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/2023.7/tutorials/phylogeny/rep-seqs.qza
Save as: rep-seqs.qza
wget \
-O "rep-seqs.qza" \
"https://data.qiime2.org/2023.7/tutorials/phylogeny/rep-seqs.qza"
curl -sL \
"https://data.qiime2.org/2023.7/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 5632 -N 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmps8ic0956 -n q2
Partition: 0 with name: No Name Provided
Base frequencies: 0.243 0.182 0.319 0.256
Inference[0]: Time 0.694150 CAT-based likelihood -1246.336487, best rearrangement setting 5
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -1393.279601 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmps8ic0956/RAxML_result.q2
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -1393.279601 ....
Final GAMMA-based Score of best tree -1387.732940
Program execution info written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmps8ic0956/RAxML_info.q2
Best-scoring ML tree written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmps8ic0956/RAxML_bestTree.q2
Overall execution time: 1.289140 secs or 0.000358 hours or 0.000015 days
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: raxmlHPC -m GTRCAT -p 5632 -N 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmps8ic0956 -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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpempjhtrb -n q2
Partition: 0 with name: No Name Provided
Base frequencies: 0.243 0.182 0.319 0.256
Inference[0]: Time 0.641981 CAT-based likelihood -1238.242991, best rearrangement setting 5
Inference[1]: Time 0.531342 CAT-based likelihood -1249.502284, best rearrangement setting 5
Inference[2]: Time 0.535570 CAT-based likelihood -1242.978035, best rearrangement setting 5
Inference[3]: Time 0.672965 CAT-based likelihood -1243.159855, best rearrangement setting 5
Inference[4]: Time 0.508695 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/tmpempjhtrb/RAxML_result.q2.RUN.0
Inference[1] final GAMMA-based Likelihood: -1392.813982 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpempjhtrb/RAxML_result.q2.RUN.1
Inference[2] final GAMMA-based Likelihood: -1388.073642 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpempjhtrb/RAxML_result.q2.RUN.2
Inference[3] final GAMMA-based Likelihood: -1387.945266 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpempjhtrb/RAxML_result.q2.RUN.3
Inference[4] final GAMMA-based Likelihood: -1387.557031 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpempjhtrb/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/tmpempjhtrb/RAxML_info.q2
Best-scoring ML tree written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpempjhtrb/RAxML_bestTree.q2
Overall execution time: 3.613343 secs or 0.001004 hours or 0.000042 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpempjhtrb -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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiq04em7j -n q2bootstrap
Time for BS model parameter optimization 0.054064
Bootstrap[0]: Time 0.181707 seconds, bootstrap likelihood -1199.758796, best rearrangement setting 12
Bootstrap[1]: Time 0.124338 seconds, bootstrap likelihood -1344.229251, best rearrangement setting 6
Bootstrap[2]: Time 0.115059 seconds, bootstrap likelihood -1295.343000, best rearrangement setting 8
Bootstrap[3]: Time 0.098479 seconds, bootstrap likelihood -1273.768320, best rearrangement setting 8
Bootstrap[4]: Time 0.116205 seconds, bootstrap likelihood -1253.402952, best rearrangement setting 6
Bootstrap[5]: Time 0.121214 seconds, bootstrap likelihood -1260.866113, best rearrangement setting 10
Bootstrap[6]: Time 0.119067 seconds, bootstrap likelihood -1293.636299, best rearrangement setting 14
Bootstrap[7]: Time 0.107628 seconds, bootstrap likelihood -1227.178693, best rearrangement setting 6
Bootstrap[8]: Time 0.118524 seconds, bootstrap likelihood -1321.820787, best rearrangement setting 13
Bootstrap[9]: Time 0.126695 seconds, bootstrap likelihood -1147.233446, best rearrangement setting 6
Bootstrap[10]: Time 0.090047 seconds, bootstrap likelihood -1220.766493, best rearrangement setting 13
Bootstrap[11]: Time 0.127921 seconds, bootstrap likelihood -1200.006355, best rearrangement setting 8
Bootstrap[12]: Time 0.132948 seconds, bootstrap likelihood -1346.392834, best rearrangement setting 14
Bootstrap[13]: Time 0.108550 seconds, bootstrap likelihood -1301.111096, best rearrangement setting 14
Bootstrap[14]: Time 0.116437 seconds, bootstrap likelihood -1262.253559, best rearrangement setting 11
Bootstrap[15]: Time 0.114979 seconds, bootstrap likelihood -1215.017551, best rearrangement setting 14
Bootstrap[16]: Time 0.109636 seconds, bootstrap likelihood -1238.832009, best rearrangement setting 7
Bootstrap[17]: Time 0.105585 seconds, bootstrap likelihood -1393.989732, best rearrangement setting 12
Bootstrap[18]: Time 0.104946 seconds, bootstrap likelihood -1173.921002, best rearrangement setting 15
Bootstrap[19]: Time 0.109499 seconds, bootstrap likelihood -1185.726976, best rearrangement setting 11
Bootstrap[20]: Time 0.097726 seconds, bootstrap likelihood -1158.491940, best rearrangement setting 6
Bootstrap[21]: Time 0.090471 seconds, bootstrap likelihood -1154.664272, best rearrangement setting 11
Bootstrap[22]: Time 0.105639 seconds, bootstrap likelihood -1244.159837, best rearrangement setting 10
Bootstrap[23]: Time 0.125237 seconds, bootstrap likelihood -1211.171036, best rearrangement setting 15
Bootstrap[24]: Time 0.106640 seconds, bootstrap likelihood -1261.440677, best rearrangement setting 12
Bootstrap[25]: Time 0.107126 seconds, bootstrap likelihood -1331.836715, best rearrangement setting 15
Bootstrap[26]: Time 0.110708 seconds, bootstrap likelihood -1129.144509, best rearrangement setting 5
Bootstrap[27]: Time 0.134422 seconds, bootstrap likelihood -1226.624056, best rearrangement setting 7
Bootstrap[28]: Time 0.132725 seconds, bootstrap likelihood -1221.046176, best rearrangement setting 12
Bootstrap[29]: Time 0.089861 seconds, bootstrap likelihood -1211.791204, best rearrangement setting 14
Bootstrap[30]: Time 0.112077 seconds, bootstrap likelihood -1389.442380, best rearrangement setting 5
Bootstrap[31]: Time 0.113762 seconds, bootstrap likelihood -1303.638592, best rearrangement setting 12
Bootstrap[32]: Time 0.121138 seconds, bootstrap likelihood -1172.859456, best rearrangement setting 12
Bootstrap[33]: Time 0.110006 seconds, bootstrap likelihood -1244.617135, best rearrangement setting 9
Bootstrap[34]: Time 0.099157 seconds, bootstrap likelihood -1211.871717, best rearrangement setting 15
Bootstrap[35]: Time 0.130204 seconds, bootstrap likelihood -1299.862912, best rearrangement setting 5
Bootstrap[36]: Time 0.102713 seconds, bootstrap likelihood -1141.967505, best rearrangement setting 5
Bootstrap[37]: Time 0.122422 seconds, bootstrap likelihood -1283.923198, best rearrangement setting 12
Bootstrap[38]: Time 0.098769 seconds, bootstrap likelihood -1304.250946, best rearrangement setting 5
Bootstrap[39]: Time 0.103022 seconds, bootstrap likelihood -1407.084376, best rearrangement setting 15
Bootstrap[40]: Time 0.113169 seconds, bootstrap likelihood -1277.946299, best rearrangement setting 13
Bootstrap[41]: Time 0.111611 seconds, bootstrap likelihood -1279.006200, best rearrangement setting 7
Bootstrap[42]: Time 0.105443 seconds, bootstrap likelihood -1160.274606, best rearrangement setting 6
Bootstrap[43]: Time 0.128511 seconds, bootstrap likelihood -1216.079259, best rearrangement setting 14
Bootstrap[44]: Time 0.099653 seconds, bootstrap likelihood -1382.278311, best rearrangement setting 8
Bootstrap[45]: Time 0.111733 seconds, bootstrap likelihood -1099.004439, best rearrangement setting 11
Bootstrap[46]: Time 0.090937 seconds, bootstrap likelihood -1296.527478, best rearrangement setting 8
Bootstrap[47]: Time 0.131870 seconds, bootstrap likelihood -1291.322658, best rearrangement setting 9
Bootstrap[48]: Time 0.088528 seconds, bootstrap likelihood -1161.908080, best rearrangement setting 6
Bootstrap[49]: Time 0.118519 seconds, bootstrap likelihood -1257.348428, best rearrangement setting 13
Bootstrap[50]: Time 0.137860 seconds, bootstrap likelihood -1309.422533, best rearrangement setting 13
Bootstrap[51]: Time 0.103916 seconds, bootstrap likelihood -1197.633097, best rearrangement setting 11
Bootstrap[52]: Time 0.114719 seconds, bootstrap likelihood -1347.123005, best rearrangement setting 8
Bootstrap[53]: Time 0.100418 seconds, bootstrap likelihood -1234.934890, best rearrangement setting 14
Bootstrap[54]: Time 0.116185 seconds, bootstrap likelihood -1227.092434, best rearrangement setting 6
Bootstrap[55]: Time 0.116643 seconds, bootstrap likelihood -1280.635747, best rearrangement setting 7
Bootstrap[56]: Time 0.100294 seconds, bootstrap likelihood -1225.911449, best rearrangement setting 6
Bootstrap[57]: Time 0.094664 seconds, bootstrap likelihood -1236.213347, best rearrangement setting 11
Bootstrap[58]: Time 0.144060 seconds, bootstrap likelihood -1393.245723, best rearrangement setting 14
Bootstrap[59]: Time 0.108086 seconds, bootstrap likelihood -1212.039371, best rearrangement setting 6
Bootstrap[60]: Time 0.099846 seconds, bootstrap likelihood -1248.692011, best rearrangement setting 10
Bootstrap[61]: Time 0.109855 seconds, bootstrap likelihood -1172.820979, best rearrangement setting 13
Bootstrap[62]: Time 0.126656 seconds, bootstrap likelihood -1126.745788, best rearrangement setting 14
Bootstrap[63]: Time 0.100105 seconds, bootstrap likelihood -1267.434444, best rearrangement setting 12
Bootstrap[64]: Time 0.097109 seconds, bootstrap likelihood -1340.680748, best rearrangement setting 5
Bootstrap[65]: Time 0.098473 seconds, bootstrap likelihood -1072.671059, best rearrangement setting 5
Bootstrap[66]: Time 0.127313 seconds, bootstrap likelihood -1234.294838, best rearrangement setting 8
Bootstrap[67]: Time 0.120335 seconds, bootstrap likelihood -1109.249439, best rearrangement setting 15
Bootstrap[68]: Time 0.096427 seconds, bootstrap likelihood -1314.493588, best rearrangement setting 8
Bootstrap[69]: Time 0.095392 seconds, bootstrap likelihood -1173.850035, best rearrangement setting 13
Bootstrap[70]: Time 0.100580 seconds, bootstrap likelihood -1231.066465, best rearrangement setting 10
Bootstrap[71]: Time 0.103531 seconds, bootstrap likelihood -1146.861379, best rearrangement setting 9
Bootstrap[72]: Time 0.087171 seconds, bootstrap likelihood -1148.753369, best rearrangement setting 8
Bootstrap[73]: Time 0.102115 seconds, bootstrap likelihood -1333.374056, best rearrangement setting 9
Bootstrap[74]: Time 0.091284 seconds, bootstrap likelihood -1259.382378, best rearrangement setting 5
Bootstrap[75]: Time 0.099588 seconds, bootstrap likelihood -1319.944496, best rearrangement setting 6
