: -1385.313 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0258379 secs using 99.96% CPU
Optimizing NNI: done in 0.0120051 secs using 99.94% CPU
Optimizing NNI: done in 0.0139091 secs using 99.96% CPU
Optimizing NNI: done in 0.018894 secs using 99.9% CPU
Optimizing NNI: done in 0.012435 secs using 99.85% CPU
Optimizing NNI: done in 0.0148401 secs using 99.59% CPU
Optimizing NNI: done in 0.015933 secs using 99.75% CPU
Optimizing NNI: done in 0.0123899 secs using 99.91% CPU
Optimizing NNI: done in 0.0114479 secs using 99.94% CPU
Optimizing NNI: done in 0.015007 secs using 99.95% CPU
Iteration 100 / LogL: -1385.638 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0048058 secs using 99.94% CPU
Optimizing NNI: done in 0.014385 secs using 99.94% CPU
Optimizing NNI: done in 0.0126531 secs using 99.68% CPU
TREE SEARCH COMPLETED AFTER 103 ITERATIONS / Time: 0h:0m:1s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1385.311
Optimal log-likelihood: -1385.306
Rate parameters: A-C: 0.39455 A-G: 1.56658 A-T: 1.00000 C-G: 0.39455 C-T: 1.56658 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.721,0.402) (0.279,2.541)
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1385.306
Total tree length: 6.843
Total number of iterations: 103
CPU time used for tree search: 2.017 sec (0h:0m:2s)
Wall-clock time used for tree search: 1.842 sec (0h:0m:1s)
Total CPU time used: 2.050 sec (0h:0m:2s)
Total wall-clock time used: 1.870 sec (0h:0m:1s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_3p9smci/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_3p9smci/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_3p9smci/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_3p9smci/q2iqtree.log
Date and Time: Tue May 30 15:52:23 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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp_3p9smci/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 2.2.2.3 COVID-edition for Mac OS X 64-bit built May 16 2023
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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpai8vj51t/q2iqtree -nt 1
Seed: 766545 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Tue May 30 15:52:33 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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000324011 secs using 82.71% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000467062 secs using 78.15% 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 7.29561e-05 secs using 78.13% 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, 1.291 / LogL: -1395.188
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.008, 1.381 / LogL: -1395.457
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.009, 1.392 / LogL: -1395.524
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.009, 1.388 / LogL: -1395.518
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.008, 1.379 / LogL: -1395.488
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.009, 1.379 / LogL: -1395.523
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.008, 1.373 / LogL: -1395.471
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.008, 1.374 / LogL: -1395.489
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.009, 1.373 / LogL: -1395.500
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.009, 1.378 / LogL: -1395.504
Optimal pinv,alpha: 0.000, 1.291 / LogL: -1395.188
Parameters optimization took 0.548 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00149798 secs using 98.4% CPU
Computing ML distances took 0.001588 sec (of wall-clock time) 0.001540 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.00679e-05 secs using 97.87% CPU
Constructing RapidNJ tree: done in 8.98838e-05 secs using 142.4% CPU
Computing RapidNJ tree took 0.000213 sec (of wall-clock time) 0.000253 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.870
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.115 second
Computing log-likelihood of 98 initial trees ... 0.142 seconds
Current best score: -1392.870
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.020704 secs using 98.47% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.263
Optimizing NNI: done in 0.0301561 secs using 98.55% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.263
Optimizing NNI: done in 0.0153739 secs using 98.59% CPU
Optimizing NNI: done in 0.015609 secs using 98.46% CPU
Optimizing NNI: done in 0.014956 secs using 98.74% CPU
Optimizing NNI: done in 0.015147 secs using 98.75% CPU
Optimizing NNI: done in 0.0152869 secs using 98.63% CPU
Optimizing NNI: done in 0.0158391 secs using 98.26% CPU
Optimizing NNI: done in 0.0152011 secs using 98.24% CPU
Optimizing NNI: done in 0.0151141 secs using 98.27% CPU
Iteration 10 / LogL: -1387.729 / Time: 0h:0m:1s
Optimizing NNI: done in 0.0298769 secs using 98.04% CPU
Optimizing NNI: done in 0.0294471 secs using 98.61% CPU
Optimizing NNI: done in 0.028826 secs using 98.44% CPU
Optimizing NNI: done in 0.027941 secs using 98.48% CPU
Optimizing NNI: done in 0.0282001 secs using 98.01% CPU
Optimizing NNI: done in 0.0280249 secs using 98.08% CPU
Optimizing NNI: done in 0.0279129 secs using 98.02% CPU
Optimizing NNI: done in 0.028039 secs using 97.87% CPU
Optimizing NNI: done in 0.0291181 secs using 98.03% CPU
Optimizing NNI: done in 0.027884 secs using 98.5% CPU
Iteration 20 / LogL: -1387.281 / Time: 0h:0m:1s
Finish initializing candidate tree set (1)
Current best tree score: -1387.263 / CPU time: 0.739
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0454268 secs using 98.59% CPU
Optimizing NNI: done in 0.0250061 secs using 98.33% CPU
Optimizing NNI: done in 0.0270782 secs using 98.53% CPU
Optimizing NNI: done in 0.011255 secs using 98.89% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.258
Optimizing NNI: done in 0.0234551 secs using 98.19% CPU
Optimizing NNI: done in 0.0402811 secs using 98.31% CPU
Optimizing NNI: done in 0.0215099 secs using 98.34% CPU
Optimizing NNI: done in 0.0205638 secs using 98.55% CPU
Optimizing NNI: done in 0.0310519 secs using 98.42% CPU
Optimizing NNI: done in 0.0378149 secs using 98.47% CPU
Iteration 30 / LogL: -1396.173 / Time: 0h:0m:1s (0h:0m:3s left)
Optimizing NNI: done in 0.0212851 secs using 97.57% CPU
Optimizing NNI: done in 0.0270371 secs using 98.69% CPU
Optimizing NNI: done in 0.0216169 secs using 99.79% CPU
Optimizing NNI: done in 0.0211928 secs using 99.96% CPU
Optimizing NNI: done in 0.035429 secs using 99.7% CPU
Optimizing NNI: done in 0.019351 secs using 99.96% CPU
Optimizing NNI: done in 0.020118 secs using 99.96% CPU
Optimizing NNI: done in 0.019578 secs using 99.96% CPU
Optimizing NNI: done in 0.0288 secs using 99.97% CPU
Optimizing NNI: done in 0.052918 secs using 99.8% CPU
Iteration 40 / LogL: -1387.355 / Time: 0h:0m:1s (0h:0m:2s left)
Optimizing NNI: done in 0.0497129 secs using 99.95% CPU
Optimizing NNI: done in 0.025872 secs using 99.96% CPU
Optimizing NNI: done in 0.0291641 secs using 99.87% CPU
Optimizing NNI: done in 0.00683904 secs using 99.37% CPU
Optimizing NNI: done in 0.021862 secs using 99.96% CPU
Optimizing NNI: done in 0.031146 secs using 99.95% CPU
Optimizing NNI: done in 0.027683 secs using 99.97% CPU
Optimizing NNI: done in 0.013629 secs using 99.95% CPU
Optimizing NNI: done in 0.020963 secs using 99.72% CPU
Optimizing NNI: done in 0.0312068 secs using 99.83% CPU
Iteration 50 / LogL: -1387.370 / Time: 0h:0m:2s (0h:0m:2s left)
Optimizing NNI: done in 0.013196 secs using 99.7% CPU
Optimizing NNI: done in 0.030015 secs using 99.95% CPU
Optimizing NNI: done in 0.040519 secs using 99.84% CPU
Optimizing NNI: done in 0.0270841 secs using 99.9% CPU
Optimizing NNI: done in 0.0286169 secs using 99.97% CPU
Optimizing NNI: done in 0.0295131 secs using 99.63% CPU
Optimizing NNI: done in 0.0260248 secs using 99.95% CPU
Optimizing NNI: done in 0.0675709 secs using 99.74% CPU
Optimizing NNI: done in 0.029608 secs using 99.67% CPU
Optimizing NNI: done in 0.030736 secs using 99.94% CPU
Iteration 60 / LogL: -1387.277 / Time: 0h:0m:2s (0h:0m:1s left)
Optimizing NNI: done in 0.0292549 secs using 99.65% CPU
Optimizing NNI: done in 0.0296581 secs using 99.94% CPU
Optimizing NNI: done in 0.03 secs using 99.96% CPU
Optimizing NNI: done in 0.0221078 secs using 99.96% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.256
Optimizing NNI: done in 0.0237441 secs using 99.5% CPU
Optimizing NNI: done in 0.014998 secs using 99.91% CPU
Optimizing NNI: done in 0.0377011 secs using 99.86% CPU
Optimizing NNI: done in 0.023231 secs using 99.96% CPU
Optimizing NNI: done in 0.00939107 secs using 99.96% CPU
Optimizing NNI: done in 0.0437522 secs using 99.91% CPU
Iteration 70 / LogL: -1387.354 / Time: 0h:0m:2s (0h:0m:1s left)
Optimizing NNI: done in 0.0418921 secs using 99.87% CPU
Optimizing NNI: done in 0.0489969 secs using 99.85% CPU
Optimizing NNI: done in 0.018914 secs using 99.71% CPU
Optimizing NNI: done in 0.0213368 secs using 99.9% CPU
Optimizing NNI: done in 0.025836 secs using 99.97% CPU
Optimizing NNI: done in 0.0357771 secs using 99.96% CPU
Optimizing NNI: done in 0.0292509 secs using 99.96% CPU
Optimizing NNI: done in 0.027853 secs using 99.73% CPU
Optimizing NNI: done in 0.029712 secs using 99.96% CPU
Optimizing NNI: done in 0.0347071 secs using 99.86% CPU
Iteration 80 / LogL: -1387.393 / Time: 0h:0m:3s (0h:0m:0s left)
Optimizing NNI: done in 0.0180008 secs using 99.96% CPU
Optimizing NNI: done in 0.015439 secs using 99.96% CPU
Optimizing NNI: done in 0.0226979 secs using 99.72% CPU
