Phylogenetic inference with q2-phylogeny¶
Phylogenetic inference with q2-phylogeny
Note
This tutorial assumes, you’ve read through the QIIME 2 Overview documentation and have at least worked through some of the other Tutorials.
Inferring phylogenies¶
Several downstream diversity metrics, available within QIIME 2, require that a phylogenetic tree be constructed using the Operational Taxonomic Units (OTUs) or Amplicon Sequence Variants (ASVs) being investigated.
But how do we proceed to construct a phylogeny from our sequence data?
Well, there are two phylogeny-based approaches we can use. Deciding upon which to use is largely dependent on your study questions:
1. A reference-based fragment insertion approach. Which, is likely the ideal choice. Especially, if your reference phylogeny (and associated representative sequences) encompass neighboring relatives of which your sequences can be reliably inserted. Any sequences that do not match well enough to the reference are not inserted. For example, this approach may not work well if your data contain sequences that are not well represented within your reference phylogeny (e.g. missing clades, etc.). For more information, check out these great fragment insertion examples.
2. A de novo approach. Marker genes that can be globally aligned across divergent taxa, are usually amenable to sequence alignment and phylogenetic investigation through this approach. Be mindful of the length of your sequences when constructing a de novo phylogeny, short reads many not have enough phylogenetic information to capture a meaningful phylogeny. This community tutorial will focus on the de novo approaches.
Here, you will learn how to make use of de novo phylogenetic approaches to:
generate a sequence alignment within QIIME 2
mask the alignment if needed
construct a phylogenetic tree
root the phylogenetic tree
If you would like to substitute any of the steps outlined here by making use of tools external to QIIME 2, please see the import, export, and filtering documentation where appropriate.
Sequence Alignment¶
Prior to constructing a phylogeny we must generate a multiple sequence alignment (MSA). When constructing a MSA we are making a statement about the putative homology of the aligned residues (columns of the MSA) by virtue of their sequence similarity.
The number of algorithms to construct a MSA are legion. We will make use of MAFFT (Multiple Alignment using Fast Fourier Transform)) via the q2-alignment plugin. For more information checkout the MAFFT paper.
Let’s start by creating a directory to work in:
mkdir qiime2-phylogeny-tutorial
cd qiime2-phylogeny-tutorial
Next, download the data:
Please select a download option that is most appropriate for your environment:
Download URL: https://data.qiime2.org/2022.2/tutorials/phylogeny/rep-seqs.qza
Save as: rep-seqs.qza
wget \
-O "rep-seqs.qza" \
"https://data.qiime2.org/2022.2/tutorials/phylogeny/rep-seqs.qza"
curl -sL \
"https://data.qiime2.org/2022.2/tutorials/phylogeny/rep-seqs.qza" > \
"rep-seqs.qza"
Run MAFFT
qiime alignment mafft \
--i-sequences rep-seqs.qza \
--o-alignment aligned-rep-seqs.qza
Reducing alignment ambiguity: masking and reference alignments¶
Why mask an alignment?
Masking helps to eliminate alignment columns that are phylogenetically uninformative or misleading before phylogenetic analysis. Much of the time alignment errors can introduce noise and confound phylogenetic inference. It is common practice to mask (remove) these ambiguously aligned regions prior to performing phylogenetic inference. In particular, David Lane’s (1991) chapter 16S/23S rRNA sequencing proposed masking SSU data prior to phylogenetic analysis. However, knowing how to deal with ambiguously aligned regions and when to apply masks largely depends on the marker genes being analyzed and the question being asked of the data.
Note
Keep in mind that this is still an active area of discussion, as highlighted by the following non-exhaustive list of articles: Wu et al. 2012, Ashkenazy et al. 2018, Schloss 2010, Tan et al. 2015, Rajan 2015.
How to mask alignment.
For our purposes, we’ll assume that we have ambiguously aligned columns in the
MAFFT alignment we produced above. The default settings for the
--p-min-conservation of the
alignment mask approximates the
Lane mask filtering of QIIME 1. Keep an eye out for updates to the alignment
plugin.
qiime alignment mask \
--i-alignment aligned-rep-seqs.qza \
--o-masked-alignment masked-aligned-rep-seqs.qza
Reference based alignments
There are a variety of tools such as PyNAST) (using NAST), Infernal, and SINA, etc., that attempt to reduce the amount of ambiguously aligned regions by using curated reference alignments (e.g. 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. For a more in-depth and eloquent overview of reference-based alignment approaches, check out the great SINA community tutorial).
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 2484 -N 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-nawidg6k/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpc7yohcap -n q2
Partition: 0 with name: No Name Provided
Base frequencies: 0.243 0.182 0.319 0.256
Inference[0]: Time 0.592248 CAT-based likelihood -1241.820506, best rearrangement setting 5
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -1388.324170 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpc7yohcap/RAxML_result.q2
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -1388.324170 ....
Final GAMMA-based Score of best tree -1387.275825
Program execution info written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpc7yohcap/RAxML_info.q2
Best-scoring ML tree written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpc7yohcap/RAxML_bestTree.q2
Overall execution time: 1.216451 secs or 0.000338 hours or 0.000014 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 2484 -N 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-nawidg6k/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpc7yohcap -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-archive-4cki8dpr/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxaucj8f9 -n q2
Partition: 0 with name: No Name Provided
Base frequencies: 0.243 0.182 0.319 0.256
Inference[0]: Time 0.591545 CAT-based likelihood -1238.242991, best rearrangement setting 5
Inference[1]: Time 0.512294 CAT-based likelihood -1249.502284, best rearrangement setting 5
Inference[2]: Time 0.514611 CAT-based likelihood -1242.978035, best rearrangement setting 5
Inference[3]: Time 0.655594 CAT-based likelihood -1243.159855, best rearrangement setting 5
Inference[4]: Time 0.495589 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/tmpxaucj8f9/RAxML_result.q2.RUN.0
Inference[1] final GAMMA-based Likelihood: -1392.813982 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxaucj8f9/RAxML_result.q2.RUN.1
Inference[2] final GAMMA-based Likelihood: -1388.073642 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxaucj8f9/RAxML_result.q2.RUN.2
Inference[3] final GAMMA-based Likelihood: -1387.945266 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxaucj8f9/RAxML_result.q2.RUN.3
Inference[4] final GAMMA-based Likelihood: -1387.557031 tree written to file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxaucj8f9/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/tmpxaucj8f9/RAxML_info.q2
Best-scoring ML tree written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxaucj8f9/RAxML_bestTree.q2
Overall execution time: 3.525764 secs or 0.000979 hours or 0.000041 days
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: raxmlHPC -m GTRCAT -p 1723 -N 5 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-4cki8dpr/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpxaucj8f9 -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-archive-w58qsbgd/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpdq267zdp -n q2bootstrap
Time for BS model parameter optimization 0.053214
Bootstrap[0]: Time 0.176107 seconds, bootstrap likelihood -1199.758796, best rearrangement setting 12
Bootstrap[1]: Time 0.116814 seconds, bootstrap likelihood -1344.229251, best rearrangement setting 6
Bootstrap[2]: Time 0.107875 seconds, bootstrap likelihood -1295.343000, best rearrangement setting 8
Bootstrap[3]: Time 0.095814 seconds, bootstrap likelihood -1273.768320, best rearrangement setting 8
Bootstrap[4]: Time 0.111717 seconds, bootstrap likelihood -1253.402952, best rearrangement setting 6
Bootstrap[5]: Time 0.114141 seconds, bootstrap likelihood -1260.866113, best rearrangement setting 10
Bootstrap[6]: Time 0.111630 seconds, bootstrap likelihood -1293.636299, best rearrangement setting 14
Bootstrap[7]: Time 0.102155 seconds, bootstrap likelihood -1227.178693, best rearrangement setting 6
Bootstrap[8]: Time 0.110671 seconds, bootstrap likelihood -1321.820787, best rearrangement setting 13
Bootstrap[9]: Time 0.117030 seconds, bootstrap likelihood -1147.233446, best rearrangement setting 6
Bootstrap[10]: Time 0.085221 seconds, bootstrap likelihood -1220.766493, best rearrangement setting 13
Bootstrap[11]: Time 0.119856 seconds, bootstrap likelihood -1200.006355, best rearrangement setting 8
Bootstrap[12]: Time 0.132877 seconds, bootstrap likelihood -1346.392834, best rearrangement setting 14
Bootstrap[13]: Time 0.112091 seconds, bootstrap likelihood -1301.111096, best rearrangement setting 14
Bootstrap[14]: Time 0.117228 seconds, bootstrap likelihood -1262.253559, best rearrangement setting 11
Bootstrap[15]: Time 0.114450 seconds, bootstrap likelihood -1215.017551, best rearrangement setting 14
Bootstrap[16]: Time 0.108611 seconds, bootstrap likelihood -1238.832009, best rearrangement setting 7
Bootstrap[17]: Time 0.098844 seconds, bootstrap likelihood -1393.989732, best rearrangement setting 12
Bootstrap[18]: Time 0.103680 seconds, bootstrap likelihood -1173.921002, best rearrangement setting 15
Bootstrap[19]: Time 0.106273 seconds, bootstrap likelihood -1185.726976, best rearrangement setting 11
Bootstrap[20]: Time 0.097301 seconds, bootstrap likelihood -1158.491940, best rearrangement setting 6
Bootstrap[21]: Time 0.096399 seconds, bootstrap likelihood -1154.664272, best rearrangement setting 11
Bootstrap[22]: Time 0.105059 seconds, bootstrap likelihood -1244.159837, best rearrangement setting 10
Bootstrap[23]: Time 0.123990 seconds, bootstrap likelihood -1211.171036, best rearrangement setting 15
Bootstrap[24]: Time 0.104976 seconds, bootstrap likelihood -1261.440677, best rearrangement setting 12
Bootstrap[25]: Time 0.106219 seconds, bootstrap likelihood -1331.836715, best rearrangement setting 15
Bootstrap[26]: Time 0.109160 seconds, bootstrap likelihood -1129.144509, best rearrangement setting 5
Bootstrap[27]: Time 0.133407 seconds, bootstrap likelihood -1226.624056, best rearrangement setting 7
Bootstrap[28]: Time 0.133844 seconds, bootstrap likelihood -1221.046176, best rearrangement setting 12
Bootstrap[29]: Time 0.088228 seconds, bootstrap likelihood -1211.791204, best rearrangement setting 14
Bootstrap[30]: Time 0.110866 seconds, bootstrap likelihood -1389.442380, best rearrangement setting 5
Bootstrap[31]: Time 0.112616 seconds, bootstrap likelihood -1303.638592, best rearrangement setting 12
Bootstrap[32]: Time 0.119959 seconds, bootstrap likelihood -1172.859456, best rearrangement setting 12
Bootstrap[33]: Time 0.105513 seconds, bootstrap likelihood -1244.617135, best rearrangement setting 9
Bootstrap[34]: Time 0.101130 seconds, bootstrap likelihood -1211.871717, best rearrangement setting 15
Bootstrap[35]: Time 0.120824 seconds, bootstrap likelihood -1299.862912, best rearrangement setting 5
Bootstrap[36]: Time 0.097998 seconds, bootstrap likelihood -1141.967505, best rearrangement setting 5
Bootstrap[37]: Time 0.120680 seconds, bootstrap likelihood -1283.923198, best rearrangement setting 12
Bootstrap[38]: Time 0.094161 seconds, bootstrap likelihood -1304.250946, best rearrangement setting 5
Bootstrap[39]: Time 0.096817 seconds, bootstrap likelihood -1407.084376, best rearrangement setting 15
Bootstrap[40]: Time 0.110331 seconds, bootstrap likelihood -1277.946299, best rearrangement setting 13
Bootstrap[41]: Time 0.109308 seconds, bootstrap likelihood -1279.006200, best rearrangement setting 7
Bootstrap[42]: Time 0.104607 seconds, bootstrap likelihood -1160.274606, best rearrangement setting 6
Bootstrap[43]: Time 0.132777 seconds, bootstrap likelihood -1216.079259, best rearrangement setting 14
Bootstrap[44]: Time 0.094301 seconds, bootstrap likelihood -1382.278311, best rearrangement setting 8
Bootstrap[45]: Time 0.111346 seconds, bootstrap likelihood -1099.004439, best rearrangement setting 11
Bootstrap[46]: Time 0.090018 seconds, bootstrap likelihood -1296.527478, best rearrangement setting 8
Bootstrap[47]: Time 0.129902 seconds, bootstrap likelihood -1291.322658, best rearrangement setting 9
Bootstrap[48]: Time 0.094719 seconds, bootstrap likelihood -1161.908080, best rearrangement setting 6