Bootstrap[76]: Time 0.111140 seconds, bootstrap likelihood -1309.042165, best rearrangement setting 14
Bootstrap[77]: Time 0.135155 seconds, bootstrap likelihood -1232.061289, best rearrangement setting 8
Bootstrap[78]: Time 0.107177 seconds, bootstrap likelihood -1261.333984, best rearrangement setting 9
Bootstrap[79]: Time 0.114820 seconds, bootstrap likelihood -1194.644341, best rearrangement setting 13
Bootstrap[80]: Time 0.101512 seconds, bootstrap likelihood -1214.037389, best rearrangement setting 9
Bootstrap[81]: Time 0.114018 seconds, bootstrap likelihood -1224.527657, best rearrangement setting 8
Bootstrap[82]: Time 0.131956 seconds, bootstrap likelihood -1241.464826, best rearrangement setting 11
Bootstrap[83]: Time 0.099149 seconds, bootstrap likelihood -1230.730558, best rearrangement setting 6
Bootstrap[84]: Time 0.106501 seconds, bootstrap likelihood -1219.034592, best rearrangement setting 10
Bootstrap[85]: Time 0.111692 seconds, bootstrap likelihood -1280.071994, best rearrangement setting 8
Bootstrap[86]: Time 0.097407 seconds, bootstrap likelihood -1444.747777, best rearrangement setting 9
Bootstrap[87]: Time 0.095685 seconds, bootstrap likelihood -1245.890035, best rearrangement setting 14
Bootstrap[88]: Time 0.111665 seconds, bootstrap likelihood -1287.832766, best rearrangement setting 7
Bootstrap[89]: Time 0.102463 seconds, bootstrap likelihood -1325.245976, best rearrangement setting 5
Bootstrap[90]: Time 0.115857 seconds, bootstrap likelihood -1227.883697, best rearrangement setting 5
Bootstrap[91]: Time 0.112054 seconds, bootstrap likelihood -1273.489392, best rearrangement setting 8
Bootstrap[92]: Time 0.046768 seconds, bootstrap likelihood -1234.725870, best rearrangement setting 7
Bootstrap[93]: Time 0.131415 seconds, bootstrap likelihood -1235.733064, best rearrangement setting 11
Bootstrap[94]: Time 0.101405 seconds, bootstrap likelihood -1204.319488, best rearrangement setting 15
Bootstrap[95]: Time 0.104308 seconds, bootstrap likelihood -1183.328582, best rearrangement setting 11
Bootstrap[96]: Time 0.110157 seconds, bootstrap likelihood -1196.298898, best rearrangement setting 13
Bootstrap[97]: Time 0.119032 seconds, bootstrap likelihood -1339.251746, best rearrangement setting 12
Bootstrap[98]: Time 0.045984 seconds, bootstrap likelihood -1404.363552, best rearrangement setting 7
Bootstrap[99]: Time 0.059831 seconds, bootstrap likelihood -1270.157811, best rearrangement setting 7
Overall Time for 100 Rapid Bootstraps 10.956089 seconds
Average Time per Rapid Bootstrap 0.109561 seconds
Starting ML Search ...
Fast ML optimization finished
Fast ML search Time: 4.402093 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: 2.234023 seconds
Thorough ML search Time: 0.561927 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 7.203642 secs or 0.002001 hours
Combined Bootstrap and ML search took 18.159930 secs or 0.005044 hours
Drawing Bootstrap Support Values on best-scoring ML tree ...
Found 1 tree in File /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiq04em7j/RAxML_bestTree.q2bootstrap
Found 1 tree in File /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiq04em7j/RAxML_bestTree.q2bootstrap
Program execution info written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiq04em7j/RAxML_info.q2bootstrap
All 100 bootstrapped trees written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiq04em7j/RAxML_bootstrap.q2bootstrap
Best-scoring ML tree written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiq04em7j/RAxML_bestTree.q2bootstrap
Best-scoring ML tree with support values written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiq04em7j/RAxML_bipartitions.q2bootstrap
Best-scoring ML tree with support values as branch labels written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiq04em7j/RAxML_bipartitionsBranchLabels.q2bootstrap
Overall execution time for full ML analysis: 18.173805 secs or 0.005048 hours or 0.000210 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpiq04em7j -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 2.2.3 COVID-edition for Mac OS X 64-bit built Aug 13 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpii9ep6kr/q2iqtree -nt 1
Seed: 12862 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Fri Aug 18 10:24:38 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000213861 secs using 84.63% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000482082 secs using 77.37% 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 89.13% 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 75.39% 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 0.028537 secs using 99.25% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1391.885
2. Current log-likelihood: -1390.523
Optimal log-likelihood: -1389.769
Rate parameters: A-C: 0.33285 A-G: 2.23820 A-T: 2.09603 C-G: 1.18764 C-T: 3.18096 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: 1.359
Parameters optimization took 2 rounds (0.013 sec)
Time for fast ML tree search: 0.066 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 484 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1405.418 45 2900.835 2925.478 3052.304
2 GTR+F+I 1403.836 46 2899.673 2925.565 3054.508
3 GTR+F+G4 1388.331 46 2868.662 2894.554 3023.497
4 GTR+F+I+G4 1388.704 47 2871.408 2898.589 3029.609
5 GTR+F+R2 1382.562 47 2859.124 2886.305 3017.325
6 GTR+F+R3 1382.602 49 2863.203 2893.081 3028.136
14 GTR+F+I+R2 1382.708 48 2861.416 2889.925 3022.983
15 GTR+F+I+R3 1382.679 50 2865.358 2896.646 3033.657
25 SYM+G4 1388.448 43 2862.897 2885.155 3007.634
27 SYM+R2 1384.041 44 2856.081 2879.513 3004.184
36 SYM+I+R2 1384.179 45 2858.357 2883.000 3009.826
47 TVM+F+G4 1389.408 45 2868.815 2893.458 3020.284
49 TVM+F+R2 1384.278 46 2860.555 2886.448 3015.390
58 TVM+F+I+R2 1384.278 47 2862.557 2889.737 3020.757
69 TVMe+G4 1388.431 42 2860.861 2881.984 3002.232
71 TVMe+R2 1384.070 43 2854.141 2876.399 2998.878
80 TVMe+I+R2 1384.207 44 2856.414 2879.846 3004.517
91 TIM3+F+G4 1392.277 44 2872.555 2895.987 3020.658
93 TIM3+F+R2 1385.911 45 2861.822 2886.465 3013.291
102 TIM3+F+I+R2 1386.044 46 2864.089 2889.981 3018.924
113 TIM3e+G4 1391.664 41 2865.328 2885.351 3003.333
115 TIM3e+R2 1386.836 42 2857.673 2878.795 2999.044
124 TIM3e+I+R2 1386.991 43 2859.982 2882.241 3004.719
135 TIM2+F+G4 1395.130 44 2878.260 2901.692 3026.363
137 TIM2+F+R2 1388.182 45 2866.364 2891.007 3017.833
146 TIM2+F+I+R2 1388.318 46 2868.637 2894.529 3023.472
157 TIM2e+G4 1398.824 41 2879.647 2899.670 3017.652
159 TIM2e+R2 1393.016 42 2870.033 2891.156 3011.404
168 TIM2e+I+R2 1393.107 43 2872.215 2894.473 3016.952
179 TIM+F+G4 1391.782 44 2871.563 2894.995 3019.666
181 TIM+F+R2 1385.369 45 2860.738 2885.381 3012.207
190 TIM+F+I+R2 1385.497 46 2862.994 2888.887 3017.829
201 TIMe+G4 1396.021 41 2874.043 2894.066 3012.048
203 TIMe+R2 1390.461 42 2864.921 2886.044 3006.292
212 TIMe+I+R2 1390.568 43 2867.135 2889.394 3011.872
223 TPM3u+F+G4 1393.267 43 2872.534 2894.792 3017.271
225 TPM3u+F+R2 1387.637 44 2863.274 2886.706 3011.377
234 TPM3u+F+I+R2 1387.756 45 2865.513 2890.156 3016.982
245 TPM3+G4 1391.670 40 2863.340 2882.300 2997.979
247 TPM3+R2 1386.891 41 2855.783 2875.806 2993.788
256 TPM3+I+R2 1387.026 42 2858.051 2879.174 2999.422
267 TPM2u+F+G4 1396.100 43 2878.200 2900.458 3022.937
269 TPM2u+F+R2 1389.793 44 2867.586 2891.018 3015.689
278 TPM2u+F+I+R2 1389.878 45 2869.756 2894.399 3021.225
289 TPM2+G4 1398.841 40 2877.682 2896.641 3012.321
291 TPM2+R2 1393.061 41 2868.123 2888.146 3006.128
300 TPM2+I+R2 1393.137 42 2870.275 2891.397 3011.646
311 K3Pu+F+G4 1392.937 43 2871.874 2894.133 3016.611
313 K3Pu+F+R2 1387.034 44 2862.067 2885.499 3010.170
322 K3Pu+F+I+R2 1387.111 45 2864.221 2888.864 3015.690
333 K3P+G4 1396.021 40 2872.041 2891.001 3006.680
335 K3P+R2 1390.496 41 2862.992 2883.015 3000.997
344 K3P+I+R2 1390.601 42 2865.202 2886.325 3006.573
355 TN+F+G4 1395.486 43 2876.972 2899.230 3021.709
357 TN+F+R2 1388.575 44 2865.151 2888.583 3013.254
366 TN+F+I+R2 1388.715 45 2867.429 2892.072 3018.898
377 TNe+G4 1398.826 40 2877.651 2896.611 3012.290
379 TNe+R2 1393.014 41 2868.027 2888.050 3006.032
388 TNe+I+R2 1393.104 42 2870.208 2891.331 3011.579
399 HKY+F+G4 1396.476 42 2876.951 2898.074 3018.322
401 HKY+F+R2 1390.188 43 2866.375 2888.634 3011.112
410 HKY+F+I+R2 1390.281 44 2868.561 2891.993 3016.664
421 K2P+G4 1398.841 39 2875.682 2893.613 3006.955
423 K2P+R2 1393.061 40 2866.123 2885.082 3000.762
432 K2P+I+R2 1393.137 41 2868.274 2888.297 3006.279
443 F81+F+G4 1406.476 41 2894.952 2914.975 3032.957
445 F81+F+R2 1401.149 42 2886.297 2907.420 3027.668
454 F81+F+I+R2 1401.264 43 2888.528 2910.787 3033.265
465 JC+G4 1408.763 38 2893.527 2910.464 3021.434
467 JC+R2 1403.897 39 2885.793 2903.724 3017.066
476 JC+I+R2 1403.935 40 2887.870 2906.829 3022.509
Akaike Information Criterion: TVMe+R2
Corrected Akaike Information Criterion: TPM3+R2
Bayesian Information Criterion: TPM3+R2
Best-fit model: TPM3+R2 chosen according to BIC
All model information printed to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpii9ep6kr/q2iqtree.model.gz
CPU time for ModelFinder: 1.416 seconds (0h:0m:1s)
Wall-clock time for ModelFinder: 1.433 seconds (0h:0m:1s)
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1386.891
Optimal log-likelihood: -1386.887
Rate parameters: A-C: 0.39145 A-G: 1.51425 A-T: 1.00000 C-G: 0.39145 C-T: 1.51425 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.718,0.396) (0.282,2.538)
Parameters optimization took 1 rounds (0.004 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000976086 secs using 97.84% CPU
Computing ML distances took 0.001067 sec (of wall-clock time) 0.001019 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.29289e-05 secs using 92.58% CPU
Constructing RapidNJ tree: done in 9.29832e-05 secs using 135.5% CPU
Computing RapidNJ tree took 0.000221 sec (of wall-clock time) 0.000251 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.864
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.104 second
Computing log-likelihood of 98 initial trees ... 0.087 seconds
Current best score: -1386.887
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00594401 secs using 99.95% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.310
Optimizing NNI: done in 0.0128658 secs using 99.94% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.308
Optimizing NNI: done in 0.0123861 secs using 99.94% CPU
Optimizing NNI: done in 0.010685 secs using 99.94% CPU
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Optimizing NNI: done in 0.0136619 secs using 99.89% CPU
Optimizing NNI: done in 0.0121131 secs using 99.94% CPU
Iteration 10 / LogL: -1385.340 / Time: 0h:0m:0s
Optimizing NNI: done in 0.012265 secs using 99.95% CPU