Optimizing NNI: done in 0.022011 secs using 99.83% CPU
Optimizing NNI: done in 0.030921 secs using 99.96% CPU
Optimizing NNI: done in 0.034971 secs using 99.96% CPU
Optimizing NNI: done in 0.039851 secs using 99.9% CPU
Optimizing NNI: done in 0.0353479 secs using 99.88% CPU
Optimizing NNI: done in 0.035526 secs using 99.96% CPU
Optimizing NNI: done in 0.027806 secs using 99.96% CPU
Iteration 90 / LogL: -1387.299 / Time: 0h:0m:3s (0h:0m:0s left)
Optimizing NNI: done in 0.020067 secs using 99.85% CPU
Optimizing NNI: done in 0.01038 secs using 99.92% CPU
Optimizing NNI: done in 0.0235581 secs using 99.8% CPU
Optimizing NNI: done in 0.0217609 secs using 99.96% CPU
Optimizing NNI: done in 0.034394 secs using 99.95% CPU
Optimizing NNI: done in 0.0199752 secs using 99.96% CPU
Optimizing NNI: done in 0.0119879 secs using 99.51% CPU
Optimizing NNI: done in 0.027209 secs using 99.83% CPU
Optimizing NNI: done in 0.0291822 secs using 99.95% CPU
Optimizing NNI: done in 0.0162199 secs using 99.96% CPU
Iteration 100 / LogL: -1387.613 / Time: 0h:0m:3s (0h:0m:0s left)
Optimizing NNI: done in 0.0462942 secs using 99.89% CPU
Optimizing NNI: done in 0.028749 secs using 99.82% CPU
TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:3s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.256
Optimal log-likelihood: -1387.253
Rate parameters: A-C: 0.32711 A-G: 2.23257 A-T: 2.11096 C-G: 1.15859 C-T: 3.23991 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: 1.329
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1387.253
Total tree length: 6.696
Total number of iterations: 102
CPU time used for tree search: 3.237 sec (0h:0m:3s)
Wall-clock time used for tree search: 3.080 sec (0h:0m:3s)
Total CPU time used: 3.804 sec (0h:0m:3s)
Total wall-clock time used: 3.653 sec (0h:0m:3s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpai8vj51t/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpai8vj51t/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpai8vj51t/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpai8vj51t/q2iqtree.log
Date and Time: Tue May 30 15:52:37 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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpai8vj51t/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 2.2.2.3 COVID-edition for Mac OS X 64-bit built May 16 2023
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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl89k1sj3/q2iqtree -nt 1 -fast
Seed: 159290 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Tue May 30 15:52:48 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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000324011 secs using 80.86% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.00061512 secs using 78.03% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Analyzing sequences: done in 2.71797e-05 secs using 88.3% CPU
Checking for duplicate sequences: done in 9.20296e-05 secs using 76.06% CPU
---> START RUN NUMBER 1 (seed: 159290)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.00 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.50)
1. Initial log-likelihood: -1492.10
2. Current log-likelihood: -1401.82
3. Current log-likelihood: -1396.52
4. Current log-likelihood: -1395.12
5. Current log-likelihood: -1394.39
Optimal log-likelihood: -1393.82
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 (0.048 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00237203 secs using 98.82% CPU
Computing ML distances took 0.002507 sec (of wall-clock time) 0.002440 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 6.79493e-05 secs using 91.24% CPU
Constructing RapidNJ tree: done in 0.000139952 secs using 157.2% CPU
Computing RapidNJ tree took 0.000302 sec (of wall-clock time) 0.000348 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.794
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| INITIALIZING CANDIDATE TREE SET |
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Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0241919 secs using 192% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.214
Optimizing NNI: done in 0.0234208 secs using 193.7% CPU
Finish initializing candidate tree set (3)
Current best tree score: -1388.214 / CPU time: 0.126
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
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| FINALIZING TREE SEARCH |
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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 (0.027 sec)
BEST SCORE FOUND : -1387.519
Total tree length: 6.815
Total number of iterations: 2
CPU time used for tree search: 0.175 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.127 sec (0h:0m:0s)
Total CPU time used: 0.302 sec (0h:0m:0s)
Total wall-clock time used: 0.226 sec (0h:0m:0s)
---> START RUN NUMBER 2 (seed: 160290)
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: -1493.167
2. Current log-likelihood: -1403.041
3. Current log-likelihood: -1398.313
4. Current log-likelihood: -1396.957
5. Current log-likelihood: -1396.228
Optimal log-likelihood: -1395.709
Rate parameters: A-C: 0.23146 A-G: 2.06957 A-T: 1.96268 C-G: 1.07937 C-T: 2.84174 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.322
Parameters optimization took 5 rounds (0.042 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00159788 secs using 97.25% CPU
Computing ML distances took 0.001695 sec (of wall-clock time) 0.001621 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 6.41346e-05 secs using 81.08% CPU
Constructing RapidNJ tree: done in 9.60827e-05 secs using 148.8% CPU
Computing RapidNJ tree took 0.000226 sec (of wall-clock time) 0.000258 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.184
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| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.024229 secs using 192.7% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.955
Optimizing NNI: done in 0.0146892 secs using 193.2% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.955 / CPU time: 0.057
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
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| 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 (0.024 sec)
BEST SCORE FOUND : -1387.423
Total tree length: 6.744
Total number of iterations: 2
CPU time used for tree search: 0.109 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.057 sec (0h:0m:0s)
Total CPU time used: 0.254 sec (0h:0m:0s)
Total wall-clock time used: 0.143 sec (0h:0m:0s)
---> START RUN NUMBER 3 (seed: 161290)
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: -1492.199
2. Current log-likelihood: -1404.591
3. Current log-likelihood: -1399.228
4. Current log-likelihood: -1397.831
5. Current log-likelihood: -1397.074
Optimal log-likelihood: -1396.495
Rate parameters: A-C: 0.24620 A-G: 2.08306 A-T: 1.99581 C-G: 1.06240 C-T: 2.85598 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: 1.432
Parameters optimization took 5 rounds (0.051 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00156403 secs using 191.7% CPU
Computing ML distances took 0.001683 sec (of wall-clock time) 0.003182 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 7.10487e-05 secs using 78.82% CPU
Constructing RapidNJ tree: done in 0.000161886 secs using 135.3% CPU
Computing RapidNJ tree took 0.000340 sec (of wall-clock time) 0.000360 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.972
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0212009 secs using 192.6% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.188
Optimizing NNI: done in 0.0317261 secs using 192.7% CPU
UPDATE BEST LOG-LIKELIHOOD: -1388.187
Finish initializing candidate tree set (3)
Current best tree score: -1388.187 / CPU time: 0.064
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
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| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.187
2. Current log-likelihood: -1387.966
3. Current log-likelihood: -1387.806
4. Current log-likelihood: -1387.687
5. Current log-likelihood: -1387.596
6. Current log-likelihood: -1387.525
7. Current log-likelihood: -1387.471
Optimal log-likelihood: -1387.426
Rate parameters: A-C: 0.33228 A-G: 2.23741 A-T: 2.11202 C-G: 1.16006 C-T: 3.23503 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 (0.030 sec)
BEST SCORE FOUND : -1387.426
Total tree length: 6.737
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: 0.314 sec (0h:0m:0s)
Total wall-clock time used: 0.165 sec (0h:0m:0s)
---> START RUN NUMBER 4 (seed: 162290)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1493.259
2. Current log-likelihood: -1403.078
3. Current log-likelihood: -1398.354
4. Current log-likelihood: -1396.979
5. Current log-likelihood: -1396.262
Optimal log-likelihood: -1395.753
Rate parameters: A-C: 0.24339 A-G: 2.10097 A-T: 1.98595 C-G: 1.09180 C-T: 2.82193 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.355
Parameters optimization took 5 rounds (0.044 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00165701 secs using 192.4% CPU
Computing ML distances took 0.001803 sec (of wall-clock time) 0.003414 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 6.69956e-05 secs using 79.11% CPU
Constructing RapidNJ tree: done in 0.000144005 secs using 121.5% CPU
Computing RapidNJ tree took 0.000310 sec (of wall-clock time) 0.000305 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 0.0230169 secs using 192.4% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.961