Bootstrap[49]: Time 0.117032 seconds, bootstrap likelihood -1257.348428, best rearrangement setting 13
Bootstrap[50]: Time 0.139497 seconds, bootstrap likelihood -1309.422533, best rearrangement setting 13
Bootstrap[51]: Time 0.098654 seconds, bootstrap likelihood -1197.633097, best rearrangement setting 11
Bootstrap[52]: Time 0.111662 seconds, bootstrap likelihood -1347.123005, best rearrangement setting 8
Bootstrap[53]: Time 0.096127 seconds, bootstrap likelihood -1234.934890, best rearrangement setting 14
Bootstrap[54]: Time 0.115316 seconds, bootstrap likelihood -1227.092434, best rearrangement setting 6
Bootstrap[55]: Time 0.122265 seconds, bootstrap likelihood -1280.635747, best rearrangement setting 7
Bootstrap[56]: Time 0.099054 seconds, bootstrap likelihood -1225.911449, best rearrangement setting 6
Bootstrap[57]: Time 0.093640 seconds, bootstrap likelihood -1236.213347, best rearrangement setting 11
Bootstrap[58]: Time 0.138473 seconds, bootstrap likelihood -1393.245723, best rearrangement setting 14
Bootstrap[59]: Time 0.106545 seconds, bootstrap likelihood -1212.039371, best rearrangement setting 6
Bootstrap[60]: Time 0.093879 seconds, bootstrap likelihood -1248.692011, best rearrangement setting 10
Bootstrap[61]: Time 0.108406 seconds, bootstrap likelihood -1172.820979, best rearrangement setting 13
Bootstrap[62]: Time 0.124893 seconds, bootstrap likelihood -1126.745788, best rearrangement setting 14
Bootstrap[63]: Time 0.100164 seconds, bootstrap likelihood -1267.434444, best rearrangement setting 12
Bootstrap[64]: Time 0.095990 seconds, bootstrap likelihood -1340.680748, best rearrangement setting 5
Bootstrap[65]: Time 0.097657 seconds, bootstrap likelihood -1072.671059, best rearrangement setting 5
Bootstrap[66]: Time 0.119499 seconds, bootstrap likelihood -1234.294838, best rearrangement setting 8
Bootstrap[67]: Time 0.118478 seconds, bootstrap likelihood -1109.249439, best rearrangement setting 15
Bootstrap[68]: Time 0.092889 seconds, bootstrap likelihood -1314.493588, best rearrangement setting 8
Bootstrap[69]: Time 0.099699 seconds, bootstrap likelihood -1173.850035, best rearrangement setting 13
Bootstrap[70]: Time 0.102796 seconds, bootstrap likelihood -1231.066465, best rearrangement setting 10
Bootstrap[71]: Time 0.102971 seconds, bootstrap likelihood -1146.861379, best rearrangement setting 9
Bootstrap[72]: Time 0.087155 seconds, bootstrap likelihood -1148.753369, best rearrangement setting 8
Bootstrap[73]: Time 0.101048 seconds, bootstrap likelihood -1333.374056, best rearrangement setting 9
Bootstrap[74]: Time 0.090339 seconds, bootstrap likelihood -1259.382378, best rearrangement setting 5
Bootstrap[75]: Time 0.097645 seconds, bootstrap likelihood -1319.944496, best rearrangement setting 6
Bootstrap[76]: Time 0.110693 seconds, bootstrap likelihood -1309.042165, best rearrangement setting 14
Bootstrap[77]: Time 0.133455 seconds, bootstrap likelihood -1232.061289, best rearrangement setting 8
Bootstrap[78]: Time 0.113731 seconds, bootstrap likelihood -1261.333984, best rearrangement setting 9
Bootstrap[79]: Time 0.113266 seconds, bootstrap likelihood -1194.644341, best rearrangement setting 13
Bootstrap[80]: Time 0.100970 seconds, bootstrap likelihood -1214.037389, best rearrangement setting 9
Bootstrap[81]: Time 0.108406 seconds, bootstrap likelihood -1224.527657, best rearrangement setting 8
Bootstrap[82]: Time 0.127233 seconds, bootstrap likelihood -1241.464826, best rearrangement setting 11
Bootstrap[83]: Time 0.097603 seconds, bootstrap likelihood -1230.730558, best rearrangement setting 6
Bootstrap[84]: Time 0.112748 seconds, bootstrap likelihood -1219.034592, best rearrangement setting 10
Bootstrap[85]: Time 0.114030 seconds, bootstrap likelihood -1280.071994, best rearrangement setting 8
Bootstrap[86]: Time 0.096299 seconds, bootstrap likelihood -1444.747777, best rearrangement setting 9
Bootstrap[87]: Time 0.098558 seconds, bootstrap likelihood -1245.890035, best rearrangement setting 14
Bootstrap[88]: Time 0.106532 seconds, bootstrap likelihood -1287.832766, best rearrangement setting 7
Bootstrap[89]: Time 0.098010 seconds, bootstrap likelihood -1325.245976, best rearrangement setting 5
Bootstrap[90]: Time 0.114252 seconds, bootstrap likelihood -1227.883697, best rearrangement setting 5
Bootstrap[91]: Time 0.109930 seconds, bootstrap likelihood -1273.489392, best rearrangement setting 8
Bootstrap[92]: Time 0.045898 seconds, bootstrap likelihood -1234.725870, best rearrangement setting 7
Bootstrap[93]: Time 0.119239 seconds, bootstrap likelihood -1235.733064, best rearrangement setting 11
Bootstrap[94]: Time 0.097775 seconds, bootstrap likelihood -1204.319488, best rearrangement setting 15
Bootstrap[95]: Time 0.094776 seconds, bootstrap likelihood -1183.328582, best rearrangement setting 11
Bootstrap[96]: Time 0.108806 seconds, bootstrap likelihood -1196.298898, best rearrangement setting 13
Bootstrap[97]: Time 0.117463 seconds, bootstrap likelihood -1339.251746, best rearrangement setting 12
Bootstrap[98]: Time 0.045511 seconds, bootstrap likelihood -1404.363552, best rearrangement setting 7
Bootstrap[99]: Time 0.059061 seconds, bootstrap likelihood -1270.157811, best rearrangement setting 7
Overall Time for 100 Rapid Bootstraps 10.747096 seconds
Average Time per Rapid Bootstrap 0.107471 seconds
Starting ML Search ...
Fast ML optimization finished
Fast ML search Time: 4.271557 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: 2.206338 seconds
Thorough ML search Time: 0.580224 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 7.064088 secs or 0.001962 hours
Combined Bootstrap and ML search took 17.811479 secs or 0.004948 hours
Drawing Bootstrap Support Values on best-scoring ML tree ...
Found 1 tree in File /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpdq267zdp/RAxML_bestTree.q2bootstrap
Found 1 tree in File /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpdq267zdp/RAxML_bestTree.q2bootstrap
Program execution info written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpdq267zdp/RAxML_info.q2bootstrap
All 100 bootstrapped trees written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpdq267zdp/RAxML_bootstrap.q2bootstrap
Best-scoring ML tree written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpdq267zdp/RAxML_bestTree.q2bootstrap
Best-scoring ML tree with support values written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpdq267zdp/RAxML_bipartitions.q2bootstrap
Best-scoring ML tree with support values as branch labels written to: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpdq267zdp/RAxML_bipartitionsBranchLabels.q2bootstrap
Overall execution time for full ML analysis: 17.824805 secs or 0.004951 hours or 0.000206 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-archive-w58qsbgd/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -w /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpdq267zdp -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:
Plugin warning from phylogeny:
iqtree is deprecated and will be removed in a future version of this plugin.
IQ-TREE multicore version 2.2.0-beta COVID-edition for Mac OS X 64-bit built Dec 21 2021 built Dec 21 2021
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-archive-6hbw_zdd/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp8fqc3j5z/q2iqtree -nt 1
Seed: 129212 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Mon Feb 21 12:27:29 2022
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-6hbw_zdd/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000218868 secs using 81.33% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000463009 secs using 78.62% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 1.90735e-05 secs using 83.89% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 7.39098e-05 secs using 75.77% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 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 0.083215 secs using 99.6% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1407.502
2. Current log-likelihood: -1400.070
3. Current log-likelihood: -1396.375
4. Current log-likelihood: -1394.887
Optimal log-likelihood: -1393.863
Rate parameters: A-C: 0.18680 A-G: 2.16102 A-T: 2.20604 C-G: 1.11230 C-T: 2.82171 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.022
Gamma shape alpha: 1.074
Parameters optimization took 4 rounds (0.037 sec)
Time for fast ML tree search: 0.161 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 299 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1413.964 45 2917.928 2942.571 3069.397
2 GTR+F+I 1411.832 46 2915.664 2941.556 3070.499
3 GTR+F+G4 1392.724 46 2877.447 2903.339 3032.282
4 GTR+F+I+G4 1393.053 47 2880.106 2907.287 3038.307
5 GTR+F+R2 1386.427 47 2866.854 2894.035 3025.055
6 GTR+F+R3 1386.566 49 2871.131 2901.009 3036.064
16 SYM+G4 1393.581 43 2873.162 2895.421 3017.899
18 SYM+R2 1388.979 44 2865.958 2889.390 3014.061
29 TVM+F+G4 1393.240 45 2876.480 2901.123 3027.949
31 TVM+F+R2 1387.337 46 2866.674 2892.566 3021.508
42 TVMe+G4 1393.700 42 2871.399 2892.522 3012.770
44 TVMe+R2 1388.983 43 2863.967 2886.226 3008.704
55 TIM3+F+G4 1397.789 44 2883.579 2907.011 3031.682
57 TIM3+F+R2 1391.101 45 2872.202 2896.845 3023.671
68 TIM3e+G4 1398.114 41 2878.228 2898.251 3016.233
70 TIM3e+R2 1393.075 42 2870.150 2891.272 3011.521
81 TIM2+F+G4 1401.888 44 2891.776 2915.208 3039.879
83 TIM2+F+R2 1394.794 45 2879.587 2904.230 3031.056
94 TIM2e+G4 1407.166 41 2896.331 2916.354 3034.336
96 TIM2e+R2 1401.544 42 2887.088 2908.211 3028.459
107 TIM+F+G4 1397.999 44 2883.999 2907.431 3032.102
109 TIM+F+R2 1391.093 45 2872.186 2896.829 3023.655
120 TIMe+G4 1404.065 41 2890.130 2910.153 3028.135
122 TIMe+R2 1398.405 42 2880.810 2901.933 3022.181
133 TPM3u+F+G4 1398.298 43 2882.597 2904.855 3027.334
135 TPM3u+F+R2 1392.056 44 2872.112 2895.544 3020.215
146 TPM3+G4 1398.232 40 2876.464 2895.423 3011.103
148 TPM3+R2 1393.083 41 2868.167 2888.190 3006.172
159 TPM2u+F+G4 1402.414 43 2890.828 2913.086 3035.565
161 TPM2u+F+R2 1395.759 44 2879.518 2902.949 3027.620
172 TPM2+G4 1407.298 40 2894.595 2913.555 3029.234
174 TPM2+R2 1401.478 41 2884.955 2904.979 3022.960
185 K3Pu+F+G4 1398.695 43 2883.391 2905.650 3028.128
187 K3Pu+F+R2 1392.170 44 2872.341 2895.773 3020.444
198 K3P+G4 1404.158 40 2888.315 2907.275 3022.954
200 K3P+R2 1398.390 41 2878.779 2898.803 3016.784
211 TN+F+G4 1402.054 43 2890.109 2912.368 3034.846
213 TN+F+R2 1395.027 44 2878.054 2901.486 3026.157
224 TNe+G4 1407.200 40 2894.399 2913.359 3029.038
226 TNe+R2 1401.479 41 2884.959 2904.982 3022.964
237 HKY+F+G4 1402.597 42 2889.194 2910.317 3030.565
239 HKY+F+R2 1396.061 43 2878.122 2900.380 3022.859
250 K2P+G4 1407.335 39 2892.671 2910.602 3023.944
252 K2P+R2 1401.478 40 2882.957 2901.916 3017.596
263 F81+F+G4 1410.825 41 2903.650 2923.673 3041.655
265 F81+F+R2 1404.980 42 2893.960 2915.083 3035.331
276 JC+G4 1415.573 38 2907.146 2924.084 3035.054
278 JC+R2 1410.586 39 2899.172 2917.103 3030.445
289 UNREST+FO+G4 1388.830 50 2877.659 2908.948 3045.958
291 UNREST+FO+R2 1384.547 51 2871.093 2903.834 3042.758
Akaike Information Criterion: TVMe+R2
Corrected Akaike Information Criterion: TVMe+R2
Bayesian Information Criterion: TPM3+R2
Best-fit model: TPM3+R2 chosen according to BIC
All model information printed to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp8fqc3j5z/q2iqtree.model.gz
CPU time for ModelFinder: 1.094 seconds (0h:0m:1s)
Wall-clock time for ModelFinder: 1.098 seconds (0h:0m:1s)
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1393.083
Optimal log-likelihood: -1393.065
Rate parameters: A-C: 0.33096 A-G: 1.35570 A-T: 1.00000 C-G: 0.33096 C-T: 1.35570 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.693,0.329) (0.307,2.511)
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 0.000867844 secs using 98.06% CPU
Computing ML distances took 0.000939 sec (of wall-clock time) 0.000905 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 5.48363e-05 secs using 89.36% CPU
Constructing RapidNJ tree: done in 9.39369e-05 secs using 146.9% CPU
Computing RapidNJ tree took 0.000215 sec (of wall-clock time) 0.000257 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1402.161
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.034 second
Computing log-likelihood of 98 initial trees ... 0.102 seconds
Current best score: -1393.065
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00694299 secs using 196.8% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1392.032
Optimizing NNI: done in 0.010772 secs using 196.3% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1385.326
Optimizing NNI: done in 0.0373728 secs using 147.5% CPU
Optimizing NNI: done in 0.0406878 secs using 99.95% CPU
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Iteration 10 / LogL: -1385.915 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0481391 secs using 99.94% CPU
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WARNING: NNI search needs unusual large number of steps (20) to converge!