Optimizing NNI: done in 0.011523 secs using 99.95% CPU
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Optimizing NNI: done in 0.0113542 secs using 99.95% CPU
Optimizing NNI: done in 0.0114291 secs using 99.95% CPU
Iteration 20 / LogL: -1385.339 / Time: 0h:0m:0s
Finish initializing candidate tree set (2)
Current best tree score: -1385.308 / CPU time: 0.441
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.017689 secs using 99.68% CPU
Optimizing NNI: done in 0.0184629 secs using 99.91% CPU
Optimizing NNI: done in 0.0169821 secs using 99.96% CPU
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Optimizing NNI: done in 0.0143189 secs using 99.95% CPU
Iteration 30 / LogL: -1385.785 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.02512 secs using 99.94% CPU
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Optimizing NNI: done in 0.00812101 secs using 99.95% CPU
Optimizing NNI: done in 0.012893 secs using 99.94% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.307
Optimizing NNI: done in 0.0185492 secs using 99.59% CPU
Optimizing NNI: done in 0.018137 secs using 99.91% CPU
Iteration 40 / LogL: -1387.674 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.0203469 secs using 99.95% CPU
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Iteration 50 / LogL: -1385.935 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.0159721 secs using 99.95% CPU
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Iteration 60 / LogL: -1385.650 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0113661 secs using 99.95% CPU
Optimizing NNI: done in 0.0207469 secs using 99.96% CPU
Optimizing NNI: done in 0.014369 secs using 99.94% CPU
Optimizing NNI: done in 0.0192771 secs using 99.96% CPU
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Optimizing NNI: done in 0.016608 secs using 99.92% CPU
Optimizing NNI: done in 0.0169902 secs using 99.95% CPU
Optimizing NNI: done in 0.0137711 secs using 99.95% CPU
Iteration 70 / LogL: -1385.926 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00916696 secs using 99.94% CPU
Optimizing NNI: done in 0.0126672 secs using 99.94% CPU
Optimizing NNI: done in 0.0216401 secs using 99.94% CPU
Optimizing NNI: done in 0.012207 secs using 99.95% CPU
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Optimizing NNI: done in 0.0106571 secs using 99.93% CPU
Optimizing NNI: done in 0.0100911 secs using 99.94% CPU
Optimizing NNI: done in 0.0151031 secs using 99.94% CPU
Optimizing NNI: done in 0.0141039 secs using 99.94% CPU
Optimizing NNI: done in 0.0138299 secs using 99.94% CPU
Iteration 80 / LogL: -1385.689 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.013993 secs using 99.95% CPU
Optimizing NNI: done in 0.0144 secs using 99.94% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.306
Optimizing NNI: done in 0.015198 secs using 99.71% CPU
Optimizing NNI: done in 0.0193892 secs using 99.89% CPU
Optimizing NNI: done in 0.0120449 secs using 99.95% CPU
Optimizing NNI: done in 0.0128589 secs using 99.94% CPU
Optimizing NNI: done in 0.016242 secs using 99.96% CPU
Optimizing NNI: done in 0.0115869 secs using 99.85% CPU
Optimizing NNI: done in 0.018501 secs using 99.88% CPU
Optimizing NNI: done in 0.0158339 secs using 99.95% CPU
Iteration 90 / LogL: -1385.506 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.019448 secs using 99.93% CPU
Optimizing NNI: done in 0.0159061 secs using 99.94% CPU
Optimizing NNI: done in 0.0106981 secs using 99.94% CPU
Optimizing NNI: done in 0.0201559 secs using 99.94% CPU
Optimizing NNI: done in 0.0122938 secs using 99.95% CPU
Optimizing NNI: done in 0.01353 secs using 99.94% CPU
Optimizing NNI: done in 0.0129271 secs using 99.95% CPU
Optimizing NNI: done in 0.0131249 secs using 99.95% CPU
Optimizing NNI: done in 0.0204899 secs using 99.95% CPU
Optimizing NNI: done in 0.012388 secs using 99.95% CPU
Iteration 100 / LogL: -1385.514 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0183542 secs using 99.94% CPU
Optimizing NNI: done in 0.0172429 secs using 99.95% CPU
TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:1s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1385.306
Optimal log-likelihood: -1385.305
Rate parameters: A-C: 0.39578 A-G: 1.57585 A-T: 1.00000 C-G: 0.39578 C-T: 1.57585 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.722,0.401) (0.278,2.554)
Parameters optimization took 1 rounds (0.003 sec)
BEST SCORE FOUND : -1385.305
Total tree length: 6.876
Total number of iterations: 102
CPU time used for tree search: 1.904 sec (0h:0m:1s)
Wall-clock time used for tree search: 1.727 sec (0h:0m:1s)
Total CPU time used: 1.933 sec (0h:0m:1s)
Total wall-clock time used: 1.752 sec (0h:0m:1s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpii9ep6kr/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpii9ep6kr/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpii9ep6kr/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpii9ep6kr/q2iqtree.log
Date and Time: Fri Aug 18 10:24:41 2023
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpii9ep6kr/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 2.2.3 COVID-edition for Mac OS X 64-bit built Aug 13 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpgoght6ii/q2iqtree -nt 1
Seed: 955059 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Fri Aug 18 10:24:51 2023
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000214815 secs using 84.26% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000507832 secs using 74.43% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 1.90735e-05 secs using 89.13% 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 7.60555e-05 secs using 76.26% 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, 1.225 / LogL: -1394.494
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.008, 1.298 / LogL: -1394.737
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.008, 1.301 / LogL: -1394.733
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.008, 1.300 / LogL: -1394.723
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.008, 1.304 / LogL: -1394.760
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.007, 1.301 / LogL: -1394.713
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.008, 1.302 / LogL: -1394.729
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.008, 1.306 / LogL: -1394.742
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.008, 1.308 / LogL: -1394.745
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.008, 1.310 / LogL: -1394.754
Optimal pinv,alpha: 0.000, 1.225 / LogL: -1394.494
Parameters optimization took 0.499 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00152183 secs using 98.17% CPU
Computing ML distances took 0.001671 sec (of wall-clock time) 0.001585 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.19753e-05 secs using 80.81% CPU
Constructing RapidNJ tree: done in 9.20296e-05 secs using 143.4% CPU
Computing RapidNJ tree took 0.000224 sec (of wall-clock time) 0.000232 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.958
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.107 second
Computing log-likelihood of 98 initial trees ... 0.132 seconds
Current best score: -1392.958
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.019604 secs using 98.84% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.273
Optimizing NNI: done in 0.00985813 secs using 99.32% CPU
Optimizing NNI: done in 0.014595 secs using 98.97% CPU
Optimizing NNI: done in 0.013876 secs using 99.92% CPU
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Optimizing NNI: done in 0.0258911 secs using 99.67% CPU
Iteration 10 / LogL: -1387.285 / Time: 0h:0m:0s
Optimizing NNI: done in 0.026274 secs using 99.14% CPU
Optimizing NNI: done in 0.0259809 secs using 99.48% CPU
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Optimizing NNI: done in 0.025986 secs using 99.36% CPU
Iteration 20 / LogL: -1387.285 / Time: 0h:0m:1s
Finish initializing candidate tree set (2)
Current best tree score: -1387.273 / CPU time: 0.671
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.02264 secs using 99.05% CPU
Optimizing NNI: done in 0.0267351 secs using 98.97% CPU
Optimizing NNI: done in 0.0304461 secs using 99.41% CPU
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Iteration 30 / LogL: -1388.137 / Time: 0h:0m:1s (0h:0m:3s left)
Optimizing NNI: done in 0.0237992 secs using 99.19% CPU
Optimizing NNI: done in 0.0248449 secs using 99.37% CPU
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Iteration 40 / LogL: -1387.430 / Time: 0h:0m:1s (0h:0m:2s left)
Optimizing NNI: done in 0.032166 secs using 99.94% CPU
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Iteration 50 / LogL: -1387.430 / Time: 0h:0m:2s (0h:0m:2s left)
Optimizing NNI: done in 0.018645 secs using 99.96% CPU
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Optimizing NNI: done in 0.0295861 secs using 99.96% CPU
Optimizing NNI: done in 0.0300272 secs using 99.89% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 58: -1387.168
Optimizing NNI: done in 0.0365939 secs using 99.41% CPU
Optimizing NNI: done in 0.0379889 secs using 99.96% CPU
Iteration 60 / LogL: -1387.386 / Time: 0h:0m:2s (0h:0m:3s left)
Optimizing NNI: done in 0.024287 secs using 99.96% CPU
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Optimizing NNI: done in 0.0236099 secs using 99.97% CPU
Optimizing NNI: done in 0.0206821 secs using 99.97% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.168
Optimizing NNI: done in 0.027132 secs using 99.9% CPU
Iteration 70 / LogL: -1387.391 / Time: 0h:0m:2s (0h:0m:3s left)
Optimizing NNI: done in 0.0235119 secs using 99.97% CPU
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Optimizing NNI: done in 0.0293062 secs using 99.97% CPU
Optimizing NNI: done in 0.0515189 secs using 99.96% CPU
Iteration 80 / LogL: -1396.639 / Time: 0h:0m:2s (0h:0m:2s left)
Optimizing NNI: done in 0.0206621 secs using 99.97% CPU
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Optimizing NNI: done in 0.0318561 secs using 99.96% CPU
Optimizing NNI: done in 0.025305 secs using 99.96% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.168
Iteration 90 / LogL: -1387.168 / Time: 0h:0m:3s (0h:0m:2s left)
Optimizing NNI: done in 0.023845 secs using 99.87% CPU
Optimizing NNI: done in 0.022954 secs using 99.97% CPU
Optimizing NNI: done in 0.019871 secs using 99.97% CPU
Optimizing NNI: done in 0.036824 secs using 99.96% CPU
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Optimizing NNI: done in 0.0230849 secs using 99.97% CPU
Optimizing NNI: done in 0.038275 secs using 99.89% CPU
Iteration 100 / LogL: -1387.168 / Time: 0h:0m:3s (0h:0m:2s left)
Optimizing NNI: done in 0.051924 secs using 99.95% CPU
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Iteration 110 / LogL: -1387.338 / Time: 0h:0m:3s (0h:0m:1s left)