Optimizing NNI: done in 0.0574062 secs using 191.9% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.961 / CPU time: 0.100
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
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| 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 (0.024 sec)
BEST SCORE FOUND : -1387.424
Total tree length: 6.743
Total number of iterations: 2
CPU time used for tree search: 0.193 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.100 sec (0h:0m:0s)
Total CPU time used: 0.361 sec (0h:0m:0s)
Total wall-clock time used: 0.189 sec (0h:0m:0s)
---> START RUN NUMBER 5 (seed: 163290)
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 (0.045 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0016551 secs using 192.9% CPU
Computing ML distances took 0.001773 sec (of wall-clock time) 0.003377 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 7.20024e-05 secs using 80.55% CPU
Constructing RapidNJ tree: done in 0.000164986 secs using 138.2% CPU
Computing RapidNJ tree took 0.000338 sec (of wall-clock time) 0.000377 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 0.0231259 secs using 192.6% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.213
Optimizing NNI: done in 0.0230212 secs using 192.7% CPU
Finish initializing candidate tree set (3)
Current best tree score: -1388.213 / CPU time: 0.057
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
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| 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 (0.027 sec)
BEST SCORE FOUND : -1387.519
Total tree length: 6.816
Total number of iterations: 2
CPU time used for tree search: 0.110 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.057 sec (0h:0m:0s)
Total CPU time used: 0.284 sec (0h:0m:0s)
Total wall-clock time used: 0.149 sec (0h:0m:0s)
---> START RUN NUMBER 6 (seed: 164290)
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: -1493.167
2. Current log-likelihood: -1403.041
3. Current log-likelihood: -1398.313
4. Current log-likelihood: -1396.957
5. Current log-likelihood: -1396.228
Optimal log-likelihood: -1395.709
Rate parameters: A-C: 0.23146 A-G: 2.06957 A-T: 1.96268 C-G: 1.07937 C-T: 2.84174 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.322
Parameters optimization took 5 rounds (0.044 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00223279 secs using 193.5% CPU
Computing ML distances took 0.002335 sec (of wall-clock time) 0.004489 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 5.00679e-05 secs using 79.89% CPU
Constructing RapidNJ tree: done in 9.60827e-05 secs using 119.7% CPU
Computing RapidNJ tree took 0.000222 sec (of wall-clock time) 0.000208 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 0.027451 secs using 192.8% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.955
Optimizing NNI: done in 0.0144339 secs using 191.9% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.955 / CPU time: 0.062
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -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 (0.024 sec)
BEST SCORE FOUND : -1387.423
Total tree length: 6.744
Total number of iterations: 2
CPU time used for tree search: 0.119 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.062 sec (0h:0m:0s)
Total CPU time used: 0.290 sec (0h:0m:0s)
Total wall-clock time used: 0.152 sec (0h:0m:0s)
---> START RUN NUMBER 7 (seed: 165290)
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: 3.28731 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 (0.046 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00171185 secs using 192.8% CPU
Computing ML distances took 0.001817 sec (of wall-clock time) 0.003471 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.10216e-05 secs using 80.36% CPU
Constructing RapidNJ tree: done in 0.00010705 secs using 133.6% CPU
Computing RapidNJ tree took 0.000242 sec (of wall-clock time) 0.000249 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 0.0225301 secs using 192.9% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.217
Optimizing NNI: done in 0.036953 secs using 192.4% CPU
BETTER TREE FOUND at iteration 2: -1388.188
Finish initializing candidate tree set (4)
Current best tree score: -1388.188 / CPU time: 0.071
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
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| 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 (0.030 sec)
BEST SCORE FOUND : -1387.534
Total tree length: 7.502
Total number of iterations: 2
CPU time used for tree search: 0.136 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.071 sec (0h:0m:0s)
Total CPU time used: 0.318 sec (0h:0m:0s)
Total wall-clock time used: 0.167 sec (0h:0m:0s)
---> START RUN NUMBER 8 (seed: 166290)
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 (0.049 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00194597 secs using 167% CPU
Computing ML distances took 0.002076 sec (of wall-clock time) 0.003472 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 6.98566e-05 secs using 80.16% CPU
Constructing RapidNJ tree: done in 0.000163078 secs using 139.2% CPU
Computing RapidNJ tree took 0.000369 sec (of wall-clock time) 0.000370 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 0.0219131 secs using 192.7% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.961
Optimizing NNI: done in 0.0553298 secs using 192.1% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.961 / CPU time: 0.097
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
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| 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 (0.026 sec)
BEST SCORE FOUND : -1387.424
Total tree length: 6.743
Total number of iterations: 2
CPU time used for tree search: 0.187 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.098 sec (0h:0m:0s)
Total CPU time used: 0.370 sec (0h:0m:0s)
Total wall-clock time used: 0.194 sec (0h:0m:0s)
---> START RUN NUMBER 9 (seed: 167290)
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: -1493.459
2. Current log-likelihood: -1403.057
3. Current log-likelihood: -1398.315
4. Current log-likelihood: -1396.957
5. Current log-likelihood: -1396.224
Optimal log-likelihood: -1395.705
Rate parameters: A-C: 0.23667 A-G: 2.08551 A-T: 1.97696 C-G: 1.07651 C-T: 2.86648 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 0.00234008 secs using 192.9% CPU
Computing ML distances took 0.002480 sec (of wall-clock time) 0.004747 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 7.31945e-05 secs using 86.07% CPU
Constructing RapidNJ tree: done in 0.000164986 secs using 143.6% CPU
Computing RapidNJ tree took 0.000346 sec (of wall-clock time) 0.000400 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.170
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.024487 secs using 192.5% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.175
Optimizing NNI: done in 0.0109282 secs using 193.4% CPU
Finish initializing candidate tree set (3)
Current best tree score: -1388.175 / CPU time: 0.049
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.175
2. Current log-likelihood: -1387.959
3. Current log-likelihood: -1387.799
4. Current log-likelihood: -1387.681
5. Current log-likelihood: -1387.591
6. Current log-likelihood: -1387.521
7. Current log-likelihood: -1387.467
Optimal log-likelihood: -1387.423
Rate parameters: A-C: 0.33681 A-G: 2.27128 A-T: 2.14654 C-G: 1.17860 C-T: 3.29078 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: 1.351
Parameters optimization took 7 rounds (0.031 sec)
BEST SCORE FOUND : -1387.423
Total tree length: 6.745
Total number of iterations: 2
CPU time used for tree search: 0.095 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.049 sec (0h:0m:0s)
Total CPU time used: 0.268 sec (0h:0m:0s)
Total wall-clock time used: 0.141 sec (0h:0m:0s)
---> START RUN NUMBER 10 (seed: 168290)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1492.097
2. Current log-likelihood: -1401.816
3. Current log-likelihood: -1396.523
4. Current log-likelihood: -1395.122
5. Current log-likelihood: -1394.389
Optimal log-likelihood: -1393.818
Rate parameters: A-C: 0.27163 A-G: 2.41073 A-T: 2.17144 C-G: 1.24911 C-T: 3.27679 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.416
Parameters optimization took 5 rounds (0.043 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00163603 secs using 192.9% CPU
Computing ML distances took 0.001728 sec (of wall-clock time) 0.003317 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 6.48499e-05 secs using 83.27% CPU
Constructing RapidNJ tree: done in 9.70364e-05 secs using 158.7% CPU
Computing RapidNJ tree took 0.000230 sec (of wall-clock time) 0.000250 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 0.0221639 secs using 192.1% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.214
Optimizing NNI: done in 0.02121 secs using 192.9% CPU
Finish initializing candidate tree set (3)
Current best tree score: -1388.214 / CPU time: 0.053
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -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 (0.031 sec)
BEST SCORE FOUND : -1387.519
Total tree length: 6.815
Total number of iterations: 2
CPU time used for tree search: 0.102 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.053 sec (0h:0m:0s)
Total CPU time used: 0.282 sec (0h:0m:0s)
Total wall-clock time used: 0.148 sec (0h:0m:0s)
---> SUMMARIZE RESULTS FROM 10 RUNS
Run 9 gave best log-likelihood: -1387.423
Total CPU time for 10 runs: 3.082 seconds.
Total wall-clock time for 10 runs: 1.699 seconds.