Optimizing NNI: done in 0.0321341 secs using 99.95% CPU
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Optimizing NNI: done in 0.0498161 secs using 99.95% CPU
Iteration 20 / LogL: -1516.381 / Time: 0h:0m:1s
Finish initializing candidate tree set (19)
Current best tree score: -1385.326 / CPU time: 0.996
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0171871 secs using 99.46% CPU
Optimizing NNI: done in 0.017936 secs using 99.88% CPU
Optimizing NNI: done in 0.024523 secs using 99.82% CPU
Optimizing NNI: done in 0.0178671 secs using 99.9% CPU
Optimizing NNI: done in 0.0147061 secs using 99.93% CPU
BETTER TREE FOUND at iteration 25: -1385.323
Optimizing NNI: done in 0.011766 secs using 99.75% CPU
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Iteration 30 / LogL: -1385.326 / Time: 0h:0m:1s (0h:0m:3s left)
Optimizing NNI: done in 0.00935483 secs using 99.94% CPU
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Iteration 40 / LogL: -1385.719 / Time: 0h:0m:1s (0h:0m:2s left)
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Iteration 50 / LogL: -1385.720 / Time: 0h:0m:1s (0h:0m:2s left)
Optimizing NNI: done in 0.012754 secs using 99.95% CPU
Optimizing NNI: done in 0.00704193 secs using 99.93% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.322
Optimizing NNI: done in 0.0149901 secs using 99.82% CPU
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Iteration 60 / LogL: -1385.920 / Time: 0h:0m:1s (0h:0m:1s left)
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Iteration 70 / LogL: -1385.930 / Time: 0h:0m:1s (0h:0m:1s left)
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Iteration 80 / LogL: -1385.720 / Time: 0h:0m:1s (0h:0m:1s left)
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Optimizing NNI: done in 0.0133619 secs using 99.95% CPU
Optimizing NNI: done in 0.0149641 secs using 99.93% CPU
Optimizing NNI: done in 0.019809 secs using 99.95% CPU
Optimizing NNI: done in 0.017031 secs using 99.96% CPU
Optimizing NNI: done in 0.0162499 secs using 99.96% CPU
Optimizing NNI: done in 0.0218918 secs using 99.95% CPU
Iteration 90 / LogL: -1385.323 / Time: 0h:0m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.010711 secs using 99.94% CPU
Optimizing NNI: done in 0.016731 secs using 99.95% CPU
Optimizing NNI: done in 0.0140181 secs using 99.94% CPU
Optimizing NNI: done in 0.0178919 secs using 99.95% CPU
Optimizing NNI: done in 0.00527692 secs using 99.96% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.322
Optimizing NNI: done in 0.020215 secs using 99.81% CPU
Optimizing NNI: done in 0.016995 secs using 99.89% CPU
Optimizing NNI: done in 0.015146 secs using 99.95% CPU
Optimizing NNI: done in 0.0159302 secs using 99.95% CPU
Optimizing NNI: done in 0.018604 secs using 99.95% CPU
Iteration 100 / LogL: -1394.070 / Time: 0h:0m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.0194921 secs using 99.63% CPU
Optimizing NNI: done in 0.0156829 secs using 99.96% CPU
Optimizing NNI: done in 0.0148799 secs using 99.93% CPU
Optimizing NNI: done in 0.013876 secs using 99.95% CPU
Optimizing NNI: done in 0.0189519 secs using 99.94% CPU
Optimizing NNI: done in 0.016773 secs using 99.94% CPU
Optimizing NNI: done in 0.0163388 secs using 99.95% CPU
Optimizing NNI: done in 0.0117059 secs using 99.94% CPU
Optimizing NNI: done in 0.0272141 secs using 99.77% CPU
Optimizing NNI: done in 0.0124669 secs using 99.95% CPU
Iteration 110 / LogL: -1385.719 / Time: 0h:0m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.015934 secs using 99.94% CPU
Optimizing NNI: done in 0.0188909 secs using 99.94% CPU
Optimizing NNI: done in 0.0114579 secs using 99.95% CPU
Optimizing NNI: done in 0.01649 secs using 99.95% CPU
Optimizing NNI: done in 0.024936 secs using 99.84% CPU
Optimizing NNI: done in 0.0149262 secs using 99.84% CPU
Optimizing NNI: done in 0.0164611 secs using 99.93% CPU
Optimizing NNI: done in 0.0224798 secs using 99.96% CPU
Optimizing NNI: done in 0.0155289 secs using 99.94% CPU
Optimizing NNI: done in 0.0137899 secs using 99.94% CPU
Iteration 120 / LogL: -1469.954 / Time: 0h:0m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.0174961 secs using 99.77% CPU
Optimizing NNI: done in 0.0112441 secs using 99.78% CPU
Optimizing NNI: done in 0.0139301 secs using 99.93% CPU
Optimizing NNI: done in 0.0102959 secs using 99.94% CPU
Optimizing NNI: done in 0.0131249 secs using 99.95% CPU
Optimizing NNI: done in 0.012594 secs using 99.94% CPU
TREE SEARCH COMPLETED AFTER 126 ITERATIONS / Time: 0h:0m:2s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1385.322
Optimal log-likelihood: -1385.311
Rate parameters: A-C: 0.39450 A-G: 1.57508 A-T: 1.00000 C-G: 0.39450 C-T: 1.57508 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.717,0.394) (0.283,2.537)
Parameters optimization took 1 rounds (0.004 sec)
BEST SCORE FOUND : -1385.311
Total tree length: 6.965
Total number of iterations: 126
CPU time used for tree search: 2.912 sec (0h:0m:2s)
Wall-clock time used for tree search: 2.734 sec (0h:0m:2s)
Total CPU time used: 2.940 sec (0h:0m:2s)
Total wall-clock time used: 2.758 sec (0h:0m:2s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp8fqc3j5z/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp8fqc3j5z/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp8fqc3j5z/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp8fqc3j5z/q2iqtree.log
Date and Time: Mon Feb 21 12:27:32 2022
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-6hbw_zdd/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp8fqc3j5z/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:
Plugin warning from phylogeny:
iqtree is deprecated and will be removed in a future version of this plugin.
IQ-TREE multicore version 2.2.0-beta COVID-edition for Mac OS X 64-bit built Dec 21 2021 built Dec 21 2021
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-archive-eofzjwbk/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp9wt85luo/q2iqtree -nt 1
Seed: 744872 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Mon Feb 21 12:27:42 2022
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-eofzjwbk/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000217915 secs using 85.35% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000464916 secs using 78.94% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 1.88351e-05 secs using 84.95% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 7.39098e-05 secs using 75.77% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 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, 0.397 / LogL: -1823.354
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.019, 0.465 / LogL: -1823.521
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.030, 0.492 / LogL: -1823.178
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.035, 0.500 / LogL: -1822.673
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.038, 0.499 / LogL: -1822.073
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.037, 0.491 / LogL: -1821.357
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.038, 0.488 / LogL: -1820.740
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.039, 0.482 / LogL: -1820.015
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.040, 0.477 / LogL: -1819.309
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.041, 0.471 / LogL: -1818.588
Optimal pinv,alpha: 0.041, 0.471 / LogL: -1818.588
Parameters optimization took 0.629 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00232697 secs using 99.14% CPU
Computing ML distances took 0.002411 sec (of wall-clock time) 0.002363 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 5.57899e-05 secs using 89.62% CPU
Constructing RapidNJ tree: done in 0.000108004 secs using 141.7% CPU
Computing RapidNJ tree took 0.000232 sec (of wall-clock time) 0.000274 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1413.667
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.034 second
Computing log-likelihood of 98 initial trees ... 0.145 seconds
Current best score: -1413.667
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.012588 secs using 194.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.651
Optimizing NNI: done in 0.0629721 secs using 99.96% CPU
Optimizing NNI: done in 0.083672 secs using 99.95% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -1387.488
Optimizing NNI: done in 0.071444 secs using 99.97% CPU
Optimizing NNI: done in 0.0655179 secs using 99.97% CPU
Optimizing NNI: done in 0.0531249 secs using 99.97% CPU
Optimizing NNI: done in 0.0723941 secs using 99.96% CPU
WARNING: NNI search needs unusual large number of steps (20) to converge!
Optimizing NNI: done in 0.06691 secs using 99.97% CPU
Optimizing NNI: done in 0.036448 secs using 99.96% CPU
Optimizing NNI: done in 0.0721941 secs using 99.97% CPU
Iteration 10 / LogL: -1520.689 / Time: 0h:0m:1s
Optimizing NNI: done in 0.0863349 secs using 99.97% CPU
Optimizing NNI: done in 0.066752 secs using 99.91% CPU
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Optimizing NNI: done in 0.079345 secs using 99.96% CPU
Optimizing NNI: done in 0.0805988 secs using 99.97% CPU
WARNING: NNI search needs unusual large number of steps (20) to converge!