Optimizing NNI: done in 0.0356638 secs using 99.97% CPU
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Optimizing NNI: done in 0.029211 secs using 99.95% CPU
Iteration 120 / LogL: -1387.168 / Time: 0h:0m:4s (0h:0m:1s left)
Optimizing NNI: done in 0.0263431 secs using 99.77% CPU
Optimizing NNI: done in 0.029017 secs using 99.91% CPU
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Optimizing NNI: done in 0.0286691 secs using 99.96% CPU
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Iteration 130 / LogL: -1387.169 / Time: 0h:0m:4s (0h:0m:0s left)
Optimizing NNI: done in 0.031728 secs using 99.84% CPU
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Iteration 140 / LogL: -1387.190 / Time: 0h:0m:4s (0h:0m:0s left)
Optimizing NNI: done in 0.049181 secs using 99.96% CPU
Optimizing NNI: done in 0.0285971 secs using 99.88% CPU
Optimizing NNI: done in 0.025883 secs using 99.81% CPU
Optimizing NNI: done in 0.0277052 secs using 99.96% CPU
Optimizing NNI: done in 0.0226371 secs using 99.96% CPU
Optimizing NNI: done in 0.023592 secs using 99.97% CPU
Optimizing NNI: done in 0.0358009 secs using 99.96% CPU
Optimizing NNI: done in 0.01525 secs using 99.96% CPU
Optimizing NNI: done in 0.0210891 secs using 99.95% CPU
Optimizing NNI: done in 0.0161691 secs using 99.96% CPU
Iteration 150 / LogL: -1387.351 / Time: 0h:0m:4s (0h:0m:0s left)
Optimizing NNI: done in 0.019784 secs using 99.97% CPU
Optimizing NNI: done in 0.017163 secs using 99.96% CPU
Optimizing NNI: done in 0.0250831 secs using 99.96% CPU
Optimizing NNI: done in 0.044266 secs using 99.96% CPU
Optimizing NNI: done in 0.0193148 secs using 99.96% CPU
Optimizing NNI: done in 0.0237679 secs using 99.96% CPU
Optimizing NNI: done in 0.0127249 secs using 99.95% CPU
Optimizing NNI: done in 0.0191779 secs using 99.97% CPU
Optimizing NNI: done in 0.0300472 secs using 99.96% CPU
TREE SEARCH COMPLETED AFTER 159 ITERATIONS / Time: 0h:0m:5s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.168
Optimal log-likelihood: -1387.167
Rate parameters: A-C: 0.34333 A-G: 2.30501 A-T: 2.12422 C-G: 1.22369 C-T: 3.18866 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.000
Gamma shape alpha: 1.285
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1387.167
Total tree length: 7.602
Total number of iterations: 159
CPU time used for tree search: 4.822 sec (0h:0m:4s)
Wall-clock time used for tree search: 4.656 sec (0h:0m:4s)
Total CPU time used: 5.340 sec (0h:0m:5s)
Total wall-clock time used: 5.178 sec (0h:0m:5s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpgoght6ii/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpgoght6ii/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpgoght6ii/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpgoght6ii/q2iqtree.log
Date and Time: Fri Aug 18 10:24:57 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpgoght6ii/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 2.2.3 COVID-edition for Mac OS X 64-bit built Aug 13 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpydy2ru20/q2iqtree -nt 1 -fast
Seed: 815653 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Fri Aug 18 10:25:07 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000236988 secs using 83.55% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000481844 secs using 77% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Analyzing sequences: done in 2.09808e-05 secs using 85.79% CPU
Checking for duplicate sequences: done in 7.29561e-05 secs using 75.39% CPU
---> START RUN NUMBER 1 (seed: 815653)
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: -1492.49
2. Current log-likelihood: -1404.61
3. Current log-likelihood: -1399.22
4. Current log-likelihood: -1397.82
5. Current log-likelihood: -1397.06
Optimal log-likelihood: -1396.48
Rate parameters: A-C: 0.24153 A-G: 2.03298 A-T: 1.94373 C-G: 1.02159 C-T: 2.79340 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.438
Parameters optimization took 5 rounds (0.039 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00158787 secs using 96.29% CPU
Computing ML distances took 0.001691 sec (of wall-clock time) 0.001600 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 8.51154e-05 secs using 62.27% CPU
Constructing RapidNJ tree: done in 9.39369e-05 secs using 162.9% CPU
Computing RapidNJ tree took 0.000288 sec (of wall-clock time) 0.000295 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.204
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0202479 secs using 191.1% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.198
Optimizing NNI: done in 0.029295 secs using 191.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -1388.190
Finish initializing candidate tree set (3)
Current best tree score: -1388.190 / CPU time: 0.060
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.190
2. Current log-likelihood: -1387.968
3. Current log-likelihood: -1387.808
4. Current log-likelihood: -1387.688
5. Current log-likelihood: -1387.597
6. Current log-likelihood: -1387.526
7. Current log-likelihood: -1387.471
Optimal log-likelihood: -1387.426
Rate parameters: A-C: 0.33201 A-G: 2.23761 A-T: 2.11213 C-G: 1.16005 C-T: 3.23466 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.356
Parameters optimization took 7 rounds (0.027 sec)
BEST SCORE FOUND : -1387.426
Total tree length: 6.737
Total number of iterations: 2
CPU time used for tree search: 0.115 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.061 sec (0h:0m:0s)
Total CPU time used: 0.228 sec (0h:0m:0s)
Total wall-clock time used: 0.146 sec (0h:0m:0s)
---> START RUN NUMBER 2 (seed: 816653)
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 (0.041 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00166893 secs using 187.7% CPU
Computing ML distances took 0.001760 sec (of wall-clock time) 0.003277 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.50747e-05 secs using 88.97% CPU
Constructing RapidNJ tree: done in 9.799e-05 secs using 155.1% CPU
Computing RapidNJ tree took 0.000226 sec (of wall-clock time) 0.000248 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 0.020123 secs using 191.1% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.214
Optimizing NNI: done in 0.020519 secs using 191.7% CPU
Finish initializing candidate tree set (3)
Current best tree score: -1388.214 / CPU time: 0.049
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.214
2. Current log-likelihood: -1388.015
3. Current log-likelihood: -1387.868
4. Current log-likelihood: -1387.760
5. Current log-likelihood: -1387.676
6. Current log-likelihood: -1387.611
7. Current log-likelihood: -1387.560
Optimal log-likelihood: -1387.519
Rate parameters: A-C: 0.35522 A-G: 2.35151 A-T: 2.13874 C-G: 1.20261 C-T: 3.36909 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.362
Parameters optimization took 7 rounds (0.026 sec)
BEST SCORE FOUND : -1387.519
Total tree length: 6.815
Total number of iterations: 2
CPU time used for tree search: 0.094 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.049 sec (0h:0m:0s)
Total CPU time used: 0.256 sec (0h:0m:0s)
Total wall-clock time used: 0.135 sec (0h:0m:0s)
---> START RUN NUMBER 3 (seed: 817653)
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: 2.06956 A-T: 1.96268 C-G: 1.07937 C-T: 2.84174 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.322
Parameters optimization took 5 rounds (0.039 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00155497 secs using 192% CPU
Computing ML distances took 0.001644 sec (of wall-clock time) 0.003133 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 5.38826e-05 secs using 89.08% CPU
Constructing RapidNJ tree: done in 9.39369e-05 secs using 146.9% CPU
Computing RapidNJ tree took 0.000212 sec (of wall-clock time) 0.000254 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 0.022157 secs using 190.5% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.955
Optimizing NNI: done in 0.0111599 secs using 191.8% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.955 / CPU time: 0.050
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1387.955
2. Current log-likelihood: -1387.798
3. Current log-likelihood: -1387.680
4. Current log-likelihood: -1387.590
5. Current log-likelihood: -1387.521
6. Current log-likelihood: -1387.467
Optimal log-likelihood: -1387.423
Rate parameters: A-C: 0.33566 A-G: 2.27095 A-T: 2.14605 C-G: 1.17829 C-T: 3.29012 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.352
Parameters optimization took 6 rounds (0.023 sec)
BEST SCORE FOUND : -1387.423
Total tree length: 6.744
Total number of iterations: 2
CPU time used for tree search: 0.096 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.051 sec (0h:0m:0s)
Total CPU time used: 0.247 sec (0h:0m:0s)
Total wall-clock time used: 0.131 sec (0h:0m:0s)
---> START RUN NUMBER 4 (seed: 818653)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1493.167
2. Current log-likelihood: -1403.041
3. Current log-likelihood: -1398.313
4. Current log-likelihood: -1396.957
5. Current log-likelihood: -1396.228
Optimal log-likelihood: -1395.709
Rate parameters: A-C: 0.23146 A-G: 2.06957 A-T: 1.96268 C-G: 1.07937 C-T: 2.84174 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.322
Parameters optimization took 5 rounds (0.040 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00159311 secs using 191.2% CPU
Computing ML distances took 0.001682 sec (of wall-clock time) 0.003203 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000104904 secs using 59.1% CPU
Constructing RapidNJ tree: done in 0.000101089 secs using 148.4% CPU
Computing RapidNJ tree took 0.000294 sec (of wall-clock time) 0.000286 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 0.022656 secs using 189.3% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.955
Optimizing NNI: done in 0.011559 secs using 190.1% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.955 / CPU time: 0.051
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1387.955
2. Current log-likelihood: -1387.798
3. Current log-likelihood: -1387.680
4. Current log-likelihood: -1387.590
5. Current log-likelihood: -1387.521
6. Current log-likelihood: -1387.467
Optimal log-likelihood: -1387.423
Rate parameters: A-C: 0.33566 A-G: 2.27095 A-T: 2.14605 C-G: 1.17829 C-T: 3.29012 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.352
Parameters optimization took 6 rounds (0.022 sec)
BEST SCORE FOUND : -1387.423
Total tree length: 6.744
Total number of iterations: 2
CPU time used for tree search: 0.097 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.051 sec (0h:0m:0s)
Total CPU time used: 0.249 sec (0h:0m:0s)
Total wall-clock time used: 0.132 sec (0h:0m:0s)
---> START RUN NUMBER 5 (seed: 819653)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1492.389
2. Current log-likelihood: -1401.890