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl89k1sj3/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl89k1sj3/q2iqtree.treefile
Trees from independent runs: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl89k1sj3/q2iqtree.runtrees
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl89k1sj3/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl89k1sj3/q2iqtree.log
Date and Time: Tue May 30 15:52:49 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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpl89k1sj3/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 2.2.2.3 COVID-edition for Mac OS X 64-bit built May 16 2023
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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxhxlfai3/q2iqtree -nt 1 -alrt 1000 -abayes -lbp 1000
Seed: 610019 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Tue May 30 15:53:00 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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000225067 secs using 83.97% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000479937 secs using 78.34% 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 7.20024e-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, 1.282 / LogL: -1392.553
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.008, 1.377 / LogL: -1392.829
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.009, 1.391 / LogL: -1392.898
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.009, 1.388 / LogL: -1392.889
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.008, 1.383 / LogL: -1392.853
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.009, 1.384 / LogL: -1392.879
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.007, 1.379 / LogL: -1392.828
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.008, 1.382 / LogL: -1392.844
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.008, 1.383 / LogL: -1392.849
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.008, 1.384 / LogL: -1392.858
Optimal pinv,alpha: 0.000, 1.282 / LogL: -1392.553
Parameters optimization took 0.530 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00158715 secs using 96.21% CPU
Computing ML distances took 0.001709 sec (of wall-clock time) 0.001609 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 7.29561e-05 secs using 91.84% CPU
Constructing RapidNJ tree: done in 0.000126839 secs using 138.8% CPU
Computing RapidNJ tree took 0.000294 sec (of wall-clock time) 0.000312 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.710
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.123 second
Computing log-likelihood of 98 initial trees ... 0.142 seconds
Current best score: -1392.553
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.015476 secs using 98.15% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.261
Optimizing NNI: done in 0.023756 secs using 98.22% CPU
Optimizing NNI: done in 0.015209 secs using 98.71% CPU
Optimizing NNI: done in 0.0155921 secs using 97.69% CPU
Optimizing NNI: done in 0.015548 secs using 98.03% CPU
Optimizing NNI: done in 0.0177879 secs using 98.11% CPU
Optimizing NNI: done in 0.0155871 secs using 98.34% CPU
Optimizing NNI: done in 0.0150139 secs using 98.77% CPU
Optimizing NNI: done in 0.027786 secs using 98.05% CPU
Optimizing NNI: done in 0.027621 secs using 98.46% CPU
Iteration 10 / LogL: -1387.282 / Time: 0h:0m:1s
Optimizing NNI: done in 0.027195 secs using 98.54% CPU
Optimizing NNI: done in 0.0281141 secs using 97.88% CPU
Optimizing NNI: done in 0.027801 secs using 98.21% CPU
Optimizing NNI: done in 0.0280862 secs using 98.24% CPU
Optimizing NNI: done in 0.030457 secs using 98.43% CPU
Optimizing NNI: done in 0.0306678 secs using 98.14% CPU
Optimizing NNI: done in 0.0290031 secs using 97.69% CPU
Optimizing NNI: done in 0.027735 secs using 98.46% CPU
Optimizing NNI: done in 0.0208399 secs using 98.78% CPU
Optimizing NNI: done in 0.0210309 secs using 99.17% CPU
Iteration 20 / LogL: -1387.267 / Time: 0h:0m:1s
Finish initializing candidate tree set (2)
Current best tree score: -1387.261 / CPU time: 0.746
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.02742 secs using 98.66% CPU
Optimizing NNI: done in 0.048559 secs using 98.36% CPU
Optimizing NNI: done in 0.038543 secs using 98.52% CPU
Optimizing NNI: done in 0.038573 secs using 98.31% CPU
Optimizing NNI: done in 0.0460198 secs using 98.53% CPU
Optimizing NNI: done in 0.00966191 secs using 98.39% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.256
Optimizing NNI: done in 0.0358629 secs using 98.3% CPU
Optimizing NNI: done in 0.0207918 secs using 99.05% CPU
Optimizing NNI: done in 0.042906 secs using 97.82% CPU
Optimizing NNI: done in 0.0174341 secs using 98.89% CPU
Iteration 30 / LogL: -1387.350 / Time: 0h:0m:1s (0h:0m:3s left)
Optimizing NNI: done in 0.0271809 secs using 98.84% CPU
Optimizing NNI: done in 0.04387 secs using 99.71% CPU
Optimizing NNI: done in 0.0424731 secs using 99.7% CPU
Optimizing NNI: done in 0.030077 secs using 99.95% CPU
Optimizing NNI: done in 0.03037 secs using 99.66% CPU
Optimizing NNI: done in 0.0204189 secs using 99.52% CPU
Optimizing NNI: done in 0.029588 secs using 99.94% CPU
Optimizing NNI: done in 0.015224 secs using 99.8% CPU
Optimizing NNI: done in 0.022908 secs using 99.75% CPU
Optimizing NNI: done in 0.035377 secs using 99.83% CPU
Iteration 40 / LogL: -1387.353 / Time: 0h:0m:1s (0h:0m:3s left)
Optimizing NNI: done in 0.024847 secs using 99.38% CPU
Optimizing NNI: done in 0.0419331 secs using 99.9% CPU
Optimizing NNI: done in 0.02968 secs using 99.76% CPU
Optimizing NNI: done in 0.020123 secs using 99.95% CPU
Optimizing NNI: done in 0.0214682 secs using 99.7% CPU
Optimizing NNI: done in 0.0351949 secs using 99.86% CPU
Optimizing NNI: done in 0.0250871 secs using 99.96% CPU
Optimizing NNI: done in 0.01893 secs using 99.82% CPU
Optimizing NNI: done in 0.040895 secs using 99.81% CPU
Optimizing NNI: done in 0.039254 secs using 99.84% CPU
Iteration 50 / LogL: -1387.354 / Time: 0h:0m:2s (0h:0m:2s left)
Optimizing NNI: done in 0.05039 secs using 99.83% CPU
Optimizing NNI: done in 0.0403972 secs using 99.88% CPU
Optimizing NNI: done in 0.0268171 secs using 99.85% CPU
Optimizing NNI: done in 0.015574 secs using 99.95% CPU
Optimizing NNI: done in 0.0217841 secs using 99.97% CPU
Optimizing NNI: done in 0.031467 secs using 99.97% CPU
Optimizing NNI: done in 0.0204091 secs using 99.86% CPU
Optimizing NNI: done in 0.0349021 secs using 99.87% CPU
Optimizing NNI: done in 0.039808 secs using 99.96% CPU
Optimizing NNI: done in 0.0300429 secs using 99.96% CPU
Iteration 60 / LogL: -1387.368 / Time: 0h:0m:2s (0h:0m:1s left)
Optimizing NNI: done in 0.025542 secs using 99.88% CPU
Optimizing NNI: done in 0.0430992 secs using 99.8% CPU
Optimizing NNI: done in 0.025321 secs using 99.89% CPU
Optimizing NNI: done in 0.062423 secs using 99.79% CPU
Optimizing NNI: done in 0.0235651 secs using 99.8% CPU
Optimizing NNI: done in 0.029206 secs using 99.93% CPU
Optimizing NNI: done in 0.024086 secs using 99.96% CPU
Optimizing NNI: done in 0.0346279 secs using 99.73% CPU
Optimizing NNI: done in 0.0342431 secs using 99.81% CPU
Optimizing NNI: done in 0.032861 secs using 99.83% CPU
Iteration 70 / LogL: -1406.641 / Time: 0h:0m:2s (0h:0m:1s left)
Optimizing NNI: done in 0.0255451 secs using 99.96% CPU
Optimizing NNI: done in 0.065995 secs using 99.91% CPU
Optimizing NNI: done in 0.0368462 secs using 99.96% CPU
Optimizing NNI: done in 0.0339179 secs using 99.96% CPU
Optimizing NNI: done in 0.037333 secs using 99.96% CPU
Optimizing NNI: done in 0.0335131 secs using 99.91% CPU
Optimizing NNI: done in 0.0348022 secs using 99.96% CPU
Optimizing NNI: done in 0.036412 secs using 99.96% CPU
Optimizing NNI: done in 0.0306211 secs using 99.94% CPU
Optimizing NNI: done in 0.0274839 secs using 99.92% CPU
Iteration 80 / LogL: -1387.351 / Time: 0h:0m:3s (0h:0m:0s left)
Optimizing NNI: done in 0.019819 secs using 99.96% CPU
Optimizing NNI: done in 0.0400741 secs using 99.96% CPU
Optimizing NNI: done in 0.028903 secs using 99.75% CPU
Optimizing NNI: done in 0.019995 secs using 99.73% CPU
Optimizing NNI: done in 0.0645459 secs using 99.85% CPU
Optimizing NNI: done in 0.020077 secs using 99.79% CPU
Optimizing NNI: done in 0.0267749 secs using 99.91% CPU
Optimizing NNI: done in 0.0487092 secs using 99.95% CPU
Optimizing NNI: done in 0.0307319 secs using 99.95% CPU
Optimizing NNI: done in 0.037535 secs using 99.86% CPU
Iteration 90 / LogL: -1397.939 / Time: 0h:0m:3s (0h:0m:0s left)
Optimizing NNI: done in 0.025681 secs using 99.78% CPU
Optimizing NNI: done in 0.026412 secs using 99.94% CPU
Optimizing NNI: done in 0.0205891 secs using 99.64% CPU
Optimizing NNI: done in 0.0208521 secs using 99.53% CPU
Optimizing NNI: done in 0.0306361 secs using 99.52% CPU
Optimizing NNI: done in 0.0458012 secs using 99.2% CPU
Optimizing NNI: done in 0.0377021 secs using 99.94% CPU
Optimizing NNI: done in 0.0401771 secs using 99.69% CPU
Optimizing NNI: done in 0.0116379 secs using 99.96% CPU
Optimizing NNI: done in 0.03385 secs using 99.96% CPU
Iteration 100 / LogL: -1406.556 / Time: 0h:0m:3s (0h:0m:0s left)
Optimizing NNI: done in 0.049793 secs using 99.92% CPU
Optimizing NNI: done in 0.015516 secs using 99.87% CPU
TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:3s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.256
Optimal log-likelihood: -1387.252
Rate parameters: A-C: 0.33726 A-G: 2.27742 A-T: 2.15644 C-G: 1.18302 C-T: 3.31088 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: 1.315
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1387.252
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...