Optimizing NNI: done in 0.087435 secs using 99.68% CPU
Optimizing NNI: done in 0.033854 secs using 99.96% CPU
Optimizing NNI: done in 0.05759 secs using 99.97% CPU
Optimizing NNI: done in 0.0561099 secs using 99.97% CPU
Iteration 20 / LogL: -1406.637 / Time: 0h:0m:2s
Finish initializing candidate tree set (18)
Current best tree score: -1387.488 / CPU time: 1.583
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.035645 secs using 99.86% CPU
Optimizing NNI: done in 0.0300579 secs using 99.93% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 22: -1387.351
Optimizing NNI: done in 0.028111 secs using 99.8% CPU
Optimizing NNI: done in 0.023325 secs using 99.82% CPU
Optimizing NNI: done in 0.0288851 secs using 99.89% CPU
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -1387.280
Optimizing NNI: done in 0.016644 secs using 99.76% CPU
Optimizing NNI: done in 0.0260649 secs using 99.96% CPU
Optimizing NNI: done in 0.0418391 secs using 99.86% CPU
Optimizing NNI: done in 0.0690269 secs using 99.95% CPU
Optimizing NNI: done in 0.0420132 secs using 99.89% CPU
Iteration 30 / LogL: -1388.256 / Time: 0h:0m:2s (0h:0m:8s left)
Optimizing NNI: done in 0.0316679 secs using 99.96% CPU
Optimizing NNI: done in 0.0232692 secs using 99.94% CPU
BETTER TREE FOUND at iteration 32: -1387.280
Optimizing NNI: done in 0.0393538 secs using 99.75% CPU
Optimizing NNI: done in 0.0490012 secs using 99.96% CPU
Optimizing NNI: done in 0.033406 secs using 99.96% CPU
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Optimizing NNI: done in 0.019891 secs using 99.96% CPU
Iteration 40 / LogL: -1387.559 / Time: 0h:0m:2s (0h:0m:6s left)
Optimizing NNI: done in 0.0206971 secs using 99.96% CPU
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Iteration 50 / LogL: -1396.567 / Time: 0h:0m:3s (0h:0m:5s left)
Optimizing NNI: done in 0.026777 secs using 99.96% CPU
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Optimizing NNI: done in 0.0162742 secs using 99.92% CPU
Optimizing NNI: done in 0.0200601 secs using 99.84% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.280
Optimizing NNI: done in 0.043077 secs using 99.86% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.279
Optimizing NNI: done in 0.0270021 secs using 99.84% CPU
Optimizing NNI: done in 0.0692711 secs using 99.96% CPU
Iteration 60 / LogL: -1387.448 / Time: 0h:0m:3s (0h:0m:4s left)
Optimizing NNI: done in 0.0345271 secs using 99.96% CPU
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Optimizing NNI: done in 0.034019 secs using 99.96% CPU
Optimizing NNI: done in 0.0409889 secs using 99.97% CPU
Iteration 70 / LogL: -1387.320 / Time: 0h:0m:3s (0h:0m:3s left)
Optimizing NNI: done in 0.0189939 secs using 99.95% CPU
Optimizing NNI: done in 0.0210509 secs using 99.95% CPU
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Optimizing NNI: done in 0.0320351 secs using 99.95% CPU
Iteration 80 / LogL: -1387.509 / Time: 0h:0m:4s (0h:0m:2s left)
Optimizing NNI: done in 0.02055 secs using 99.97% CPU
Optimizing NNI: done in 0.00681686 secs using 99.99% CPU
Optimizing NNI: done in 0.018805 secs using 99.97% CPU
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Optimizing NNI: done in 0.028795 secs using 99.79% CPU
Optimizing NNI: done in 0.019119 secs using 99.86% CPU
Iteration 90 / LogL: -1387.280 / Time: 0h:0m:4s (0h:0m:2s left)
Optimizing NNI: done in 0.022809 secs using 99.84% CPU
Optimizing NNI: done in 0.0243859 secs using 99.96% CPU
Optimizing NNI: done in 0.0474122 secs using 99.96% CPU
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Optimizing NNI: done in 0.0314069 secs using 99.96% CPU
Optimizing NNI: done in 0.031337 secs using 99.96% CPU
Iteration 100 / LogL: -1387.283 / Time: 0h:0m:4s (0h:0m:1s left)
Optimizing NNI: done in 0.024379 secs using 99.96% CPU
Optimizing NNI: done in 0.0291388 secs using 99.96% CPU
Optimizing NNI: done in 0.047951 secs using 99.96% CPU
Optimizing NNI: done in 0.0291979 secs using 99.97% CPU
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Optimizing NNI: done in 0.0246079 secs using 99.97% CPU
Optimizing NNI: done in 0.039984 secs using 99.96% CPU
Optimizing NNI: done in 0.0258222 secs using 99.96% CPU
Optimizing NNI: done in 0.030107 secs using 99.97% CPU
Iteration 110 / LogL: -1387.280 / Time: 0h:0m:5s (0h:0m:1s left)
Optimizing NNI: done in 0.029587 secs using 99.96% CPU
Optimizing NNI: done in 0.0211229 secs using 99.81% CPU
Optimizing NNI: done in 0.040602 secs using 99.96% CPU
Optimizing NNI: done in 0.0358291 secs using 99.96% CPU
Optimizing NNI: done in 0.0370009 secs using 99.96% CPU
Optimizing NNI: done in 0.0192761 secs using 99.97% CPU
Optimizing NNI: done in 0.0296869 secs using 99.96% CPU
Optimizing NNI: done in 0.020494 secs using 99.96% CPU
Optimizing NNI: done in 0.030174 secs using 99.82% CPU
Optimizing NNI: done in 0.0353281 secs using 99.96% CPU
Iteration 120 / LogL: -1387.305 / Time: 0h:0m:5s (0h:0m:0s left)
Optimizing NNI: done in 0.0112879 secs using 99.95% CPU
Optimizing NNI: done in 0.0254529 secs using 99.97% CPU
Optimizing NNI: done in 0.026248 secs using 99.85% CPU
Optimizing NNI: done in 0.0428178 secs using 99.86% CPU
Optimizing NNI: done in 0.0295799 secs using 99.96% CPU
Optimizing NNI: done in 0.038702 secs using 99.96% CPU
Optimizing NNI: done in 0.040941 secs using 99.96% CPU
Optimizing NNI: done in 0.029923 secs using 99.96% CPU
Optimizing NNI: done in 0.0334852 secs using 99.97% CPU
Optimizing NNI: done in 0.0299928 secs using 99.96% CPU
Iteration 130 / LogL: -1387.323 / Time: 0h:0m:5s (0h:0m:0s left)
Optimizing NNI: done in 0.0317531 secs using 99.97% CPU
Optimizing NNI: done in 0.02036 secs using 99.96% CPU
Optimizing NNI: done in 0.043314 secs using 99.96% CPU
TREE SEARCH COMPLETED AFTER 133 ITERATIONS / Time: 0h:0m:5s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.279
2. Current log-likelihood: -1387.261
3. Current log-likelihood: -1387.245
4. Current log-likelihood: -1387.233
5. Current log-likelihood: -1387.222
Optimal log-likelihood: -1387.213
Rate parameters: A-C: 0.34958 A-G: 2.33258 A-T: 2.15590 C-G: 1.24042 C-T: 3.23753 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.001
Gamma shape alpha: 1.287
Parameters optimization took 5 rounds (0.017 sec)
BEST SCORE FOUND : -1387.213
Total tree length: 7.621
Total number of iterations: 133
CPU time used for tree search: 5.295 sec (0h:0m:5s)
Wall-clock time used for tree search: 5.118 sec (0h:0m:5s)
Total CPU time used: 5.964 sec (0h:0m:5s)
Total wall-clock time used: 5.784 sec (0h:0m:5s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp9wt85luo/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp9wt85luo/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp9wt85luo/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp9wt85luo/q2iqtree.log
Date and Time: Mon Feb 21 12:27:48 2022
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-eofzjwbk/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmp9wt85luo/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:
Plugin warning from phylogeny:
iqtree is deprecated and will be removed in a future version of this plugin.