3. Current log-likelihood: -1396.534
4. Current log-likelihood: -1395.117
5. Current log-likelihood: -1394.389
Optimal log-likelihood: -1393.814
Rate parameters: A-C: 0.27026 A-G: 2.39526 A-T: 2.16931 C-G: 1.24752 C-T: 3.29290 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.415
Parameters optimization took 5 rounds (0.040 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00200701 secs using 192.5% CPU
Computing ML distances took 0.002110 sec (of wall-clock time) 0.004049 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 6.19888e-05 secs using 74.21% CPU
Constructing RapidNJ tree: done in 9.799e-05 secs using 142.9% CPU
Computing RapidNJ tree took 0.000287 sec (of wall-clock time) 0.000264 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 0.0198479 secs using 192% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.213
Optimizing NNI: done in 0.020195 secs using 191.2% CPU
Finish initializing candidate tree set (3)
Current best tree score: -1388.213 / 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: -1388.213
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: 0.093 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.049 sec (0h:0m:0s)
Total CPU time used: 0.254 sec (0h:0m:0s)
Total wall-clock time used: 0.134 sec (0h:0m:0s)
---> START RUN NUMBER 6 (seed: 820653)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1493.167
2. Current log-likelihood: -1403.041
3. Current log-likelihood: -1398.313
4. Current log-likelihood: -1396.957
5. Current log-likelihood: -1396.228
Optimal log-likelihood: -1395.709
Rate parameters: A-C: 0.23146 A-G: 2.06957 A-T: 1.96268 C-G: 1.07937 C-T: 2.84174 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.322
Parameters optimization took 5 rounds (0.039 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00158405 secs using 191.5% CPU
Computing ML distances took 0.001680 sec (of wall-clock time) 0.003206 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 7.08103e-05 secs using 88.97% CPU
Constructing RapidNJ tree: done in 9.67979e-05 secs using 156% CPU
Computing RapidNJ tree took 0.000255 sec (of wall-clock time) 0.000284 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 0.022053 secs using 191.1% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.955
Optimizing NNI: done in 0.0118551 secs using 191.3% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.955 / CPU time: 0.051
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1387.955
2. Current log-likelihood: -1387.798
3. Current log-likelihood: -1387.680
4. Current log-likelihood: -1387.590
5. Current log-likelihood: -1387.521
6. Current log-likelihood: -1387.467
Optimal log-likelihood: -1387.423
Rate parameters: A-C: 0.33566 A-G: 2.27095 A-T: 2.14605 C-G: 1.17829 C-T: 3.29012 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.352
Parameters optimization took 6 rounds (0.023 sec)
BEST SCORE FOUND : -1387.423
Total tree length: 6.744
Total number of iterations: 2
CPU time used for tree search: 0.097 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.051 sec (0h:0m:0s)
Total CPU time used: 0.248 sec (0h:0m:0s)
Total wall-clock time used: 0.131 sec (0h:0m:0s)
---> START RUN NUMBER 7 (seed: 821653)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1493.167
2. Current log-likelihood: -1403.041
3. Current log-likelihood: -1398.313
4. Current log-likelihood: -1396.957
5. Current log-likelihood: -1396.228
Optimal log-likelihood: -1395.709
Rate parameters: A-C: 0.23146 A-G: 2.06956 A-T: 1.96268 C-G: 1.07937 C-T: 2.84174 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.322
Parameters optimization took 5 rounds (0.039 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0016129 secs using 191.1% CPU
Computing ML distances took 0.001698 sec (of wall-clock time) 0.003220 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 5.19753e-05 secs using 94.28% CPU
Constructing RapidNJ tree: done in 9.29832e-05 secs using 148.4% CPU
Computing RapidNJ tree took 0.000214 sec (of wall-clock time) 0.000243 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 0.022815 secs using 191.8% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.955
Optimizing NNI: done in 0.012449 secs using 191.7% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.955 / CPU time: 0.052
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1387.955
2. Current log-likelihood: -1387.798
3. Current log-likelihood: -1387.680
4. Current log-likelihood: -1387.590
5. Current log-likelihood: -1387.521
6. Current log-likelihood: -1387.467
Optimal log-likelihood: -1387.423
Rate parameters: A-C: 0.33566 A-G: 2.27095 A-T: 2.14605 C-G: 1.17829 C-T: 3.29012 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.352
Parameters optimization took 6 rounds (0.022 sec)
BEST SCORE FOUND : -1387.423
Total tree length: 6.744
Total number of iterations: 2
CPU time used for tree search: 0.100 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.052 sec (0h:0m:0s)
Total CPU time used: 0.250 sec (0h:0m:0s)
Total wall-clock time used: 0.132 sec (0h:0m:0s)
---> START RUN NUMBER 8 (seed: 822653)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1493.167
2. Current log-likelihood: -1403.041
3. Current log-likelihood: -1398.313
4. Current log-likelihood: -1396.957
5. Current log-likelihood: -1396.228
Optimal log-likelihood: -1395.709
Rate parameters: A-C: 0.23146 A-G: 2.06956 A-T: 1.96268 C-G: 1.07937 C-T: 2.84174 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.322
Parameters optimization took 5 rounds (0.039 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00153685 secs using 191.8% CPU
Computing ML distances took 0.001626 sec (of wall-clock time) 0.003081 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 5.29289e-05 secs using 86.91% CPU
Constructing RapidNJ tree: done in 0.000132084 secs using 137.8% CPU
Computing RapidNJ tree took 0.000276 sec (of wall-clock time) 0.000302 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 0.0224791 secs using 190.7% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.955
Optimizing NNI: done in 0.0120571 secs using 190.6% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.955 / CPU time: 0.052
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1387.955
2. Current log-likelihood: -1387.798
3. Current log-likelihood: -1387.680
4. Current log-likelihood: -1387.590
5. Current log-likelihood: -1387.521
6. Current log-likelihood: -1387.467
Optimal log-likelihood: -1387.423
Rate parameters: A-C: 0.33566 A-G: 2.27095 A-T: 2.14605 C-G: 1.17829 C-T: 3.29012 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.352
Parameters optimization took 6 rounds (0.023 sec)
BEST SCORE FOUND : -1387.423
Total tree length: 6.744
Total number of iterations: 2
CPU time used for tree search: 0.098 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.052 sec (0h:0m:0s)
Total CPU time used: 0.250 sec (0h:0m:0s)
Total wall-clock time used: 0.132 sec (0h:0m:0s)
---> START RUN NUMBER 9 (seed: 823653)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1493.167
2. Current log-likelihood: -1403.041
3. Current log-likelihood: -1398.313
4. Current log-likelihood: -1396.957
5. Current log-likelihood: -1396.228
Optimal log-likelihood: -1395.709
Rate parameters: A-C: 0.23146 A-G: 2.06956 A-T: 1.96268 C-G: 1.07937 C-T: 2.84174 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 (0.040 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00155807 secs using 189.6% CPU
Computing ML distances took 0.001648 sec (of wall-clock time) 0.003106 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 4.88758e-05 secs using 81.84% CPU
Constructing RapidNJ tree: done in 0.000100136 secs using 129.8% CPU
Computing RapidNJ tree took 0.000228 sec (of wall-clock time) 0.000239 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 0.0234692 secs using 191% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.955
Optimizing NNI: done in 0.012069 secs using 190.9% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.955 / CPU time: 0.052
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1387.955
2. Current log-likelihood: -1387.798
3. Current log-likelihood: -1387.680
4. Current log-likelihood: -1387.590
5. Current log-likelihood: -1387.521
6. Current log-likelihood: -1387.467
Optimal log-likelihood: -1387.423
Rate parameters: A-C: 0.33566 A-G: 2.27095 A-T: 2.14605 C-G: 1.17829 C-T: 3.29012 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.352
Parameters optimization took 6 rounds (0.023 sec)
BEST SCORE FOUND : -1387.423
Total tree length: 6.744
Total number of iterations: 2
CPU time used for tree search: 0.100 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.053 sec (0h:0m:0s)
Total CPU time used: 0.253 sec (0h:0m:0s)
Total wall-clock time used: 0.134 sec (0h:0m:0s)
---> START RUN NUMBER 10 (seed: 824653)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1492.097
2. Current log-likelihood: -1401.816
3. Current log-likelihood: -1396.523
4. Current log-likelihood: -1395.122
5. Current log-likelihood: -1394.389
Optimal log-likelihood: -1393.818
Rate parameters: A-C: 0.27163 A-G: 2.41073 A-T: 2.17144 C-G: 1.24911 C-T: 3.27679 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.416
Parameters optimization took 5 rounds (0.041 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00150609 secs using 192.2% CPU
Computing ML distances took 0.001594 sec (of wall-clock time) 0.003033 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.10216e-05 secs using 82.32% CPU
Constructing RapidNJ tree: done in 9.39369e-05 secs using 118.2% CPU
Computing RapidNJ tree took 0.000218 sec (of wall-clock time) 0.000216 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 0.02069 secs using 191.1% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.214
Optimizing NNI: done in 0.0209949 secs using 191.5% CPU
Finish initializing candidate tree set (3)
Current best tree score: -1388.214 / CPU time: 0.051
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.214
2. Current log-likelihood: -1388.015
3. Current log-likelihood: -1387.868
4. Current log-likelihood: -1387.760
5. Current log-likelihood: -1387.676
6. Current log-likelihood: -1387.611
7. Current log-likelihood: -1387.560
Optimal log-likelihood: -1387.519
Rate parameters: A-C: 0.35522 A-G: 2.35151 A-T: 2.13874 C-G: 1.20261 C-T: 3.36909 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.362
Parameters optimization took 7 rounds (0.026 sec)
BEST SCORE FOUND : -1387.519
Total tree length: 6.815
Total number of iterations: 2
CPU time used for tree search: 0.096 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.051 sec (0h:0m:0s)
Total CPU time used: 0.257 sec (0h:0m:0s)
Total wall-clock time used: 0.136 sec (0h:0m:0s)
---> SUMMARIZE RESULTS FROM 10 RUNS
Run 8 gave best log-likelihood: -1387.423
Total CPU time for 10 runs: 2.527 seconds.