0.057 sec.
Total tree length: 6.745
Total number of iterations: 102
CPU time used for tree search: 3.583 sec (0h:0m:3s)
Wall-clock time used for tree search: 3.428 sec (0h:0m:3s)
Total CPU time used: 4.186 sec (0h:0m:4s)
Total wall-clock time used: 4.038 sec (0h:0m:4s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxhxlfai3/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxhxlfai3/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxhxlfai3/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxhxlfai3/q2iqtree.log
Date and Time: Tue May 30 15:53:04 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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxhxlfai3/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 2.2.2.3 COVID-edition for Mac OS X 64-bit built May 16 2023
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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpko4rlnj9/q2iqtree -nt 1 -nstop 200 -pers 0.200000
Seed: 303682 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Tue May 30 15:53:15 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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000320911 secs using 75.72% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000484943 secs using 76.71% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 1.90735e-05 secs using 83.89% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 7.41482e-05 secs using 76.87% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.0386369 secs using 97.58% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1389.605
Optimal log-likelihood: -1388.791
Rate parameters: A-C: 0.37331 A-G: 2.35436 A-T: 2.13670 C-G: 1.23381 C-T: 3.29661 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.034
Gamma shape alpha: 1.400
Parameters optimization took 1 rounds (0.006 sec)
Time for fast ML tree search: 0.074 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 484 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1402.600 45 2895.200 2919.842 3046.668
2 GTR+F+I 1401.121 46 2894.242 2920.134 3049.077
3 GTR+F+G4 1387.358 46 2866.716 2892.608 3021.551
4 GTR+F+I+G4 1387.726 47 2869.452 2896.633 3027.653
5 GTR+F+R2 1382.364 47 2858.729 2885.910 3016.930
6 GTR+F+R3 1382.420 49 2862.840 2892.718 3027.773
14 GTR+F+I+R2 1382.418 48 2860.837 2889.346 3022.403
15 GTR+F+I+R3 1382.449 50 2864.899 2896.187 3033.197
25 SYM+G4 1387.134 43 2860.269 2882.528 3005.006
27 SYM+R2 1383.095 44 2854.189 2877.621 3002.292
36 SYM+I+R2 1383.227 45 2856.454 2881.097 3007.923
47 TVM+F+G4 1388.357 45 2866.713 2891.356 3018.182
49 TVM+F+R2 1383.789 46 2859.578 2885.470 3014.413
58 TVM+F+I+R2 1383.812 47 2861.625 2888.805 3019.826
69 TVMe+G4 1387.122 42 2858.245 2879.368 2999.616
71 TVMe+R2 1383.079 43 2852.159 2874.418 2996.896
80 TVMe+I+R2 1383.224 44 2854.449 2877.881 3002.552
91 TIM3+F+G4 1391.377 44 2870.754 2894.186 3018.857
93 TIM3+F+R2 1385.912 45 2861.825 2886.468 3013.294
102 TIM3+F+I+R2 1386.041 46 2864.082 2889.975 3018.917
113 TIM3e+G4 1390.358 41 2862.715 2882.738 3000.720
115 TIM3e+R2 1385.918 42 2855.836 2876.959 2997.207
124 TIM3e+I+R2 1386.073 43 2858.145 2880.404 3002.882
135 TIM2+F+G4 1393.635 44 2875.270 2898.702 3023.373
137 TIM2+F+R2 1387.681 45 2865.362 2890.005 3016.831
146 TIM2+F+I+R2 1387.782 46 2867.564 2893.456 3022.399
157 TIM2e+G4 1396.795 41 2875.589 2895.613 3013.594
159 TIM2e+R2 1391.574 42 2867.148 2888.270 3008.519
168 TIM2e+I+R2 1391.651 43 2869.302 2891.561 3014.039
179 TIM+F+G4 1390.363 44 2868.726 2892.158 3016.829
181 TIM+F+R2 1384.933 45 2859.866 2884.509 3011.335
190 TIM+F+I+R2 1385.016 46 2862.032 2887.925 3016.867
201 TIMe+G4 1394.002 41 2870.005 2890.028 3008.010
203 TIMe+R2 1389.000 42 2862.000 2883.123 3003.371
212 TIMe+I+R2 1389.095 43 2864.190 2886.449 3008.927
223 TPM3u+F+G4 1392.306 43 2870.611 2892.870 3015.348
225 TPM3u+F+R2 1387.329 44 2862.659 2886.091 3010.762
234 TPM3u+F+I+R2 1387.462 45 2864.923 2889.566 3016.392
245 TPM3+G4 1390.374 40 2860.748 2879.708 2995.387
247 TPM3+R2 1385.925 41 2853.851 2873.874 2991.856
256 TPM3+I+R2 1386.070 42 2856.140 2877.263 2997.511
267 TPM2u+F+G4 1394.533 43 2875.067 2897.325 3019.804
269 TPM2u+F+R2 1389.057 44 2866.113 2889.545 3014.216
278 TPM2u+F+I+R2 1389.101 45 2868.201 2892.844 3019.670
289 TPM2+G4 1396.823 40 2873.646 2892.605 3008.285
291 TPM2+R2 1391.578 41 2865.155 2885.178 3003.160
300 TPM2+I+R2 1391.649 42 2867.297 2888.420 3008.668
311 K3Pu+F+G4 1391.381 43 2868.762 2891.021 3013.499
313 K3Pu+F+R2 1386.371 44 2860.742 2884.174 3008.845
322 K3Pu+F+I+R2 1386.425 45 2862.850 2887.493 3014.319
333 K3P+G4 1394.015 40 2868.030 2886.989 3002.669
335 K3P+R2 1389.002 41 2860.004 2880.028 2998.009
344 K3P+I+R2 1389.099 42 2862.197 2883.320 3003.568
355 TN+F+G4 1394.038 43 2874.077 2896.336 3018.814
357 TN+F+R2 1388.241 44 2864.483 2887.915 3012.586
366 TN+F+I+R2 1388.289 45 2866.578 2891.221 3018.047
377 TNe+G4 1396.791 40 2873.582 2892.542 3008.221
379 TNe+R2 1391.586 41 2865.172 2885.195 3003.177
388 TNe+I+R2 1391.666 42 2867.332 2888.454 3008.703
399 HKY+F+G4 1394.951 42 2873.902 2895.024 3015.273
401 HKY+F+R2 1389.609 43 2865.217 2887.476 3009.954
410 HKY+F+I+R2 1389.663 44 2867.327 2890.759 3015.430
421 K2P+G4 1396.825 39 2871.649 2889.580 3002.922
423 K2P+R2 1391.594 40 2863.189 2882.148 2997.828
432 K2P+I+R2 1391.664 41 2865.327 2885.351 3003.332
443 F81+F+G4 1405.743 41 2893.486 2913.509 3031.491
445 F81+F+R2 1400.805 42 2885.611 2906.733 3026.982
454 F81+F+I+R2 1400.908 43 2887.816 2910.075 3032.553
465 JC+G4 1407.650 38 2891.299 2908.236 3019.206
467 JC+R2 1402.858 39 2883.715 2901.646 3014.988
476 JC+I+R2 1402.926 40 2885.851 2904.811 3020.490
Akaike Information Criterion: TVMe+R2
Corrected Akaike Information Criterion: TPM3+R2
Bayesian Information Criterion: TPM3+R2
Best-fit model: TPM3+R2 chosen according to BIC
All model information printed to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpko4rlnj9/q2iqtree.model.gz
CPU time for ModelFinder: 1.467 seconds (0h:0m:1s)
Wall-clock time for ModelFinder: 1.495 seconds (0h:0m:1s)
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1385.925
Optimal log-likelihood: -1385.924
Rate parameters: A-C: 0.40868 A-G: 1.56206 A-T: 1.00000 C-G: 0.40868 C-T: 1.56206 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.716,0.409) (0.284,2.490)
Parameters optimization took 1 rounds (0.004 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000975132 secs using 97.83% CPU
Computing ML distances took 0.001061 sec (of wall-clock time) 0.001017 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 7.20024e-05 secs using 77.78% CPU
Constructing RapidNJ tree: done in 9.39369e-05 secs using 144.8% CPU
Computing RapidNJ tree took 0.000239 sec (of wall-clock time) 0.000267 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.820
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.116 second
Computing log-likelihood of 98 initial trees ... 0.095 seconds
Current best score: -1385.924
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00463891 secs using 99.96% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.880
Optimizing NNI: done in 0.0123601 secs using 99.94% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1385.311
Optimizing NNI: done in 0.012295 secs using 99.78% CPU
Optimizing NNI: done in 0.0121899 secs using 99.92% CPU
Optimizing NNI: done in 0.012104 secs using 99.94% CPU
Optimizing NNI: done in 0.0123429 secs using 99.71% CPU
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Optimizing NNI: done in 0.0143149 secs using 99.94% CPU
Optimizing NNI: done in 0.0141301 secs using 99.95% CPU
Optimizing NNI: done in 0.0137489 secs using 99.82% CPU
Iteration 10 / LogL: -1385.344 / Time: 0h:0m:0s
Optimizing NNI: done in 0.013458 secs using 99.37% CPU
Optimizing NNI: done in 0.012229 secs using 99.93% CPU