IQ-TREE multicore version 2.2.0-beta COVID-edition for Mac OS X 64-bit built Dec 21 2021 built Dec 21 2021
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-archive-831ch4_r/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpic_js0rc/q2iqtree -nt 1 -fast
Seed: 370492 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Mon Feb 21 12:27:58 2022
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-831ch4_r/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000235081 secs using 84.23% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000504971 secs using 78.62% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Analyzing sequences: done in 2.00272e-05 secs using 84.88% CPU
Checking for duplicate sequences: done in 7.89165e-05 secs using 74.76% CPU
---> START RUN NUMBER 1 (seed: 370492)
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: -2058.24
2. Current log-likelihood: -1852.37
3. Current log-likelihood: -1841.32
4. Current log-likelihood: -1839.47
Optimal log-likelihood: -1838.94
Rate parameters: A-C: 0.00010 A-G: 1.78167 A-T: 2.22392 C-G: 1.90153 C-T: 4.54949 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.055
Gamma shape alpha: 0.549
Parameters optimization took 4 rounds (0.049 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00205183 secs using 99.13% CPU
Computing ML distances took 0.002139 sec (of wall-clock time) 0.002090 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 5.50747e-05 secs using 88.97% CPU
Constructing RapidNJ tree: done in 9.58443e-05 secs using 153.4% CPU
Computing RapidNJ tree took 0.000218 sec (of wall-clock time) 0.000249 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1409.513
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0124321 secs using 196.1% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1389.026
Optimizing NNI: done in 0.087559 secs using 196.8% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 2: -1387.969
Finish initializing candidate tree set (4)
Current best tree score: -1387.969 / CPU time: 0.149
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: -1387.969
2. Current log-likelihood: -1387.834
3. Current log-likelihood: -1387.726
4. Current log-likelihood: -1387.647
5. Current log-likelihood: -1387.587
Optimal log-likelihood: -1387.539
Rate parameters: A-C: 0.37899 A-G: 2.35435 A-T: 2.15803 C-G: 1.24720 C-T: 3.34425 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.006
Gamma shape alpha: 1.311
Parameters optimization took 5 rounds (0.018 sec)
BEST SCORE FOUND : -1387.539
Total tree length: 7.606
Total number of iterations: 2
CPU time used for tree search: 0.294 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.149 sec (0h:0m:0s)
Total CPU time used: 0.402 sec (0h:0m:0s)
Total wall-clock time used: 0.237 sec (0h:0m:0s)
---> START RUN NUMBER 2 (seed: 371492)
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: -2171.038
2. Current log-likelihood: -1980.051
3. Current log-likelihood: -1923.533
4. Current log-likelihood: -1921.371
5. Current log-likelihood: -1920.591
Optimal log-likelihood: -1920.191
Rate parameters: A-C: 0.46540 A-G: 4.42811 A-T: 5.73340 C-G: 5.22017 C-T: 12.34775 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.047
Gamma shape alpha: 0.513
Parameters optimization took 5 rounds (0.057 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00223708 secs using 99.59% CPU
Computing ML distances took 0.002306 sec (of wall-clock time) 0.002280 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 4.91142e-05 secs using 93.66% CPU
Constructing RapidNJ tree: done in 9.29832e-05 secs using 154.9% CPU
Computing RapidNJ tree took 0.000212 sec (of wall-clock time) 0.000257 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1409.567
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0124841 secs using 196.3% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.647
Optimizing NNI: done in 0.0856218 secs using 196.7% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1388.647 / CPU time: 0.151
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: -1388.647
2. Current log-likelihood: -1388.179
3. Current log-likelihood: -1387.902
4. Current log-likelihood: -1387.788
5. Current log-likelihood: -1387.693
6. Current log-likelihood: -1387.615
7. Current log-likelihood: -1387.549
Optimal log-likelihood: -1387.509
Rate parameters: A-C: 0.33876 A-G: 2.32970 A-T: 2.21066 C-G: 1.20503 C-T: 3.38894 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.003
Gamma shape alpha: 1.331
Parameters optimization took 7 rounds (0.031 sec)
BEST SCORE FOUND : -1387.509
Total tree length: 6.865
Total number of iterations: 2
CPU time used for tree search: 0.296 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.151 sec (0h:0m:0s)
Total CPU time used: 0.464 sec (0h:0m:0s)
Total wall-clock time used: 0.257 sec (0h:0m:0s)
---> START RUN NUMBER 3 (seed: 372492)
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: -2203.030
2. Current log-likelihood: -1920.171
3. Current log-likelihood: -1891.219
4. Current log-likelihood: -1888.241
5. Current log-likelihood: -1886.789
6. Current log-likelihood: -1886.096
Optimal log-likelihood: -1885.699
Rate parameters: A-C: 2.27921 A-G: 13.94801 A-T: 16.57646 C-G: 25.00127 C-T: 56.30754 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: 0.448
Parameters optimization took 6 rounds (0.076 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00232387 secs using 99.62% CPU
Computing ML distances took 0.002401 sec (of wall-clock time) 0.002368 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 4.91142e-05 secs using 93.66% CPU
Constructing RapidNJ tree: done in 9.01222e-05 secs using 157.6% CPU
Computing RapidNJ tree took 0.000206 sec (of wall-clock time) 0.000255 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1417.785
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.024498 secs using 196.5% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.937
Optimizing NNI: done in 0.0829699 secs using 196.6% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.937 / CPU time: 0.177
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: -1387.937
2. Current log-likelihood: -1387.806
3. Current log-likelihood: -1387.711
4. Current log-likelihood: -1387.646
Optimal log-likelihood: -1387.595
Rate parameters: A-C: 0.35123 A-G: 2.25319 A-T: 2.13485 C-G: 1.20366 C-T: 3.24072 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.006
Gamma shape alpha: 1.288
Parameters optimization took 4 rounds (0.018 sec)
BEST SCORE FOUND : -1387.595
Total tree length: 7.711
Total number of iterations: 2
CPU time used for tree search: 0.347 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.177 sec (0h:0m:0s)
Total CPU time used: 0.493 sec (0h:0m:0s)
Total wall-clock time used: 0.288 sec (0h:0m:0s)
---> START RUN NUMBER 4 (seed: 373492)
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: -2172.151
2. Current log-likelihood: -1968.935
3. Current log-likelihood: -1955.145
4. Current log-likelihood: -1953.495
5. Current log-likelihood: -1952.567
6. Current log-likelihood: -1952.022
Optimal log-likelihood: -1951.639
Rate parameters: A-C: 0.37558 A-G: 3.11091 A-T: 3.56840 C-G: 4.00162 C-T: 10.74161 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.041
Gamma shape alpha: 0.492
Parameters optimization took 6 rounds (0.065 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00247717 secs using 99.59% CPU
Computing ML distances took 0.002555 sec (of wall-clock time) 0.002525 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 4.91142e-05 secs using 93.66% CPU
Constructing RapidNJ tree: done in 8.91685e-05 secs using 158.1% CPU
Computing RapidNJ tree took 0.000208 sec (of wall-clock time) 0.000252 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1411.154
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.012377 secs using 196.6% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.631
Optimizing NNI: done in 0.0792961 secs using 196.8% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1388.631 / CPU time: 0.139
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: -1388.631
2. Current log-likelihood: -1388.163
3. Current log-likelihood: -1387.885
4. Current log-likelihood: -1387.774
5. Current log-likelihood: -1387.684
6. Current log-likelihood: -1387.608
7. Current log-likelihood: -1387.544
Optimal log-likelihood: -1387.503
Rate parameters: A-C: 0.34579 A-G: 2.34534 A-T: 2.22721 C-G: 1.21402 C-T: 3.41641 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.003
Gamma shape alpha: 1.325
Parameters optimization took 7 rounds (0.030 sec)
BEST SCORE FOUND : -1387.503
Total tree length: 6.881
Total number of iterations: 2
CPU time used for tree search: 0.274 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.140 sec (0h:0m:0s)
Total CPU time used: 0.419 sec (0h:0m:0s)
Total wall-clock time used: 0.251 sec (0h:0m:0s)
---> START RUN NUMBER 5 (seed: 374492)
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: -2187.914
2. Current log-likelihood: -1945.256
3. Current log-likelihood: -1911.107
4. Current log-likelihood: -1909.125
5. Current log-likelihood: -1908.529
Optimal log-likelihood: -1907.968
Rate parameters: A-C: 0.00010 A-G: 3.20756 A-T: 4.13615 C-G: 3.02646 C-T: 8.43244 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.050
Gamma shape alpha: 0.524
Parameters optimization took 5 rounds (0.059 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00328207 secs using 99.48% CPU
Computing ML distances took 0.003382 sec (of wall-clock time) 0.003340 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 6.10352e-05 secs using 95.03% CPU
Constructing RapidNJ tree: done in 8.89301e-05 secs using 159.7% CPU
Computing RapidNJ tree took 0.000223 sec (of wall-clock time) 0.000253 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1409.387
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0127108 secs using 196.9% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.656
Optimizing NNI: done in 0.079556 secs using 196.7% CPU
WARNING: NNI search needs unusual large number of steps (20) to converge!
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 2: -1387.820
Finish initializing candidate tree set (4)
Current best tree score: -1387.820 / CPU time: 0.145
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: -1387.820
2. Current log-likelihood: -1387.691
3. Current log-likelihood: -1387.591
4. Current log-likelihood: -1387.518
5. Current log-likelihood: -1387.463
Optimal log-likelihood: -1387.420
Rate parameters: A-C: 0.33318 A-G: 2.27456 A-T: 2.14928 C-G: 1.18018 C-T: 3.29473 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.353
Parameters optimization took 5 rounds (0.021 sec)
BEST SCORE FOUND : -1387.420
Total tree length: 6.716
Total number of iterations: 2
CPU time used for tree search: 0.286 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.145 sec (0h:0m:0s)
Total CPU time used: 0.435 sec (0h:0m:0s)
Total wall-clock time used: 0.245 sec (0h:0m:0s)
---> START RUN NUMBER 6 (seed: 375492)
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: -2249.937
2. Current log-likelihood: -1972.913
3. Current log-likelihood: -1926.884
4. Current log-likelihood: -1924.378
5. Current log-likelihood: -1923.567
Optimal log-likelihood: -1923.172
Rate parameters: A-C: 0.07579 A-G: 4.99960 A-T: 6.87531 C-G: 6.70939 C-T: 15.72924 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.043
Gamma shape alpha: 0.491
Parameters optimization took 5 rounds (0.054 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00222087 secs using 99.65% CPU
Computing ML distances took 0.002298 sec (of wall-clock time) 0.002264 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 4.79221e-05 secs using 93.9% CPU
Constructing RapidNJ tree: done in 8.91685e-05 secs using 160.4% CPU
Computing RapidNJ tree took 0.000205 sec (of wall-clock time) 0.000229 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1412.673
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0142901 secs using 196.1% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.598
Optimizing NNI: done in 0.0776949 secs using 196.7% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1388.598 / CPU time: 0.145
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: -1388.598
2. Current log-likelihood: -1388.147
3. Current log-likelihood: -1387.880
4. Current log-likelihood: -1387.770
5. Current log-likelihood: -1387.679
6. Current log-likelihood: -1387.604
7. Current log-likelihood: -1387.540
Optimal log-likelihood: -1387.504
Rate parameters: A-C: 0.33979 A-G: 2.34210 A-T: 2.22344 C-G: 1.21181 C-T: 3.41009 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.003
Gamma shape alpha: 1.329
Parameters optimization took 7 rounds (0.029 sec)
BEST SCORE FOUND : -1387.504
Total tree length: 6.870
Total number of iterations: 2
CPU time used for tree search: 0.284 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.145 sec (0h:0m:0s)
Total CPU time used: 0.444 sec (0h:0m:0s)
Total wall-clock time used: 0.244 sec (0h:0m:0s)
---> START RUN NUMBER 7 (seed: 376492)
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: -2131.292
2. Current log-likelihood: -1886.623
3. Current log-likelihood: -1865.156
4. Current log-likelihood: -1863.099
5. Current log-likelihood: -1862.535
Optimal log-likelihood: -1862.269
Rate parameters: A-C: 0.00010 A-G: 11.57685 A-T: 13.13277 C-G: 13.16951 C-T: 33.38440 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.046
Gamma shape alpha: 0.507
Parameters optimization took 5 rounds (0.066 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00230598 secs using 99.61% CPU
Computing ML distances took 0.002374 sec (of wall-clock time) 0.002349 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 4.81606e-05 secs using 118.4% CPU
Constructing RapidNJ tree: done in 8.70228e-05 secs using 148.2% CPU
Computing RapidNJ tree took 0.000204 sec (of wall-clock time) 0.000259 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1413.332
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.012778 secs using 196.3% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.666
Optimizing NNI: done in 0.0874641 secs using 196.7% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1388.666 / CPU time: 0.167
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: -1388.666
2. Current log-likelihood: -1388.191
3. Current log-likelihood: -1387.908
4. Current log-likelihood: -1387.792
5. Current log-likelihood: -1387.694
6. Current log-likelihood: -1387.614
7. Current log-likelihood: -1387.548
Optimal log-likelihood: -1387.508
Rate parameters: A-C: 0.33790 A-G: 2.30927 A-T: 2.19120 C-G: 1.19469 C-T: 3.35969 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.003
Gamma shape alpha: 1.331
Parameters optimization took 7 rounds (0.030 sec)
BEST SCORE FOUND : -1387.508
Total tree length: 6.868
Total number of iterations: 2
CPU time used for tree search: 0.328 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.167 sec (0h:0m:0s)
Total CPU time used: 0.497 sec (0h:0m:0s)
Total wall-clock time used: 0.281 sec (0h:0m:0s)
---> START RUN NUMBER 8 (seed: 377492)
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: -2233.377
2. Current log-likelihood: -2020.208
3. Current log-likelihood: -1962.287
4. Current log-likelihood: -1960.737
5. Current log-likelihood: -1960.047
Optimal log-likelihood: -1959.712
Rate parameters: A-C: 0.31227 A-G: 3.44049 A-T: 5.31178 C-G: 4.20904 C-T: 9.70999 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.050
Gamma shape alpha: 0.507
Parameters optimization took 5 rounds (0.064 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.002177 secs using 99.59% CPU
Computing ML distances took 0.002254 sec (of wall-clock time) 0.002219 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 6.07967e-05 secs using 87.18% CPU
Constructing RapidNJ tree: done in 0.000108957 secs using 140.4% CPU
Computing RapidNJ tree took 0.000251 sec (of wall-clock time) 0.000284 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1410.338
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0127189 secs using 196.8% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.673
Optimizing NNI: done in 0.086112 secs using 196.9% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1388.673 / CPU time: 0.143
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: -1388.673
2. Current log-likelihood: -1388.193
3. Current log-likelihood: -1387.914
4. Current log-likelihood: -1387.796
5. Current log-likelihood: -1387.700
6. Current log-likelihood: -1387.620
7. Current log-likelihood: -1387.553
Optimal log-likelihood: -1387.512
Rate parameters: A-C: 0.33851 A-G: 2.32579 A-T: 2.20683 C-G: 1.20313 C-T: 3.38371 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: 1.332
Parameters optimization took 7 rounds (0.030 sec)
BEST SCORE FOUND : -1387.512
Total tree length: 6.860
Total number of iterations: 2
CPU time used for tree search: 0.281 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.143 sec (0h:0m:0s)
Total CPU time used: 0.436 sec (0h:0m:0s)
Total wall-clock time used: 0.259 sec (0h:0m:0s)
---> START RUN NUMBER 9 (seed: 378492)
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: -2175.200
2. Current log-likelihood: -1916.392
3. Current log-likelihood: -1903.171
4. Current log-likelihood: -1900.276
5. Current log-likelihood: -1899.281
6. Current log-likelihood: -1898.755
Optimal log-likelihood: -1898.367
Rate parameters: A-C: 0.78587 A-G: 6.84248 A-T: 6.68372 C-G: 10.82602 C-T: 22.74524 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.033
Gamma shape alpha: 0.441
Parameters optimization took 6 rounds (0.073 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.0023241 secs using 99.61% CPU
Computing ML distances took 0.002400 sec (of wall-clock time) 0.002366 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 92.58% CPU
Constructing RapidNJ tree: done in 8.91685e-05 secs using 160.4% CPU
Computing RapidNJ tree took 0.000216 sec (of wall-clock time) 0.000268 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1416.063
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0246129 secs using 196.6% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.822
Optimizing NNI: done in 0.0805068 secs using 195.9% CPU
WARNING: NNI search needs unusual large number of steps (20) to converge!