Total wall-clock time for 10 runs: 1.366 seconds.
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpydy2ru20/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpydy2ru20/q2iqtree.treefile
Trees from independent runs: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpydy2ru20/q2iqtree.runtrees
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpydy2ru20/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpydy2ru20/q2iqtree.log
Date and Time: Fri Aug 18 10:25:09 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpydy2ru20/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 2.2.3 COVID-edition for Mac OS X 64-bit built Aug 13 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpnbj20lwv/q2iqtree -nt 1 -alrt 1000 -abayes -lbp 1000
Seed: 966964 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Fri Aug 18 10:25:19 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000226974 secs using 82.83% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000462055 secs using 78.35% 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 2.12193e-05 secs using 84.83% 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, 1.239 / LogL: -1394.544
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.010, 1.340 / LogL: -1394.887
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.010, 1.353 / LogL: -1394.887
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.009, 1.352 / LogL: -1394.871
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.009, 1.348 / LogL: -1394.836
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.009, 1.351 / LogL: -1394.862
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.010, 1.352 / LogL: -1394.884
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.008, 1.346 / LogL: -1394.826
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.009, 1.347 / LogL: -1394.838
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.009, 1.348 / LogL: -1394.841
Optimal pinv,alpha: 0.000, 1.239 / LogL: -1394.544
Parameters optimization took 0.484 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00154996 secs using 97.81% CPU
Computing ML distances took 0.001653 sec (of wall-clock time) 0.001586 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.19753e-05 secs using 92.35% CPU
Constructing RapidNJ tree: done in 0.000100851 secs using 142.8% CPU
Computing RapidNJ tree took 0.000231 sec (of wall-clock time) 0.000267 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.870
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.112 second
Computing log-likelihood of 98 initial trees ... 0.133 seconds
Current best score: -1392.870
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.0190849 secs using 99.27% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.265
Optimizing NNI: done in 0.0220208 secs using 98.72% CPU
Optimizing NNI: done in 0.0146549 secs using 98.66% CPU
Optimizing NNI: done in 0.0139999 secs using 99.52% CPU
Optimizing NNI: done in 0.014122 secs using 99.52% CPU
Optimizing NNI: done in 0.0141509 secs using 99.17% CPU
Optimizing NNI: done in 0.0143919 secs using 99.06% CPU
Optimizing NNI: done in 0.0147951 secs using 98.42% CPU
Optimizing NNI: done in 0.0144489 secs using 98.94% CPU
Optimizing NNI: done in 0.0264108 secs using 98.92% CPU
Iteration 10 / LogL: -1387.282 / Time: 0h:0m:0s
Optimizing NNI: done in 0.026 secs using 99.12% CPU
Optimizing NNI: done in 0.0255609 secs using 99.55% CPU
Optimizing NNI: done in 0.0264871 secs using 98.82% CPU
Optimizing NNI: done in 0.027168 secs using 98.28% CPU
Optimizing NNI: done in 0.02738 secs using 96.42% CPU
Optimizing NNI: done in 0.0262239 secs using 99.16% CPU
Optimizing NNI: done in 0.0257239 secs using 99.62% CPU
Optimizing NNI: done in 0.026042 secs using 99.03% CPU
Optimizing NNI: done in 0.0260901 secs using 99.19% CPU
Optimizing NNI: done in 0.0261471 secs using 99.25% CPU
Iteration 20 / LogL: -1387.282 / Time: 0h:0m:1s
Finish initializing candidate tree set (1)
Current best tree score: -1387.265 / CPU time: 0.700
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.016727 secs using 99.29% CPU
Optimizing NNI: done in 0.020926 secs using 99.38% CPU
Optimizing NNI: done in 0.0528009 secs using 98.92% CPU
Optimizing NNI: done in 0.0710459 secs using 99.24% CPU
Optimizing NNI: done in 0.0709319 secs using 99.19% CPU
Optimizing NNI: done in 0.0376611 secs using 99.36% CPU
Optimizing NNI: done in 0.03544 secs using 99.38% CPU
Optimizing NNI: done in 0.020339 secs using 99.79% CPU
Optimizing NNI: done in 0.037621 secs using 99.96% CPU
Optimizing NNI: done in 0.05126 secs using 99.96% CPU
Iteration 30 / LogL: -1387.348 / Time: 0h:0m:1s (0h:0m:3s left)
Optimizing NNI: done in 0.0341651 secs using 99.96% CPU
Optimizing NNI: done in 0.02509 secs using 99.96% CPU
Optimizing NNI: done in 0.014605 secs using 99.97% CPU
Optimizing NNI: done in 0.0260789 secs using 99.96% CPU
Optimizing NNI: done in 0.046057 secs using 99.96% CPU
Optimizing NNI: done in 0.021714 secs using 99.95% CPU
Optimizing NNI: done in 0.0178099 secs using 99.96% CPU
Optimizing NNI: done in 0.0242531 secs using 99.96% CPU
Optimizing NNI: done in 0.0156519 secs using 99.97% CPU
Optimizing NNI: done in 0.0437479 secs using 99.96% CPU
Iteration 40 / LogL: -1387.348 / Time: 0h:0m:1s (0h:0m:2s left)
Optimizing NNI: done in 0.0147889 secs using 99.92% CPU
Optimizing NNI: done in 0.0467789 secs using 99.96% CPU
Optimizing NNI: done in 0.0066421 secs using 99.94% CPU
Optimizing NNI: done in 0.054738 secs using 99.96% CPU
Optimizing NNI: done in 0.0541749 secs using 99.97% CPU
Optimizing NNI: done in 0.0191569 secs using 99.96% CPU
Optimizing NNI: done in 0.019824 secs using 99.96% CPU
Optimizing NNI: done in 0.0206859 secs using 99.97% CPU
Optimizing NNI: done in 0.0250921 secs using 99.96% CPU
Optimizing NNI: done in 0.0206931 secs using 99.96% CPU
Iteration 50 / LogL: -1387.604 / Time: 0h:0m:2s (0h:0m:2s left)
Optimizing NNI: done in 0.031702 secs using 99.97% CPU
Optimizing NNI: done in 0.034533 secs using 99.96% CPU
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Optimizing NNI: done in 0.0451071 secs using 99.96% CPU
Iteration 60 / LogL: -1387.348 / Time: 0h:0m:2s (0h:0m:1s left)
Optimizing NNI: done in 0.0293322 secs using 99.97% CPU
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Optimizing NNI: done in 0.0392289 secs using 99.96% CPU
Iteration 70 / LogL: -1387.372 / Time: 0h:0m:2s (0h:0m:1s left)
Optimizing NNI: done in 0.025986 secs using 99.96% CPU
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Iteration 80 / LogL: -1387.401 / Time: 0h:0m:3s (0h:0m:0s left)
Optimizing NNI: done in 0.0271218 secs using 99.96% CPU
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Optimizing NNI: done in 0.036957 secs using 99.95% CPU
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Optimizing NNI: done in 0.0239639 secs using 99.96% CPU
Iteration 90 / LogL: -1387.347 / Time: 0h:0m:3s (0h:0m:0s left)
Optimizing NNI: done in 0.020772 secs using 99.97% CPU
Optimizing NNI: done in 0.02879 secs using 99.96% CPU
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Optimizing NNI: done in 0.043117 secs using 99.96% CPU
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Iteration 100 / LogL: -1387.375 / Time: 0h:0m:3s (0h:0m:0s left)
Optimizing NNI: done in 0.0478899 secs using 99.96% CPU
Optimizing NNI: done in 0.0258269 secs using 99.97% 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: -1387.265
Optimal log-likelihood: -1387.256
Rate parameters: A-C: 0.32869 A-G: 2.26095 A-T: 2.13921 C-G: 1.17512 C-T: 3.28909 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: 1.318
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1387.256
Testing tree branches by SH-like aLRT with 1000 replicates...
Testing tree branches by local-BP test with 1000 replicates...
Testing tree branches by aBayes parametric test...
0.055 sec.