Optimizing NNI: done in 0.012008 secs using 99.96% CPU
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Optimizing NNI: done in 0.0118999 secs using 99.94% CPU
Optimizing NNI: done in 0.0120258 secs using 99.85% CPU
Iteration 20 / LogL: -1385.343 / Time: 0h:0m:0s
Finish initializing candidate tree set (2)
Current best tree score: -1385.311 / CPU time: 0.470
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0078361 secs using 99.63% CPU
Optimizing NNI: done in 0.0147521 secs using 99.57% CPU
Optimizing NNI: done in 0.014642 secs using 99.93% CPU
Optimizing NNI: done in 0.00844789 secs using 99.89% CPU
Optimizing NNI: done in 0.0111721 secs using 99.93% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.311
Optimizing NNI: done in 0.0130959 secs using 99.76% CPU
Optimizing NNI: done in 0.0161588 secs using 99.94% CPU
Optimizing NNI: done in 0.00462008 secs using 99.91% CPU
Optimizing NNI: done in 0.013273 secs using 99.92% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.311
Optimizing NNI: done in 0.00865507 secs using 99.92% CPU
Iteration 30 / LogL: -1385.314 / Time: 0h:0m:0s (0h:0m:3s left)
Optimizing NNI: done in 0.0166988 secs using 99.73% CPU
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Optimizing NNI: done in 0.0111208 secs using 99.94% CPU
Optimizing NNI: done in 0.00479794 secs using 99.92% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.310
Optimizing NNI: done in 0.0133772 secs using 99.73% CPU
Optimizing NNI: done in 0.01491 secs using 99.66% CPU
Optimizing NNI: done in 0.013773 secs using 99.94% CPU
Iteration 40 / LogL: -1385.831 / Time: 0h:0m:0s (0h:0m:3s left)
Optimizing NNI: done in 0.00722218 secs using 99.91% CPU
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Iteration 50 / LogL: -1385.832 / Time: 0h:0m:0s (0h:0m:2s left)
Optimizing NNI: done in 0.00768185 secs using 99.94% CPU
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Iteration 60 / LogL: -1385.703 / Time: 0h:0m:0s (0h:0m:2s left)
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Iteration 70 / LogL: -1385.700 / Time: 0h:0m:1s (0h:0m:2s left)
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Iteration 80 / LogL: -1385.311 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.0135441 secs using 99.95% CPU
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Optimizing NNI: done in 0.014024 secs using 99.91% CPU
Optimizing NNI: done in 0.00556493 secs using 99.64% CPU
BETTER TREE FOUND at iteration 88: -1385.310
Optimizing NNI: done in 0.0154152 secs using 99.69% CPU
Optimizing NNI: done in 0.01195 secs using 99.89% CPU
Iteration 90 / LogL: -1385.511 / Time: 0h:0m:1s (0h:0m:3s left)
Optimizing NNI: done in 0.010745 secs using 99.93% CPU
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Iteration 100 / LogL: -1385.313 / Time: 0h:0m:1s (0h:0m:2s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.310
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UPDATE BEST LOG-LIKELIHOOD: -1385.310
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UPDATE BEST LOG-LIKELIHOOD: -1385.310
Iteration 170 / LogL: -1385.310 / Time: 0h:0m:2s (0h:0m:1s left)
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Iteration 270 / LogL: -1385.777 / Time: 0h:0m:3s (0h:0m:0s left)
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Iteration 280 / LogL: -1385.863 / Time: 0h:0m:3s (0h:0m:0s left)
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TREE SEARCH COMPLETED AFTER 289 ITERATIONS / Time: 0h:0m:3s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1385.310
Optimal log-likelihood: -1385.306
Rate parameters: A-C: 0.39448 A-G: 1.56671 A-T: 1.00000 C-G: 0.39448 C-T: 1.56671 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.721,0.402) (0.279,2.542)
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1385.306
Total tree length: 6.847
Total number of iterations: 289
CPU time used for tree search: 3.677 sec (0h:0m:3s)
Wall-clock time used for tree search: 3.628 sec (0h:0m:3s)
Total CPU time used: 3.708 sec (0h:0m:3s)
Total wall-clock time used: 3.655 sec (0h:0m:3s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpko4rlnj9/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpko4rlnj9/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpko4rlnj9/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpko4rlnj9/q2iqtree.log
Date and Time: Tue May 30 15:53:20 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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpko4rlnj9/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 2.2.2.3 COVID-edition for Mac OS X 64-bit built May 16 2023
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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxzhw88ah/q2iqtreeufboot -nt 1 -nstop 200 -pers 0.200000
Seed: 115430 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Tue May 30 15:53:31 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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000226021 secs using 82.74% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000468016 secs using 78.42% 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 2.40803e-05 secs using 78.9% 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 8.79765e-05 secs using 73.88% 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 0.0262101 secs using 98.44% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1391.311
2. Current log-likelihood: -1389.733
Optimal log-likelihood: -1388.881
Rate parameters: A-C: 0.33789 A-G: 2.29237 A-T: 2.14761 C-G: 1.19040 C-T: 3.28358 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.033
Gamma shape alpha: 1.424
Parameters optimization took 2 rounds (0.015 sec)
Time for fast ML tree search: 0.065 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 484 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1402.497 45 2894.994 2919.637 3046.463
2 GTR+F+I 1401.403 46 2894.806 2920.698 3049.641
3 GTR+F+G4 1387.279 46 2866.558 2892.450 3021.393
4 GTR+F+I+G4 1387.559 47 2869.117 2896.298 3027.318
5 GTR+F+R2 1380.611 47 2855.222 2882.402 3013.423
6 GTR+F+R3 1380.659 49 2859.317 2889.195 3024.250
14 GTR+F+I+R2 1380.757 48 2857.513 2886.023 3019.080
15 GTR+F+I+R3 1380.696 50 2861.392 2892.681 3029.691
25 SYM+G4 1387.157 43 2860.314 2882.573 3005.051
27 SYM+R2 1382.244 44 2852.489 2875.920 3000.591
36 SYM+I+R2 1382.405 45 2854.809 2879.452 3006.278
47 TVM+F+G4 1388.424 45 2866.848 2891.491 3018.317
49 TVM+F+R2 1382.481 46 2856.963 2882.855 3011.798
58 TVM+F+I+R2 1382.560 47 2859.119 2886.300 3017.320
69 TVMe+G4 1387.122 42 2858.245 2879.367 2999.616
71 TVMe+R2 1382.298 43 2850.596 2872.854 2995.333
80 TVMe+I+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+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+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+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+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+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+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+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+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+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+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+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+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+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+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+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+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+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+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/tmpxzhw88ah/q2iqtreeufboot.model.gz
CPU time for ModelFinder: 1.590 seconds (0h:0m:1s)
Wall-clock time for ModelFinder: 1.619 seconds (0h:0m:1s)
Generating 1000 samples for ultrafast bootstrap (seed: 115430)...