BETTER TREE FOUND at iteration 2: -1387.799
Finish initializing candidate tree set (4)
Current best tree score: -1387.799 / CPU time: 0.162
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: -1387.799
2. Current log-likelihood: -1387.694
3. Current log-likelihood: -1387.616
4. Current log-likelihood: -1387.559
Optimal log-likelihood: -1387.515
Rate parameters: A-C: 0.37633 A-G: 2.32817 A-T: 2.13387 C-G: 1.23254 C-T: 3.30404 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.006
Gamma shape alpha: 1.305
Parameters optimization took 4 rounds (0.017 sec)
BEST SCORE FOUND : -1387.515
Total tree length: 7.624
Total number of iterations: 2
CPU time used for tree search: 0.316 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.162 sec (0h:0m:0s)
Total CPU time used: 0.462 sec (0h:0m:0s)
Total wall-clock time used: 0.269 sec (0h:0m:0s)
---> START RUN NUMBER 10 (seed: 379492)
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: -2225.628
2. Current log-likelihood: -1974.142
3. Current log-likelihood: -1940.784
4. Current log-likelihood: -1939.115
5. Current log-likelihood: -1938.501
Optimal log-likelihood: -1938.231
Rate parameters: A-C: 0.91680 A-G: 8.16332 A-T: 9.32969 C-G: 10.41035 C-T: 21.78572 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.049
Gamma shape alpha: 0.493
Parameters optimization took 5 rounds (0.054 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00220919 secs using 99.63% CPU
Computing ML distances took 0.002287 sec (of wall-clock time) 0.002253 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 4.91142e-05 secs using 95.7% CPU
Constructing RapidNJ tree: done in 9.01222e-05 secs using 145.4% CPU
Computing RapidNJ tree took 0.000212 sec (of wall-clock time) 0.000253 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1412.123
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0128419 secs using 196.4% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.719
Optimizing NNI: done in 0.06568 secs using 196.7% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1388.719 / CPU time: 0.133
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: -1388.719
2. Current log-likelihood: -1388.216
3. Current log-likelihood: -1387.923
4. Current log-likelihood: -1387.804
5. Current log-likelihood: -1387.708
6. Current log-likelihood: -1387.627
7. Current log-likelihood: -1387.560
Optimal log-likelihood: -1387.513
Rate parameters: A-C: 0.34611 A-G: 2.34591 A-T: 2.22722 C-G: 1.21436 C-T: 3.41584 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: 1.328
Parameters optimization took 7 rounds (0.029 sec)
BEST SCORE FOUND : -1387.513
Total tree length: 6.872
Total number of iterations: 2
CPU time used for tree search: 0.262 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.133 sec (0h:0m:0s)
Total CPU time used: 0.409 sec (0h:0m:0s)
Total wall-clock time used: 0.233 sec (0h:0m:0s)
---> SUMMARIZE RESULTS FROM 10 RUNS
Run 5 gave best log-likelihood: -1387.420
Total CPU time for 10 runs: 4.492 seconds.
Total wall-clock time for 10 runs: 2.585 seconds.
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpic_js0rc/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpic_js0rc/q2iqtree.treefile
Trees from independent runs: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpic_js0rc/q2iqtree.runtrees
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpic_js0rc/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpic_js0rc/q2iqtree.log
Date and Time: Mon Feb 21 12:28:00 2022
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 10 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-831ch4_r/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpic_js0rc/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:
Plugin warning from phylogeny:
iqtree is deprecated and will be removed in a future version of this plugin.
IQ-TREE multicore version 2.2.0-beta COVID-edition for Mac OS X 64-bit built Dec 21 2021 built Dec 21 2021
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-archive-kqe1pbtc/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpg9s9mgz9/q2iqtree -nt 1 -alrt 1000 -abayes -lbp 1000
Seed: 716339 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Mon Feb 21 12:28:10 2022
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-kqe1pbtc/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000234127 secs using 85% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000509024 secs using 78.78% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 2.00272e-05 secs using 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 8.10623e-05 secs using 75.25% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Thoroughly optimizing +I+G parameters from 10 start values...
Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 0.469 / LogL: -1762.982
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.028, 0.522 / LogL: -1762.832
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.040, 0.538 / LogL: -1762.553
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.042, 0.534 / LogL: -1762.119
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.041, 0.527 / LogL: -1761.641
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.043, 0.523 / LogL: -1761.188
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.045, 0.517 / LogL: -1760.729
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.046, 0.512 / LogL: -1760.260
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.047, 0.505 / LogL: -1759.772
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.048, 0.498 / LogL: -1759.279
Optimal pinv,alpha: 0.048, 0.498 / LogL: -1759.279
Parameters optimization took 0.492 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00219703 secs using 99.13% CPU
Computing ML distances took 0.002282 sec (of wall-clock time) 0.002235 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 5.98431e-05 secs using 86.89% CPU
Constructing RapidNJ tree: done in 0.000101089 secs using 150.4% CPU
Computing RapidNJ tree took 0.000228 sec (of wall-clock time) 0.000256 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1407.925
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.037 second
Computing log-likelihood of 98 initial trees ... 0.148 seconds
Current best score: -1407.925
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.012892 secs using 146.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.668
Optimizing NNI: done in 0.0815451 secs using 99.71% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1387.498
Optimizing NNI: done in 0.0810869 secs using 99.91% CPU
Optimizing NNI: done in 0.074126 secs using 99.96% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 4: -1387.310
Optimizing NNI: done in 0.0760131 secs using 99.86% CPU
Optimizing NNI: done in 0.062387 secs using 99.96% CPU
Optimizing NNI: done in 0.0753469 secs using 99.97% CPU
Optimizing NNI: done in 0.0787661 secs using 99.96% CPU
Optimizing NNI: done in 0.0756319 secs using 99.96% CPU
Optimizing NNI: done in 0.0810931 secs using 99.97% CPU
Iteration 10 / LogL: -1507.358 / Time: 0h:0m:1s
Optimizing NNI: done in 0.0763841 secs using 99.96% CPU
Optimizing NNI: done in 0.0473402 secs using 99.9% CPU
Optimizing NNI: done in 0.09003 secs using 99.92% CPU
Optimizing NNI: done in 0.078732 secs using 99.93% CPU
WARNING: NNI search needs unusual large number of steps (20) to converge!
Optimizing NNI: done in 0.0513439 secs using 99.95% CPU
Optimizing NNI: done in 0.0851171 secs using 99.9% CPU
Optimizing NNI: done in 0.0783741 secs using 99.96% CPU
Optimizing NNI: done in 0.0659561 secs using 99.97% CPU
Optimizing NNI: done in 0.0805922 secs using 99.96% CPU
Optimizing NNI: done in 0.0702441 secs using 99.86% CPU
WARNING: NNI search needs unusual large number of steps (20) to converge!
Iteration 20 / LogL: -1393.172 / Time: 0h:0m:2s
Finish initializing candidate tree set (19)
Current best tree score: -1387.310 / CPU time: 1.690
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0517349 secs using 99.71% CPU
Optimizing NNI: done in 0.0195539 secs using 99.95% CPU
Optimizing NNI: done in 0.0162179 secs using 99.97% CPU
Optimizing NNI: done in 0.030206 secs using 99.97% CPU
Optimizing NNI: done in 0.0528839 secs using 99.87% CPU
Optimizing NNI: done in 0.015352 secs using 99.96% CPU
Optimizing NNI: done in 0.015614 secs using 99.95% CPU
Optimizing NNI: done in 0.0208011 secs using 99.96% CPU
Optimizing NNI: done in 0.0112429 secs using 99.96% CPU
Optimizing NNI: done in 0.0267608 secs using 99.96% CPU
Iteration 30 / LogL: -1387.507 / Time: 0h:0m:2s (0h:0m:6s left)
Optimizing NNI: done in 0.030647 secs using 99.96% CPU
Optimizing NNI: done in 0.023025 secs using 99.96% CPU
Optimizing NNI: done in 0.0137661 secs using 99.96% CPU
Optimizing NNI: done in 0.0327482 secs using 99.72% CPU
Optimizing NNI: done in 0.0284681 secs using 99.96% CPU
Optimizing NNI: done in 0.0346348 secs using 99.95% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.309
Optimizing NNI: done in 0.0305219 secs using 99.84% CPU
Optimizing NNI: done in 0.0432711 secs using 99.96% CPU
Optimizing NNI: done in 0.063673 secs using 99.92% CPU
Optimizing NNI: done in 0.0211139 secs using 99.97% CPU
Iteration 40 / LogL: -1387.479 / Time: 0h:0m:2s (0h:0m:4s left)
Optimizing NNI: done in 0.016181 secs using 99.97% CPU
Optimizing NNI: done in 0.0194349 secs using 99.96% CPU
Optimizing NNI: done in 0.027199 secs using 99.97% CPU
Optimizing NNI: done in 0.026778 secs using 99.84% CPU
Optimizing NNI: done in 0.021065 secs using 99.92% CPU
Optimizing NNI: done in 0.0320332 secs using 99.96% CPU
Optimizing NNI: done in 0.0254321 secs using 99.65% CPU
Optimizing NNI: done in 0.0227308 secs using 99.97% CPU
Optimizing NNI: done in 0.0282309 secs using 99.96% CPU
Optimizing NNI: done in 0.0186069 secs using 99.96% CPU
Iteration 50 / LogL: -1396.690 / Time: 0h:0m:3s (0h:0m:3s left)
Optimizing NNI: done in 0.0316188 secs using 99.96% CPU
Optimizing NNI: done in 0.0221789 secs using 99.95% CPU
Optimizing NNI: done in 0.0312622 secs using 99.96% CPU
Optimizing NNI: done in 0.017709 secs using 99.96% CPU
Optimizing NNI: done in 0.017761 secs using 99.97% CPU
Optimizing NNI: done in 0.0235729 secs using 99.97% CPU
Optimizing NNI: done in 0.029547 secs using 99.97% CPU
Optimizing NNI: done in 0.0210171 secs using 99.97% CPU
Optimizing NNI: done in 0.0413818 secs using 99.96% CPU
Optimizing NNI: done in 0.0148151 secs using 99.96% CPU