Total tree length: 6.742
Total number of iterations: 102
CPU time used for tree search: 3.401 sec (0h:0m:3s)
Wall-clock time used for tree search: 3.237 sec (0h:0m:3s)
Total CPU time used: 3.962 sec (0h:0m:3s)
Total wall-clock time used: 3.799 sec (0h:0m:3s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpnbj20lwv/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpnbj20lwv/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpnbj20lwv/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpnbj20lwv/q2iqtree.log
Date and Time: Fri Aug 18 10:25:23 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpnbj20lwv/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 2.2.3 COVID-edition for Mac OS X 64-bit built Aug 13 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpe1f_lmlg/q2iqtree -nt 1 -nstop 200 -pers 0.200000
Seed: 505480 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Fri Aug 18 10:25:34 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000216007 secs using 84.72% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.00048089 secs using 77.98% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 2.00272e-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 75% 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 0.0343349 secs using 98.98% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1389.605
Optimal log-likelihood: -1388.793
Rate parameters: A-C: 0.37543 A-G: 2.37167 A-T: 2.15334 C-G: 1.24272 C-T: 3.32366 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.034
Gamma shape alpha: 1.400
Parameters optimization took 1 rounds (0.006 sec)
Time for fast ML tree search: 0.068 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 484 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1402.600 45 2895.200 2919.843 3046.669
2 GTR+F+I 1401.121 46 2894.242 2920.135 3049.077
3 GTR+F+G4 1387.358 46 2866.716 2892.609 3021.551
4 GTR+F+I+G4 1387.726 47 2869.452 2896.633 3027.653
5 GTR+F+R2 1382.364 47 2858.729 2885.910 3016.930
6 GTR+F+R3 1382.420 49 2862.840 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/tmpe1f_lmlg/q2iqtree.model.gz
CPU time for ModelFinder: 1.388 seconds (0h:0m:1s)
Wall-clock time for ModelFinder: 1.404 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 0.000944138 secs using 97.87% CPU
Computing ML distances took 0.001059 sec (of wall-clock time) 0.001002 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.19753e-05 secs using 80.81% CPU
Constructing RapidNJ tree: done in 0.000146151 secs using 118.4% CPU
Computing RapidNJ tree took 0.000293 sec (of wall-clock time) 0.000299 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.820
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.102 second
Computing log-likelihood of 97 initial trees ... 0.084 seconds
Current best score: -1385.924
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00447297 secs using 197% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.880
Optimizing NNI: done in 0.0120451 secs using 100.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1385.311
Optimizing NNI: done in 0.0117791 secs using 99.95% CPU
Optimizing NNI: done in 0.0114112 secs using 99.95% CPU
Optimizing NNI: done in 0.012347 secs using 99.93% CPU
Optimizing NNI: done in 0.012296 secs using 99.96% CPU
Optimizing NNI: done in 0.0116198 secs using 99.95% CPU
Optimizing NNI: done in 0.011529 secs using 99.95% CPU
Optimizing NNI: done in 0.0152621 secs using 99.86% CPU
Optimizing NNI: done in 0.0114729 secs using 99.95% CPU
Iteration 10 / LogL: -1385.344 / Time: 0h:0m:0s
Optimizing NNI: done in 0.01159 secs using 99.96% CPU
Optimizing NNI: done in 0.011523 secs using 99.95% CPU
Optimizing NNI: done in 0.012228 secs using 99.94% CPU
Optimizing NNI: done in 0.012042 secs using 99.97% CPU
Optimizing NNI: done in 0.0121 secs using 99.95% CPU
Optimizing NNI: done in 0.0114551 secs using 99.9% CPU
Optimizing NNI: done in 0.0114429 secs using 99.96% CPU
Optimizing NNI: done in 0.011337 secs using 99.95% CPU
Optimizing NNI: done in 0.0114272 secs using 99.95% CPU
Optimizing NNI: done in 0.011373 secs using 99.95% CPU
Iteration 20 / LogL: -1385.335 / Time: 0h:0m:0s
Finish initializing candidate tree set (2)
Current best tree score: -1385.311 / CPU time: 0.434
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0062561 secs using 99.93% CPU
Optimizing NNI: done in 0.0106912 secs using 99.35% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.311
Optimizing NNI: done in 0.0117669 secs using 99.76% CPU
Optimizing NNI: done in 0.0139041 secs using 99.83% CPU
Optimizing NNI: done in 0.0119648 secs using 99.93% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.310
Optimizing NNI: done in 0.00507188 secs using 99.96% CPU
Optimizing NNI: done in 0.013155 secs using 99.77% CPU
Optimizing NNI: done in 0.00923705 secs using 99.95% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.309
Optimizing NNI: done in 0.00975609 secs using 99.94% CPU
Optimizing NNI: done in 0.022202 secs using 99.74% CPU
Iteration 30 / LogL: -1385.929 / Time: 0h:0m:0s (0h:0m:3s left)
Optimizing NNI: done in 0.00478101 secs using 99.96% CPU
Optimizing NNI: done in 0.010442 secs using 99.93% CPU
Optimizing NNI: done in 0.0116611 secs using 99.94% CPU
Optimizing NNI: done in 0.0125821 secs using 99.95% CPU
Optimizing NNI: done in 0.014894 secs using 99.95% CPU
Optimizing NNI: done in 0.00676799 secs using 99.93% CPU
Optimizing NNI: done in 0.00607395 secs using 99.92% CPU
Optimizing NNI: done in 0.017668 secs using 99.94% CPU
Optimizing NNI: done in 0.00479388 secs using 99.98% CPU
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Iteration 40 / LogL: -1385.506 / Time: 0h:0m:0s (0h:0m:2s left)
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Iteration 140 / LogL: -1385.811 / Time: 0h:0m:1s (0h:0m:0s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.309
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Iteration 190 / LogL: -1385.715 / Time: 0h:0m:2s (0h:0m:0s left)
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Iteration 200 / LogL: -1385.374 / Time: 0h:0m:2s (0h:0m:0s left)
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TREE SEARCH COMPLETED AFTER 203 ITERATIONS / Time: 0h:0m:2s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1385.309
Optimal log-likelihood: -1385.305
Rate parameters: A-C: 0.39448 A-G: 1.56672 A-T: 1.00000 C-G: 0.39448 C-T: 1.56672 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.721,0.402) (0.279,2.542)
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1385.305
Total tree length: 6.846
Total number of iterations: 203
CPU time used for tree search: 2.628 sec (0h:0m:2s)
Wall-clock time used for tree search: 2.453 sec (0h:0m:2s)
Total CPU time used: 2.659 sec (0h:0m:2s)
Total wall-clock time used: 2.479 sec (0h:0m:2s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpe1f_lmlg/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpe1f_lmlg/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpe1f_lmlg/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpe1f_lmlg/q2iqtree.log
Date and Time: Fri Aug 18 10:25:38 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpe1f_lmlg/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 2.2.3 COVID-edition for Mac OS X 64-bit built Aug 13 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpm7jxk46_/q2iqtreeufboot -nt 1 -nstop 200 -pers 0.200000
Seed: 48273 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Fri Aug 18 10:25:49 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000216961 secs using 84.81% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.00045681 secs using 78.37% 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 2.09808e-05 secs using 85.79% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 7.10487e-05 secs using 77.41% 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 0.034153 secs using 99.16% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1389.605
Optimal log-likelihood: -1388.793
Rate parameters: A-C: 0.37543 A-G: 2.37167 A-T: 2.15335 C-G: 1.24272 C-T: 3.32366 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.034
Gamma shape alpha: 1.400
Parameters optimization took 1 rounds (0.006 sec)
Time for fast ML tree search: 0.068 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 484 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1402.600 45 2895.200 2919.843 3046.669
2 GTR+F+I 1401.121 46 2894.242 2920.135 3049.077
3 GTR+F+G4 1387.358 46 2866.716 2892.609 3021.551
4 GTR+F+I+G4 1387.726 47 2869.452 2896.633 3027.653
5 GTR+F+R2 1382.364 47 2858.729 2885.910 3016.930
6 GTR+F+R3 1382.420 49 2862.841 2892.719 3027.773
14 GTR+F+I+R2 1382.418 48 2860.837 2889.346 3022.403
15 GTR+F+I+R3 1382.449 50 2864.898 2896.187 3033.197
25 SYM+G4 1387.134 43 2860.269 2882.528 3005.006
27 SYM+R2 1383.095 44 2854.189 2877.621 3002.292
36 SYM+I+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/tmpm7jxk46_/q2iqtreeufboot.model.gz
CPU time for ModelFinder: 1.436 seconds (0h:0m:1s)
Wall-clock time for ModelFinder: 1.580 seconds (0h:0m:1s)
Generating 1000 samples for ultrafast bootstrap (seed: 48273)...
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 0.000983953 secs using 97.97% CPU
Computing ML distances took 0.001077 sec (of wall-clock time) 0.001029 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.19753e-05 secs using 94.28% CPU
Constructing RapidNJ tree: done in 9.39369e-05 secs using 150.1% CPU
Computing RapidNJ tree took 0.000218 sec (of wall-clock time) 0.000264 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.820
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| INITIALIZING CANDIDATE TREE SET |
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Generating 98 parsimony trees... 0.106 second
Computing log-likelihood of 98 initial trees ... 0.087 seconds
Current best score: -1385.924
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.011384 secs using 99.48% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.880
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1385.311
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BETTER TREE FOUND at iteration 4: -1385.309
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Iteration 20 / LogL: -1385.335 / Time: 0h:0m:0s
Finish initializing candidate tree set (4)
Current best tree score: -1385.309 / CPU time: 0.631
Number of iterations: 20
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| OPTIMIZING CANDIDATE TREE SET |
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Iteration 50 / LogL: -1385.318 / Time: 0h:0m:1s (0h:0m:3s left)
Log-likelihood cutoff on original alignment: -1410.911
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Optimizing NNI: done in 0.00845098 secs using 99.95% CPU
Optimizing NNI: done in 0.00848484 secs using 99.97% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.309
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Iteration 70 / LogL: -1385.324 / Time: 0h:0m:1s (0h:0m:3s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.309
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Iteration 90 / LogL: -1385.848 / Time: 0h:0m:2s (0h:0m:2s left)
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Iteration 100 / LogL: -1385.316 / Time: 0h:0m:2s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -1410.911
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.993
Optimizing NNI: done in 0.00861907 secs using 99.81% CPU
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Iteration 110 / LogL: -1385.664 / Time: 0h:0m:2s (0h:0m:2s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.309
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Iteration 130 / LogL: -1385.312 / Time: 0h:0m:2s (0h:0m:1s left)
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Iteration 140 / LogL: -1385.313 / Time: 0h:0m:3s (0h:0m:1s left)
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Iteration 150 / LogL: -1385.333 / Time: 0h:0m:3s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -1410.911
Optimizing NNI: done in 0.0102091 secs using 99.93% CPU
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Iteration 170 / LogL: -1385.311 / Time: 0h:0m:3s (0h:0m:0s left)
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Iteration 180 / LogL: -1385.311 / Time: 0h:0m:3s (0h:0m:0s left)
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Iteration 190 / LogL: -1385.311 / Time: 0h:0m:4s (0h:0m:0s left)
Optimizing NNI: done in 0.0219309 secs using 99.95% CPU
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Iteration 200 / LogL: -1385.311 / Time: 0h:0m:4s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -1410.911
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.999
Optimizing NNI: done in 0.00643396 secs using 99.92% CPU
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Optimizing NNI: done in 0.0114341 secs using 99.94% CPU
TREE SEARCH COMPLETED AFTER 205 ITERATIONS / Time: 0h:0m:4s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1385.309
Optimal log-likelihood: -1385.305
Rate parameters: A-C: 0.39449 A-G: 1.56668 A-T: 1.00000 C-G: 0.39449 C-T: 1.56668 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.721,0.402) (0.279,2.542)
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1385.305
Creating bootstrap support values...
Split supports printed to NEXUS file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpm7jxk46_/q2iqtreeufboot.splits.nex
Total tree length: 6.847
Total number of iterations: 205
CPU time used for tree search: 4.670 sec (0h:0m:4s)
Wall-clock time used for tree search: 4.510 sec (0h:0m:4s)
Total CPU time used: 4.775 sec (0h:0m:4s)
Total wall-clock time used: 4.615 sec (0h:0m:4s)
Computing bootstrap consensus tree...
Reading input file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpm7jxk46_/q2iqtreeufboot.splits.nex...
20 taxa and 155 splits.