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1385.307
Optimal log-likelihood: -1385.304
Rate parameters: A-C: 0.39693 A-G: 1.57493 A-T: 1.00000 C-G: 0.39693 C-T: 1.57493 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.723,0.403) (0.277,2.560)
Parameters optimization took 1 rounds (0.004 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00102401 secs using 96.29% CPU
Computing ML distances took 0.001119 sec (of wall-clock time) 0.001051 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.48363e-05 secs using 80.24% CPU
Constructing RapidNJ tree: done in 9.29832e-05 secs using 126.9% CPU
Computing RapidNJ tree took 0.000214 sec (of wall-clock time) 0.000219 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.836
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| INITIALIZING CANDIDATE TREE SET |
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Generating 98 parsimony trees... 0.105 second
Computing log-likelihood of 97 initial trees ... 0.088 seconds
Current best score: -1385.304
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00505495 secs using 99.53% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.303
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Iteration 10 / LogL: -1385.338 / Time: 0h:0m:0s
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Iteration 20 / LogL: -1385.338 / Time: 0h:0m:0s
Finish initializing candidate tree set (1)
Current best tree score: -1385.303 / CPU time: 0.628
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
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Iteration 30 / LogL: -1385.306 / Time: 0h:0m:0s (0h:0m:4s left)
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Iteration 40 / LogL: -1385.521 / Time: 0h:0m:1s (0h:0m:4s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.303
Optimizing NNI: done in 0.0270309 secs using 99.84% CPU
Iteration 50 / LogL: -1385.304 / Time: 0h:0m:1s (0h:0m:4s left)
Log-likelihood cutoff on original alignment: -1404.361
Optimizing NNI: done in 0.0117528 secs using 99.92% CPU
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Iteration 60 / LogL: -1386.016 / Time: 0h:0m:1s (0h:0m:3s left)
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Iteration 70 / LogL: -1385.940 / Time: 0h:0m:1s (0h:0m:3s left)
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Iteration 80 / LogL: -1385.305 / Time: 0h:0m:2s (0h:0m:3s left)
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Iteration 90 / LogL: -1390.104 / Time: 0h:0m:2s (0h:0m:2s left)
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Iteration 100 / LogL: -1385.841 / Time: 0h:0m:2s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -1404.209
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.980
NOTE: UFBoot does not converge, continue at least 100 more iterations
Optimizing NNI: done in 0.0131679 secs using 99.67% CPU
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Iteration 110 / LogL: -1385.862 / Time: 0h:0m:2s (0h:0m:2s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.303
Optimizing NNI: done in 0.018568 secs using 99.71% CPU
Iteration 120 / LogL: -1385.305 / Time: 0h:0m:2s (0h:0m:1s left)
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Iteration 130 / LogL: -1385.840 / Time: 0h:0m:3s (0h:0m:1s left)
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Iteration 140 / LogL: -1385.310 / Time: 0h:0m:3s (0h:0m:1s left)
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Optimizing NNI: done in 0.01775 secs using 99.75% CPU
Iteration 150 / LogL: -1385.305 / Time: 0h:0m:3s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -1404.737
Optimizing NNI: done in 0.0151789 secs using 99.73% CPU
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Iteration 160 / LogL: -1385.517 / Time: 0h:0m:3s (0h:0m:0s left)
Optimizing NNI: done in 0.0186689 secs using 99.91% CPU
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Iteration 170 / LogL: -1385.309 / Time: 0h:0m:3s (0h:0m:0s left)
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Iteration 180 / LogL: -1385.716 / Time: 0h:0m:4s (0h:0m:0s left)
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Iteration 190 / LogL: -1385.507 / Time: 0h:0m:4s (0h:0m:0s left)
Optimizing NNI: done in 0.0130582 secs using 99.74% CPU
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Optimizing NNI: done in 0.0265181 secs using 99.91% CPU
Iteration 200 / LogL: -1394.236 / Time: 0h:0m:4s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -1404.837
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.993
Optimizing NNI: done in 0.00813389 secs using 99.96% CPU
Optimizing NNI: done in 0.00965595 secs using 99.96% CPU
TREE SEARCH COMPLETED AFTER 202 ITERATIONS / Time: 0h:0m:4s
--------------------------------------------------------------------
| 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
Creating bootstrap support values...
Split supports printed to NEXUS file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxzhw88ah/q2iqtreeufboot.splits.nex
Total tree length: 6.855
Total number of iterations: 202
CPU time used for tree search: 4.786 sec (0h:0m:4s)
Wall-clock time used for tree search: 4.626 sec (0h:0m:4s)
Total CPU time used: 4.891 sec (0h:0m:4s)
Total wall-clock time used: 4.729 sec (0h:0m:4s)
Computing bootstrap consensus tree...
Reading input file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxzhw88ah/q2iqtreeufboot.splits.nex...
20 taxa and 145 splits.
Consensus tree written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxzhw88ah/q2iqtreeufboot.contree
Reading input trees file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxzhw88ah/q2iqtreeufboot.contree
Log-likelihood of consensus tree: -1385.304
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxzhw88ah/q2iqtreeufboot.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxzhw88ah/q2iqtreeufboot.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxzhw88ah/q2iqtreeufboot.mldist
Ultrafast bootstrap approximation results written to:
Split support values: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxzhw88ah/q2iqtreeufboot.splits.nex
Consensus tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxzhw88ah/q2iqtreeufboot.contree
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxzhw88ah/q2iqtreeufboot.log
Date and Time: Tue May 30 15:53:37 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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxzhw88ah/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 2.2.2.3 COVID-edition for Mac OS X 64-bit built May 16 2023
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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxxhns4mj/q2iqtreeufboot -nt 1 -alrt 1000 -abayes -lbp 1000 -nstop 200 -pers 0.200000
Seed: 168158 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Tue May 30 15:53:48 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/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000247002 secs using 78.95% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000469923 secs using 78.1% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 2.59876e-05 secs using 80.81% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 7.41482e-05 secs using 76.87% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
Generating 1000 samples for ultrafast bootstrap (seed: 168158)...
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, 1.282 / LogL: -1392.553
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.008, 1.377 / LogL: -1392.829
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.009, 1.391 / LogL: -1392.898
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.009, 1.388 / LogL: -1392.889
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.008, 1.383 / LogL: -1392.853
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.009, 1.384 / LogL: -1392.879
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.007, 1.379 / LogL: -1392.828
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.008, 1.382 / LogL: -1392.844
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.008, 1.383 / LogL: -1392.849
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.008, 1.384 / LogL: -1392.858
Optimal pinv,alpha: 0.000, 1.282 / LogL: -1392.553
Parameters optimization took 0.526 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00156307 secs using 97.18% CPU
Computing ML distances took 0.001689 sec (of wall-clock time) 0.001607 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 6.79493e-05 secs using 89.77% CPU
Constructing RapidNJ tree: done in 0.000102043 secs using 151.9% CPU
Computing RapidNJ tree took 0.000264 sec (of wall-clock time) 0.000285 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.710
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.118 second
Computing log-likelihood of 98 initial trees ... 0.137 seconds
Current best score: -1392.553
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.0274849 secs using 98.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.261
Optimizing NNI: done in 0.034713 secs using 98.51% CPU
Optimizing NNI: done in 0.0367701 secs using 98.2% CPU
Optimizing NNI: done in 0.0224311 secs using 98.34% CPU
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Optimizing NNI: done in 0.0256691 secs using 98.36% CPU
Optimizing NNI: done in 0.0414841 secs using 98.54% CPU
Iteration 10 / LogL: -1387.282 / Time: 0h:0m:1s
Optimizing NNI: done in 0.0400019 secs using 98.65% CPU
Optimizing NNI: done in 0.0402949 secs using 98.73% CPU
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Optimizing NNI: done in 0.0332429 secs using 98.45% CPU
Iteration 20 / LogL: -1387.267 / Time: 0h:0m:1s
Finish initializing candidate tree set (3)
Current best tree score: -1387.261 / CPU time: 0.980
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0798769 secs using 98.47% CPU
Optimizing NNI: done in 0.0236859 secs using 98.35% CPU
Optimizing NNI: done in 0.0609779 secs using 99.39% CPU