Iteration 60 / LogL: -1387.309 / Time: 0h:0m:3s (0h:0m:2s left)
Optimizing NNI: done in 0.039804 secs using 99.96% CPU
Optimizing NNI: done in 0.0364778 secs using 99.96% CPU
Optimizing NNI: done in 0.0311122 secs using 99.96% CPU
Optimizing NNI: done in 0.0286188 secs using 99.96% CPU
Optimizing NNI: done in 0.0351291 secs using 99.97% CPU
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Optimizing NNI: done in 0.020098 secs using 99.96% CPU
Optimizing NNI: done in 0.0260601 secs using 99.97% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.309
Optimizing NNI: done in 0.0428321 secs using 99.87% CPU
Optimizing NNI: done in 0.031939 secs using 99.97% CPU
Iteration 70 / LogL: -1387.480 / Time: 0h:0m:3s (0h:0m:1s left)
Optimizing NNI: done in 0.02953 secs using 99.96% CPU
Optimizing NNI: done in 0.0507631 secs using 99.96% CPU
Optimizing NNI: done in 0.0276999 secs using 99.96% CPU
Optimizing NNI: done in 0.0428119 secs using 99.97% CPU
Optimizing NNI: done in 0.0296459 secs using 99.95% CPU
Optimizing NNI: done in 0.039593 secs using 99.95% CPU
Optimizing NNI: done in 0.043896 secs using 99.96% CPU
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Optimizing NNI: done in 0.022476 secs using 99.96% CPU
Optimizing NNI: done in 0.0479362 secs using 99.96% CPU
Iteration 80 / LogL: -1387.335 / Time: 0h:0m:4s (0h:0m:1s left)
Optimizing NNI: done in 0.0221879 secs using 99.97% CPU
Optimizing NNI: done in 0.0438969 secs using 99.8% CPU
Optimizing NNI: done in 0.0227799 secs using 99.95% CPU
Optimizing NNI: done in 0.018862 secs using 99.96% CPU
Optimizing NNI: done in 0.028512 secs using 99.96% CPU
Optimizing NNI: done in 0.0547352 secs using 99.96% CPU
Optimizing NNI: done in 0.0394669 secs using 99.96% CPU
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Optimizing NNI: done in 0.025537 secs using 99.97% CPU
Optimizing NNI: done in 0.0331299 secs using 99.96% CPU
Iteration 90 / LogL: -1387.342 / Time: 0h:0m:4s (0h:0m:0s left)
Optimizing NNI: done in 0.0203331 secs using 99.96% CPU
Optimizing NNI: done in 0.00887489 secs using 99.94% CPU
Optimizing NNI: done in 0.0288792 secs using 99.96% CPU
Optimizing NNI: done in 0.0318589 secs using 99.96% CPU
Optimizing NNI: done in 0.0386801 secs using 99.96% CPU
Optimizing NNI: done in 0.0191312 secs using 99.96% CPU
Optimizing NNI: done in 0.047617 secs using 99.89% CPU
Optimizing NNI: done in 0.0364361 secs using 99.96% CPU
Optimizing NNI: done in 0.0284669 secs using 99.96% CPU
Optimizing NNI: done in 0.0241051 secs using 99.87% CPU
Iteration 100 / LogL: -1387.722 / Time: 0h:0m:4s (0h:0m:0s left)
Optimizing NNI: done in 0.0293961 secs using 99.86% CPU
Optimizing NNI: done in 0.0153511 secs using 99.95% CPU
Optimizing NNI: done in 0.0292881 secs using 99.96% CPU
Optimizing NNI: done in 0.0328581 secs using 99.96% CPU
Optimizing NNI: done in 0.0261972 secs using 99.96% CPU
TREE SEARCH COMPLETED AFTER 105 ITERATIONS / Time: 0h:0m:4s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.309
2. Current log-likelihood: -1387.285
3. Current log-likelihood: -1387.265
4. Current log-likelihood: -1387.249
5. Current log-likelihood: -1387.236
6. Current log-likelihood: -1387.225
Optimal log-likelihood: -1387.216
Rate parameters: A-C: 0.35235 A-G: 2.33149 A-T: 2.15517 C-G: 1.24020 C-T: 3.23605 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.001
Gamma shape alpha: 1.288
Parameters optimization took 6 rounds (0.020 sec)
BEST SCORE FOUND : -1387.216
Testing tree branches by SH-like aLRT with 1000 replicates...
Testing tree branches by local-BP test with 1000 replicates...
Testing tree branches by aBayes parametric test...
0.056 sec.
Total tree length: 7.618
Total number of iterations: 105
CPU time used for tree search: 4.429 sec (0h:0m:4s)
Wall-clock time used for tree search: 4.251 sec (0h:0m:4s)
Total CPU time used: 5.021 sec (0h:0m:5s)
Total wall-clock time used: 4.839 sec (0h:0m:4s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpg9s9mgz9/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpg9s9mgz9/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpg9s9mgz9/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpg9s9mgz9/q2iqtree.log
Date and Time: Mon Feb 21 12:28:15 2022
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-kqe1pbtc/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpg9s9mgz9/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:
Plugin warning from phylogeny:
iqtree is deprecated and will be removed in a future version of this plugin.
IQ-TREE multicore version 2.2.0-beta COVID-edition for Mac OS X 64-bit built Dec 21 2021 built Dec 21 2021
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-archive-ledkmtyg/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfphg4jyl/q2iqtree -nt 1 -nstop 200 -pers 0.200000
Seed: 359207 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Mon Feb 21 12:28:25 2022
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-ledkmtyg/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000234127 secs using 85.85% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000464916 secs using 78.08% 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 1.78814e-05 secs using 89.48% 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 73.23% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 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 0.0886381 secs using 99.95% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1524.136
2. Current log-likelihood: -1517.825
3. Current log-likelihood: -1515.203
Optimal log-likelihood: -1513.848
Rate parameters: A-C: 0.21227 A-G: 2.66119 A-T: 2.92875 C-G: 1.46743 C-T: 4.51073 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.041
Gamma shape alpha: 0.813
Parameters optimization took 3 rounds (0.030 sec)
Time for fast ML tree search: 0.158 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 299 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1542.305 45 3174.611 3199.253 3326.079
2 GTR+F+I 1533.642 46 3159.285 3185.177 3314.120
3 GTR+F+G4 1512.431 46 3116.862 3142.754 3271.697
4 GTR+F+I+G4 1512.774 47 3119.548 3146.729 3277.749
5 GTR+F+R2 1509.949 47 3113.897 3141.078 3272.098
6 GTR+F+R3 1508.490 49 3114.980 3144.858 3279.913
16 SYM+G4 1513.646 43 3113.291 3135.550 3258.028
17 SYM+I+G4 1513.917 44 3115.835 3139.267 3263.938
18 SYM+R2 1511.175 44 3110.351 3133.782 3258.453
19 SYM+R3 1510.381 46 3112.762 3138.654 3267.597
29 TVM+F+G4 1514.066 45 3118.132 3142.774 3269.601
30 TVM+F+I+G4 1514.265 46 3120.530 3146.422 3275.365
31 TVM+F+R2 1511.878 46 3115.757 3141.649 3270.592
32 TVM+F+R3 1510.317 48 3116.635 3145.144 3278.201
42 TVMe+G4 1513.648 42 3111.296 3132.419 3252.667
43 TVMe+I+G4 1513.871 43 3113.741 3136.000 3258.478
44 TVMe+R2 1511.238 43 3108.475 3130.734 3253.212
45 TVMe+R3 1510.422 45 3110.845 3135.488 3262.314
55 TIM3+F+G4 1518.225 44 3124.451 3147.883 3272.554
56 TIM3+F+I+G4 1518.605 45 3127.210 3151.853 3278.679
57 TIM3+F+R2 1515.166 45 3120.333 3144.975 3271.802
58 TIM3+F+R3 1514.111 47 3122.223 3149.403 3280.423
68 TIM3e+G4 1518.501 41 3119.002 3139.025 3257.007
69 TIM3e+I+G4 1518.773 42 3121.546 3142.669 3262.917
70 TIM3e+R2 1515.624 42 3115.247 3136.370 3256.618
71 TIM3e+R3 1514.901 44 3117.801 3141.233 3265.904
81 TIM2+F+G4 1520.982 44 3129.964 3153.396 3278.067
82 TIM2+F+I+G4 1521.300 45 3132.600 3157.243 3284.069
83 TIM2+F+R2 1518.617 45 3127.235 3151.878 3278.704
84 TIM2+F+R3 1516.942 47 3127.885 3155.066 3286.086
94 TIM2e+G4 1526.233 41 3134.466 3154.490 3272.471
95 TIM2e+I+G4 1526.417 42 3136.835 3157.957 3278.206
96 TIM2e+R2 1524.217 42 3132.435 3153.558 3273.806
97 TIM2e+R3 1522.909 44 3133.818 3157.250 3281.921
107 TIM+F+G4 1516.284 44 3120.567 3143.999 3268.670
108 TIM+F+I+G4 1516.585 45 3123.170 3147.813 3274.639
109 TIM+F+R2 1514.514 45 3119.028 3143.670 3270.497
110 TIM+F+R3 1512.216 47 3118.432 3145.613 3276.633
120 TIMe+G4 1522.561 41 3127.121 3147.144 3265.126
121 TIMe+I+G4 1522.763 42 3129.526 3150.648 3270.897
122 TIMe+R2 1520.529 42 3125.058 3146.181 3266.429
123 TIMe+R3 1518.921 44 3125.843 3149.275 3273.946
133 TPM3u+F+G4 1519.736 43 3125.471 3147.730 3270.208
134 TPM3u+F+I+G4 1519.965 44 3127.931 3151.363 3276.034
135 TPM3u+F+R2 1516.896 44 3121.793 3145.225 3269.896
136 TPM3u+F+R3 1515.886 46 3123.773 3149.665 3278.608
146 TPM3+G4 1518.503 40 3117.007 3135.966 3251.646
147 TPM3+I+G4 1518.778 41 3119.556 3139.579 3257.561
148 TPM3+R2 1515.686 41 3113.372 3133.395 3251.377
149 TPM3+R3 1514.937 43 3115.874 3138.132 3260.611
159 TPM2u+F+G4 1522.774 43 3131.548 3153.807 3276.285
160 TPM2u+F+I+G4 1522.935 44 3133.869 3157.301 3281.972
161 TPM2u+F+R2 1520.655 44 3129.310 3152.742 3277.413
162 TPM2u+F+R3 1519.227 46 3130.453 3156.345 3285.288
172 TPM2+G4 1526.248 40 3132.495 3151.455 3267.134
173 TPM2+I+G4 1526.397 41 3134.794 3154.817 3272.799
174 TPM2+R2 1524.286 41 3130.572 3150.595 3268.577
175 TPM2+R3 1523.068 43 3132.137 3154.395 3276.874
185 K3Pu+F+G4 1518.530 43 3123.060 3145.319 3267.797
186 K3Pu+F+I+G4 1518.700 44 3125.399 3148.831 3273.502
187 K3Pu+F+R2 1516.927 44 3121.854 3145.286 3269.957
188 K3Pu+F+R3 1514.831 46 3121.663 3147.555 3276.498
198 K3P+G4 1522.597 40 3125.194 3144.154 3259.833
199 K3P+I+G4 1522.756 41 3127.512 3147.535 3265.517
200 K3P+R2 1520.703 41 3123.406 3143.430 3261.411
201 K3P+R3 1519.161 43 3124.323 3146.581 3269.060
211 TN+F+G4 1521.251 43 3128.501 3150.760 3273.238
212 TN+F+I+G4 1521.544 44 3131.087 3154.519 3279.190
213 TN+F+R2 1518.893 44 3125.786 3149.218 3273.889
214 TN+F+R3 1517.379 46 3126.758 3152.650 3281.593
224 TNe+G4 1526.252 40 3132.504 3151.464 3267.143
225 TNe+I+G4 1526.418 41 3134.835 3154.859 3272.840
226 TNe+R2 1524.087 41 3130.173 3150.196 3268.178
227 TNe+R3 1522.903 43 3131.807 3154.066 3276.544
237 HKY+F+G4 1523.019 42 3130.037 3151.160 3271.408
238 HKY+F+I+G4 1523.218 43 3132.435 3154.694 3277.172
239 HKY+F+R2 1521.075 43 3128.150 3150.409 3272.887
240 HKY+F+R3 1519.620 45 3129.239 3153.882 3280.708
250 K2P+G4 1526.267 39 3130.534 3148.465 3261.807
251 K2P+I+G4 1526.420 40 3132.840 3151.799 3267.479
252 K2P+R2 1524.288 40 3128.577 3147.536 3263.216
253 K2P+R3 1523.064 42 3130.128 3151.250 3271.499
263 F81+F+G4 1532.526 41 3147.051 3167.075 3285.056
264 F81+F+I+G4 1532.701 42 3149.403 3170.526 3290.774
265 F81+F+R2 1531.031 42 3146.062 3167.185 3287.433
266 F81+F+R3 1529.558 44 3147.116 3170.548 3295.219