Consensus tree written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpm7jxk46_/q2iqtreeufboot.contree
Reading input trees file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpm7jxk46_/q2iqtreeufboot.contree
Log-likelihood of consensus tree: -1385.306
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpm7jxk46_/q2iqtreeufboot.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpm7jxk46_/q2iqtreeufboot.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpm7jxk46_/q2iqtreeufboot.mldist
Ultrafast bootstrap approximation results written to:
Split support values: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpm7jxk46_/q2iqtreeufboot.splits.nex
Consensus tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpm7jxk46_/q2iqtreeufboot.contree
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpm7jxk46_/q2iqtreeufboot.log
Date and Time: Fri Aug 18 10:25:55 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpm7jxk46_/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 2.2.3 COVID-edition for Mac OS X 64-bit built Aug 13 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpu1dvf8uv/q2iqtreeufboot -nt 1 -alrt 1000 -abayes -lbp 1000 -nstop 200 -pers 0.200000
Seed: 843418 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Fri Aug 18 10:26:05 2023
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2/caporasolab/data/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000219107 secs using 83.98% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000507116 secs using 77.69% 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 7.51019e-05 secs using 75.9% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
Generating 1000 samples for ultrafast bootstrap (seed: 843418)...
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 0.495 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00149989 secs using 98.81% CPU
Computing ML distances took 0.001596 sec (of wall-clock time) 0.001551 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 5.19753e-05 secs using 96.2% CPU
Constructing RapidNJ tree: done in 9.41753e-05 secs using 148.7% CPU
Computing RapidNJ tree took 0.000219 sec (of wall-clock time) 0.000263 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.710
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.101 second
Computing log-likelihood of 98 initial trees ... 0.130 seconds
Current best score: -1392.553
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.022079 secs using 98.85% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.261
Optimizing NNI: done in 0.032872 secs using 99.15% CPU
Optimizing NNI: done in 0.021729 secs using 98.85% CPU
Optimizing NNI: done in 0.020848 secs using 99.69% CPU
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Optimizing NNI: done in 0.0389559 secs using 99.06% CPU
Iteration 10 / LogL: -1387.282 / Time: 0h:0m:1s
Optimizing NNI: done in 0.0379362 secs using 99.49% CPU
Optimizing NNI: done in 0.0385129 secs using 99.27% CPU
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Optimizing NNI: done in 0.03076 secs using 98.92% CPU
Iteration 20 / LogL: -1387.267 / Time: 0h:0m:1s
Finish initializing candidate tree set (2)
Current best tree score: -1387.261 / CPU time: 0.905
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0248649 secs using 99.43% CPU
Optimizing NNI: done in 0.0272501 secs using 98.8% CPU
Optimizing NNI: done in 0.0960331 secs using 99.5% CPU
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Optimizing NNI: done in 0.010375 secs using 99.95% CPU
Optimizing NNI: done in 0.011241 secs using 99.96% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.257
Optimizing NNI: done in 0.03742 secs using 99.75% CPU
Iteration 30 / LogL: -1387.356 / Time: 0h:0m:1s (0h:0m:10s left)
Optimizing NNI: done in 0.0162401 secs using 99.95% CPU
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Optimizing NNI: done in 0.0223432 secs using 99.96% CPU
Optimizing NNI: done in 0.011708 secs using 99.87% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.256
Iteration 40 / LogL: -1387.256 / Time: 0h:0m:2s (0h:0m:8s left)
Optimizing NNI: done in 0.0127189 secs using 99.68% CPU
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Optimizing NNI: done in 0.0160089 secs using 99.96% CPU
Iteration 50 / LogL: -1387.351 / Time: 0h:0m:2s (0h:0m:7s left)
Log-likelihood cutoff on original alignment: -1409.531
Optimizing NNI: done in 0.008986 secs using 99.91% CPU
Optimizing NNI: done in 0.053251 secs using 99.9% CPU
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Iteration 60 / LogL: -1387.530 / Time: 0h:0m:2s (0h:0m:6s left)
Optimizing NNI: done in 0.0269768 secs using 99.81% CPU
Optimizing NNI: done in 0.0284622 secs using 99.96% CPU
Optimizing NNI: done in 0.011569 secs using 99.98% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.256
Optimizing NNI: done in 0.0295188 secs using 99.81% CPU
Optimizing NNI: done in 0.0495069 secs using 99.97% CPU
Optimizing NNI: done in 0.02053 secs using 99.97% CPU
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Iteration 70 / LogL: -1387.357 / Time: 0h:0m:3s (0h:0m:5s left)
Optimizing NNI: done in 0.0308728 secs using 99.93% CPU
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Optimizing NNI: done in 0.032028 secs using 99.97% CPU
Iteration 80 / LogL: -1396.634 / Time: 0h:0m:3s (0h:0m:4s left)
Optimizing NNI: done in 0.0584581 secs using 99.92% CPU
Optimizing NNI: done in 0.00875902 secs using 99.97% CPU
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Iteration 90 / LogL: -1387.351 / Time: 0h:0m:3s (0h:0m:4s left)
Optimizing NNI: done in 0.0326691 secs using 99.97% CPU
Optimizing NNI: done in 0.0103021 secs using 99.96% CPU
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Optimizing NNI: done in 0.0436599 secs using 99.97% CPU
Optimizing NNI: done in 0.035604 secs using 99.97% CPU
Iteration 100 / LogL: -1387.352 / Time: 0h:0m:3s (0h:0m:3s left)
Log-likelihood cutoff on original alignment: -1409.531
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.997
Optimizing NNI: done in 0.0285001 secs using 99.97% CPU
Optimizing NNI: done in 0.048244 secs using 99.97% CPU
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Iteration 110 / LogL: -1387.351 / Time: 0h:0m:4s (0h:0m:3s left)
Optimizing NNI: done in 0.02214 secs using 99.93% CPU
Optimizing NNI: done in 0.020128 secs using 99.97% CPU
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Iteration 120 / LogL: -1387.256 / Time: 0h:0m:4s (0h:0m:3s left)
Optimizing NNI: done in 0.0553801 secs using 99.95% CPU
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Iteration 130 / LogL: -1387.834 / Time: 0h:0m:4s (0h:0m:2s left)
Optimizing NNI: done in 0.00968003 secs using 99.96% CPU
Optimizing NNI: done in 0.0283489 secs using 99.98% CPU
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Optimizing NNI: done in 0.0650141 secs using 99.97% CPU
Iteration 140 / LogL: -1387.352 / Time: 0h:0m:5s (0h:0m:2s left)
Optimizing NNI: done in 0.0357721 secs using 99.83% CPU
Optimizing NNI: done in 0.018569 secs using 99.97% CPU
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Optimizing NNI: done in 0.0172091 secs using 99.97% CPU
Iteration 150 / LogL: -1387.350 / Time: 0h:0m:5s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -1409.308
Optimizing NNI: done in 0.084183 secs using 99.95% CPU
Optimizing NNI: done in 0.048908 secs using 99.97% CPU
Optimizing NNI: done in 0.00940895 secs using 99.97% CPU
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Optimizing NNI: done in 0.0164609 secs using 99.96% CPU
Optimizing NNI: done in 0.012428 secs using 99.97% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.255
Optimizing NNI: done in 0.021178 secs using 99.83% CPU
Optimizing NNI: done in 0.0222659 secs using 99.96% CPU
Optimizing NNI: done in 0.0331252 secs using 99.96% CPU
Iteration 160 / LogL: -1387.658 / Time: 0h:0m:5s (0h:0m:1s left)
Optimizing NNI: done in 0.019428 secs using 99.97% CPU
Optimizing NNI: done in 0.057348 secs using 99.97% CPU
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Iteration 170 / LogL: -1387.356 / Time: 0h:0m:6s (0h:0m:1s left)
Optimizing NNI: done in 0.00689983 secs using 99.97% CPU
Optimizing NNI: done in 0.02843 secs using 99.95% CPU
Optimizing NNI: done in 0.00818896 secs using 99.95% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.255
Optimizing NNI: done in 0.016742 secs using 99.72% CPU
Optimizing NNI: done in 0.028348 secs using 99.95% CPU
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Iteration 180 / LogL: -1387.595 / Time: 0h:0m:6s (0h:0m:0s left)
Optimizing NNI: done in 0.0333569 secs using 99.95% CPU
Optimizing NNI: done in 0.0153961 secs using 99.97% CPU
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Optimizing NNI: done in 0.00954103 secs using 99.94% CPU
Optimizing NNI: done in 0.0161672 secs using 99.93% CPU
Iteration 190 / LogL: -1387.296 / Time: 0h:0m:6s (0h:0m:0s left)
Optimizing NNI: done in 0.0254359 secs using 99.96% CPU
Optimizing NNI: done in 0.019253 secs using 99.96% CPU
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Optimizing NNI: done in 0.0793221 secs using 99.7% CPU
Optimizing NNI: done in 0.0223298 secs using 99.97% CPU
Optimizing NNI: done in 0.020972 secs using 99.97% CPU
Optimizing NNI: done in 0.0279691 secs using 99.96% CPU
Optimizing NNI: done in 0.0493391 secs using 99.97% CPU
Optimizing NNI: done in 0.0144022 secs using 99.97% CPU
Optimizing NNI: done in 0.0134349 secs using 99.96% CPU
Iteration 200 / LogL: -1387.336 / Time: 0h:0m:6s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -1409.308
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.999
Optimizing NNI: done in 0.0307291 secs using 99.96% CPU
Optimizing NNI: done in 0.0174251 secs using 99.97% CPU
TREE SEARCH COMPLETED AFTER 202 ITERATIONS / Time: 0h:0m:7s
--------------------------------------------------------------------
| 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: 2.15656 C-G: 1.18241 C-T: 3.31127 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...
0.055 sec.
Creating bootstrap support values...
Split supports printed to NEXUS file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpu1dvf8uv/q2iqtreeufboot.splits.nex
Total tree length: 6.751
Total number of iterations: 202
CPU time used for tree search: 6.695 sec (0h:0m:6s)
Wall-clock time used for tree search: 6.540 sec (0h:0m:6s)
Total CPU time used: 7.344 sec (0h:0m:7s)
Total wall-clock time used: 7.195 sec (0h:0m:7s)
Computing bootstrap consensus tree...
Reading input file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpu1dvf8uv/q2iqtreeufboot.splits.nex...
20 taxa and 158 splits.
Consensus tree written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpu1dvf8uv/q2iqtreeufboot.contree
Reading input trees file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpu1dvf8uv/q2iqtreeufboot.contree
Log-likelihood of consensus tree: -1387.426
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpu1dvf8uv/q2iqtreeufboot.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpu1dvf8uv/q2iqtreeufboot.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpu1dvf8uv/q2iqtreeufboot.mldist
Ultrafast bootstrap approximation results written to:
Split support values: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpu1dvf8uv/q2iqtreeufboot.splits.nex
Consensus tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpu1dvf8uv/q2iqtreeufboot.contree
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpu1dvf8uv/q2iqtreeufboot.log
Date and Time: Fri Aug 18 10:26:13 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/5d3741c7-e023-4858-bd05-bcf7d25c1386/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpu1dvf8uv/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!