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Optimizing NNI: done in 0.0219879 secs using 99.96% CPU
Optimizing NNI: done in 0.011641 secs using 99.66% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.257
Optimizing NNI: done in 0.0494831 secs using 99.91% CPU
Optimizing NNI: done in 0.0285399 secs using 99.95% CPU
Optimizing NNI: done in 0.022512 secs using 99.96% CPU
Iteration 30 / LogL: -1387.263 / Time: 0h:0m:1s (0h:0m:11s left)
Optimizing NNI: done in 0.00697803 secs using 99.84% CPU
Optimizing NNI: done in 0.015311 secs using 99.6% CPU
Optimizing NNI: done in 0.013016 secs using 99.95% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.256
Optimizing NNI: done in 0.0329161 secs using 99.58% CPU
Optimizing NNI: done in 0.0134659 secs using 99.33% CPU
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Optimizing NNI: done in 0.0484128 secs using 99.9% CPU
Iteration 40 / LogL: -1387.379 / Time: 0h:0m:2s (0h:0m:8s left)
Optimizing NNI: done in 0.018183 secs using 99.96% CPU
Optimizing NNI: done in 0.031831 secs using 99.89% CPU
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Optimizing NNI: done in 0.016829 secs using 99.96% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.256
Optimizing NNI: done in 0.027303 secs using 99.51% CPU
Optimizing NNI: done in 0.024642 secs using 99.65% CPU
Optimizing NNI: done in 0.023283 secs using 99.94% CPU
Optimizing NNI: done in 0.0140059 secs using 99.98% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.255
Optimizing NNI: done in 0.013139 secs using 99.62% CPU
Iteration 50 / LogL: -1387.301 / Time: 0h:0m:2s (0h:0m:7s left)
Log-likelihood cutoff on original alignment: -1414.386
Optimizing NNI: done in 0.014267 secs using 99.94% CPU
Optimizing NNI: done in 0.0203581 secs using 99.97% CPU
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Optimizing NNI: done in 0.0170181 secs using 99.93% CPU
Optimizing NNI: done in 0.0225661 secs using 99.89% CPU
Iteration 60 / LogL: -1387.350 / Time: 0h:0m:2s (0h:0m:6s left)
Optimizing NNI: done in 0.0334949 secs using 99.97% CPU
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Optimizing NNI: done in 0.00721717 secs using 99.68% CPU
Optimizing NNI: done in 0.013768 secs using 99.92% CPU
Iteration 70 / LogL: -1387.569 / Time: 0h:0m:2s (0h:0m:5s left)
Optimizing NNI: done in 0.0136631 secs using 99.92% CPU
Optimizing NNI: done in 0.0863001 secs using 99.96% CPU
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Optimizing NNI: done in 0.0102389 secs using 99.91% CPU
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Optimizing NNI: done in 0.0138462 secs using 99.76% CPU
Optimizing NNI: done in 0.0124872 secs using 99.95% CPU
Optimizing NNI: done in 0.0391819 secs using 99.79% CPU
Iteration 80 / LogL: -1387.409 / Time: 0h:0m:3s (0h:0m:5s left)
Optimizing NNI: done in 0.012953 secs using 99.93% CPU
Optimizing NNI: done in 0.0103312 secs using 99.71% CPU
Optimizing NNI: done in 0.012229 secs using 99.92% CPU
Optimizing NNI: done in 0.0193579 secs using 99.96% CPU
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Optimizing NNI: done in 0.0244701 secs using 99.97% CPU
Optimizing NNI: done in 0.01736 secs using 99.96% CPU
Iteration 90 / LogL: -1387.256 / Time: 0h:0m:3s (0h:0m:4s left)
Optimizing NNI: done in 0.015687 secs using 99.96% CPU
Optimizing NNI: done in 0.026324 secs using 99.9% CPU
Optimizing NNI: done in 0.01489 secs using 99.9% CPU
Optimizing NNI: done in 0.010309 secs using 99.96% CPU
Optimizing NNI: done in 0.049227 secs using 99.97% CPU
Optimizing NNI: done in 0.0302401 secs using 99.97% CPU
Optimizing NNI: done in 0.0136261 secs using 99.9% CPU
Optimizing NNI: done in 0.015996 secs using 99.78% CPU
Optimizing NNI: done in 0.0149019 secs using 99.95% CPU
Optimizing NNI: done in 0.010462 secs using 99.97% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.255
Iteration 100 / LogL: -1387.255 / Time: 0h:0m:3s (0h:0m:3s left)
Log-likelihood cutoff on original alignment: -1414.723
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.994
Optimizing NNI: done in 0.030658 secs using 99.74% CPU
Optimizing NNI: done in 0.0340991 secs using 99.97% CPU
Optimizing NNI: done in 0.0191898 secs using 99.97% CPU
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Optimizing NNI: done in 0.018441 secs using 99.75% CPU
Optimizing NNI: done in 0.0161369 secs using 99.93% CPU
Iteration 110 / LogL: -1387.274 / Time: 0h:0m:4s (0h:0m:3s left)
Optimizing NNI: done in 0.0136111 secs using 99.96% CPU
Optimizing NNI: done in 0.0146539 secs using 99.97% CPU
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Optimizing NNI: done in 0.0343308 secs using 99.9% CPU
Optimizing NNI: done in 0.0182259 secs using 99.56% CPU
Iteration 120 / LogL: -1387.350 / Time: 0h:0m:4s (0h:0m:3s left)
Optimizing NNI: done in 0.021894 secs using 99.74% CPU
Optimizing NNI: done in 0.015177 secs using 99.7% CPU
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Optimizing NNI: done in 0.0105698 secs using 99.97% CPU
Optimizing NNI: done in 0.019953 secs using 99.96% CPU
Iteration 130 / LogL: -1387.285 / Time: 0h:0m:4s (0h:0m:2s left)
Optimizing NNI: done in 0.0144188 secs using 99.96% CPU
Optimizing NNI: done in 0.0201402 secs using 99.96% CPU
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Optimizing NNI: done in 0.017658 secs using 99.97% CPU
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Optimizing NNI: done in 0.0230069 secs using 99.97% CPU
Iteration 140 / LogL: -1387.350 / Time: 0h:0m:4s (0h:0m:2s left)
Optimizing NNI: done in 0.0106368 secs using 99.89% CPU
Optimizing NNI: done in 0.0100279 secs using 99.84% CPU
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Optimizing NNI: done in 0.0169139 secs using 99.93% CPU
Iteration 150 / LogL: -1387.288 / Time: 0h:0m:5s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -1414.804
Optimizing NNI: done in 0.0237391 secs using 99.96% CPU
Optimizing NNI: done in 0.022953 secs using 99.97% CPU
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Iteration 160 / LogL: -1387.273 / Time: 0h:0m:5s (0h:0m:1s left)
Optimizing NNI: done in 0.010335 secs using 99.96% CPU
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Iteration 170 / LogL: -1387.264 / Time: 0h:0m:5s (0h:0m:1s left)
Optimizing NNI: done in 0.0115809 secs using 99.84% CPU
Optimizing NNI: done in 0.0597961 secs using 99.96% CPU
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Optimizing NNI: done in 0.024879 secs using 99.96% CPU
Optimizing NNI: done in 0.0192039 secs using 99.57% CPU
Iteration 180 / LogL: -1387.371 / Time: 0h:0m:6s (0h:0m:0s left)
Optimizing NNI: done in 0.0202942 secs using 99.66% CPU
Optimizing NNI: done in 0.00735998 secs using 99.95% CPU
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Optimizing NNI: done in 0.0122778 secs using 99.96% CPU
Optimizing NNI: done in 0.0578709 secs using 99.96% CPU
Iteration 190 / LogL: -1387.398 / Time: 0h:0m:6s (0h:0m:0s left)
Optimizing NNI: done in 0.0217359 secs using 99.84% CPU
Optimizing NNI: done in 0.0156031 secs using 99.96% CPU
Optimizing NNI: done in 0.00943613 secs using 99.97% CPU
Optimizing NNI: done in 0.012588 secs using 99.96% CPU
Optimizing NNI: done in 0.0269089 secs using 99.68% CPU
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Optimizing NNI: done in 0.0277281 secs using 99.47% CPU
Optimizing NNI: done in 0.0189371 secs using 99.79% CPU
Iteration 200 / LogL: -1387.281 / Time: 0h:0m:6s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -1414.813
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.998
Optimizing NNI: done in 0.02545 secs using 99.95% CPU
Optimizing NNI: done in 0.0153031 secs using 99.96% CPU
TREE SEARCH COMPLETED AFTER 202 ITERATIONS / Time: 0h:0m:6s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.255
Optimal log-likelihood: -1387.252
Rate parameters: A-C: 0.33717 A-G: 2.27751 A-T: 2.15657 C-G: 1.18236 C-T: 3.31131 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: 1.315
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1387.252
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...
0.058 sec.
Creating bootstrap support values...
Split supports printed to NEXUS file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxxhns4mj/q2iqtreeufboot.splits.nex
Total tree length: 6.752
Total number of iterations: 202
CPU time used for tree search: 6.328 sec (0h:0m:6s)
Wall-clock time used for tree search: 6.188 sec (0h:0m:6s)
Total CPU time used: 7.008 sec (0h:0m:7s)
Total wall-clock time used: 6.877 sec (0h:0m:6s)
Computing bootstrap consensus tree...
Reading input file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxxhns4mj/q2iqtreeufboot.splits.nex...
20 taxa and 147 splits.
Consensus tree written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxxhns4mj/q2iqtreeufboot.contree
Reading input trees file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxxhns4mj/q2iqtreeufboot.contree
Log-likelihood of consensus tree: -1387.254
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxxhns4mj/q2iqtreeufboot.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxxhns4mj/q2iqtreeufboot.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxxhns4mj/q2iqtreeufboot.mldist
Ultrafast bootstrap approximation results written to:
Split support values: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxxhns4mj/q2iqtreeufboot.splits.nex
Consensus tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxxhns4mj/q2iqtreeufboot.contree
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxxhns4mj/q2iqtreeufboot.log
Date and Time: Tue May 30 15:53:55 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 -bb 1000 -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/9ba7310e-c2a5-4d8d-b965-6da092275726/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxxhns4mj/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!