276 JC+G4 1535.871 38 3147.741 3164.679 3275.648
277 JC+I+G4 1535.946 39 3149.892 3167.823 3281.165
278 JC+R2 1534.598 39 3147.196 3165.127 3278.469
279 JC+R3 1533.192 41 3148.385 3168.408 3286.390
289 UNREST+FO+G4 1509.112 50 3118.223 3149.512 3286.522
290 UNREST+FO+I+G4 1509.177 51 3120.354 3153.094 3292.018
291 UNREST+FO+R2 1506.908 51 3115.816 3148.557 3287.481
292 UNREST+FO+R3 1505.875 53 3117.750 3153.525 3296.147
Akaike Information Criterion: TVMe+R2
Corrected Akaike Information Criterion: TVMe+R2
Bayesian Information Criterion: TPM3+R2
Best-fit model: TPM3+R2 chosen according to BIC
All model information printed to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfphg4jyl/q2iqtree.model.gz
CPU time for ModelFinder: 2.583 seconds (0h:0m:2s)
Wall-clock time for ModelFinder: 2.599 seconds (0h:0m:2s)
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1515.686
Optimal log-likelihood: -1515.671
Rate parameters: A-C: 0.31536 A-G: 1.39782 A-T: 1.00000 C-G: 0.31536 C-T: 1.39782 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.670,0.272) (0.330,2.481)
Parameters optimization took 1 rounds (0.006 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00116205 secs using 98.19% CPU
Computing ML distances took 0.001256 sec (of wall-clock time) 0.001210 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 7.20024e-05 secs using 87.5% CPU
Constructing RapidNJ tree: done in 0.000121117 secs using 147% CPU
Computing RapidNJ tree took 0.000276 sec (of wall-clock time) 0.000334 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1403.144
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.034 second
Computing log-likelihood of 98 initial trees ... 0.106 seconds
Current best score: -1403.144
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.0108979 secs using 196.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.328
Optimizing NNI: done in 0.0171239 secs using 196.8% CPU
Optimizing NNI: done in 0.051857 secs using 109% CPU
Optimizing NNI: done in 0.032558 secs using 99.94% CPU
Optimizing NNI: done in 0.0426841 secs using 99.91% CPU
Optimizing NNI: done in 0.0499208 secs using 99.93% CPU
Optimizing NNI: done in 0.0438759 secs using 99.88% CPU
BETTER TREE FOUND at iteration 7: -1385.327
Optimizing NNI: done in 0.0481269 secs using 99.95% CPU
Optimizing NNI: done in 0.0381591 secs using 99.93% CPU
Optimizing NNI: done in 0.042057 secs using 99.95% CPU
Iteration 10 / LogL: -1409.351 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0355461 secs using 99.95% CPU
Optimizing NNI: done in 0.0430701 secs using 99.95% CPU
Optimizing NNI: done in 0.029876 secs using 99.95% CPU
Optimizing NNI: done in 0.049552 secs using 99.96% CPU
Optimizing NNI: done in 0.03478 secs using 99.95% CPU
Optimizing NNI: done in 0.0373609 secs using 99.95% CPU
Optimizing NNI: done in 0.0389488 secs using 99.96% CPU
Optimizing NNI: done in 0.044574 secs using 99.96% CPU
Optimizing NNI: done in 0.0551362 secs using 99.96% CPU
WARNING: NNI search needs unusual large number of steps (20) to converge!
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Iteration 20 / LogL: -1386.004 / Time: 0h:0m:0s
Finish initializing candidate tree set (20)
Current best tree score: -1385.327 / CPU time: 0.950
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
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UPDATE BEST LOG-LIKELIHOOD: -1385.326
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UPDATE BEST LOG-LIKELIHOOD: -1385.326
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Iteration 30 / LogL: -1385.884 / Time: 0h:0m:1s (0h:0m:6s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.326
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UPDATE BEST LOG-LIKELIHOOD: -1385.326
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UPDATE BEST LOG-LIKELIHOOD: -1385.325
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UPDATE BEST LOG-LIKELIHOOD: -1385.325
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Iteration 60 / LogL: -1385.325 / Time: 0h:0m:1s (0h:0m:3s left)
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Iteration 70 / LogL: -1385.723 / Time: 0h:0m:1s (0h:0m:3s left)
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Iteration 80 / LogL: -1385.328 / Time: 0h:0m:1s (0h:0m:2s left)
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Iteration 90 / LogL: -1385.326 / Time: 0h:0m:1s (0h:0m:2s left)
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Iteration 100 / LogL: -1385.326 / Time: 0h:0m:1s (0h:0m:2s left)
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Iteration 110 / LogL: -1385.422 / Time: 0h:0m:2s (0h:0m:1s left)
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Iteration 120 / LogL: -1385.329 / Time: 0h:0m:2s (0h:0m:1s left)
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Iteration 130 / LogL: -1385.402 / Time: 0h:0m:2s (0h:0m:1s left)
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Iteration 140 / LogL: -1385.336 / Time: 0h:0m:2s (0h:0m:1s left)
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Iteration 150 / LogL: -1385.327 / Time: 0h:0m:2s (0h:0m:0s left)
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Iteration 160 / LogL: -1385.329 / Time: 0h:0m:2s (0h:0m:0s left)
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Iteration 170 / LogL: -1385.325 / Time: 0h:0m:2s (0h:0m:0s left)
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Iteration 180 / LogL: -1385.497 / Time: 0h:0m:2s (0h:0m:0s left)
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Iteration 190 / LogL: -1385.329 / Time: 0h:0m:3s (0h:0m:0s left)
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Iteration 200 / LogL: -1385.327 / Time: 0h:0m:3s (0h:0m:0s left)
Optimizing NNI: done in 0.0126691 secs using 99.93% CPU
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TREE SEARCH COMPLETED AFTER 208 ITERATIONS / Time: 0h:0m:3s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1385.325
2. Current log-likelihood: -1385.314
Optimal log-likelihood: -1385.307
Rate parameters: A-C: 0.39478 A-G: 1.57080 A-T: 1.00000 C-G: 0.39478 C-T: 1.57080 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.719,0.397) (0.281,2.542)
Parameters optimization took 2 rounds (0.007 sec)
BEST SCORE FOUND : -1385.307
Total tree length: 6.922
Total number of iterations: 208
CPU time used for tree search: 3.366 sec (0h:0m:3s)
Wall-clock time used for tree search: 3.190 sec (0h:0m:3s)
Total CPU time used: 3.400 sec (0h:0m:3s)
Total wall-clock time used: 3.220 sec (0h:0m:3s)
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfphg4jyl/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfphg4jyl/q2iqtree.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfphg4jyl/q2iqtree.mldist
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfphg4jyl/q2iqtree.log
Date and Time: Mon Feb 21 12:28:31 2022
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-ledkmtyg/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfphg4jyl/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:
Plugin warning from phylogeny:
iqtree-ultrafast-bootstrap is deprecated and will be removed in a future version of this plugin.
IQ-TREE multicore version 2.2.0-beta COVID-edition for Mac OS X 64-bit built Dec 21 2021 built Dec 21 2021
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-archive-swijfhdn/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfdh4xk3s/q2iqtreeufboot -nt 1 -nstop 200 -pers 0.200000
Seed: 42654 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Mon Feb 21 12:28:41 2022
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-swijfhdn/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000217915 secs using 81.22% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000469923 secs using 78.52% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 1.88351e-05 secs using 84.95% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 7.39098e-05 secs using 75.77% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 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 0.0738082 secs using 99.93% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1415.023
2. Current log-likelihood: -1409.585
3. Current log-likelihood: -1408.297
Optimal log-likelihood: -1407.632
Rate parameters: A-C: 0.31403 A-G: 2.69368 A-T: 2.73260 C-G: 1.45424 C-T: 3.88931 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.036
Gamma shape alpha: 0.821
Parameters optimization took 3 rounds (0.023 sec)
Time for fast ML tree search: 0.133 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 299 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1434.388 45 2958.775 2983.418 3110.244
2 GTR+F+I 1428.598 46 2949.196 2975.088 3104.031
3 GTR+F+G4 1406.624 46 2905.248 2931.140 3060.083
4 GTR+F+I+G4 1406.960 47 2907.919 2935.100 3066.120
5 GTR+F+R2 1406.162 47 2906.324 2933.505 3064.525
6 GTR+F+R3 1405.397 49 2908.794 2938.672 3073.727
16 SYM+G4 1406.038 43 2898.076 2920.335 3042.813
17 SYM+I+G4 1406.329 44 2900.658 2924.090 3048.761
18 SYM+R2 1405.917 44 2899.834 2923.266 3047.937
29 TVM+F+G4 1407.601 45 2905.202 2929.845 3056.671
30 TVM+F+I+G4 1407.818 46 2907.636 2933.528 3062.471
31 TVM+F+R2 1407.037 46 2906.074 2931.966 3060.909
42 TVMe+G4 1406.052 42 2896.105 2917.228 3037.476
43 TVMe+I+G4 1406.378 43 2898.756 2921.015 3043.493
44 TVMe+R2 1405.939 43 2897.878 2920.137 3042.615
55 TIM3+F+G4 1411.680 44 2911.359 2934.791 3059.462
56 TIM3+F+I+G4 1412.041 45 2914.083 2938.725 3065.552
57 TIM3+F+R2 1410.654 45 2911.308 2935.951 3062.777
68 TIM3e+G4 1409.891 41 2901.783 2921.806 3039.788
69 TIM3e+I+G4 1410.235 42 2904.470 2925.592 3045.841
70 TIM3e+R2 1409.455 42 2902.909 2924.032 3044.280
81 TIM2+F+G4 1413.631 44 2915.263 2938.695 3063.366
82 TIM2+F+I+G4 1413.935 45 2917.870 2942.513 3069.339
83 TIM2+F+R2 1412.668 45 2915.336 2939.979 3066.805
94 TIM2e+G4 1416.338 41 2914.677 2934.700 3052.682
95 TIM2e+I+G4 1416.529 42 2917.059 2938.182 3058.430
96 TIM2e+R2 1415.338 42 2914.676 2935.798 3056.047
107 TIM+F+G4 1409.708 44 2907.416 2930.848 3055.519
108 TIM+F+I+G4 1410.020 45 2910.039 2934.682 3061.508
109 TIM+F+R2 1408.839 45 2907.678 2932.321 3059.147
120 TIMe+G4 1412.985 41 2907.970 2927.993 3045.975
121 TIMe+I+G4 1413.204 42 2910.408 2931.531 3051.779
122 TIMe+R2 1412.180 42 2908.360 2929.483 3049.731
133 TPM3u+F+G4 1412.579 43 2911.159 2933.417 3055.896
134 TPM3u+F+I+G4 1412.898 44 2913.796 2937.228 3061.899
135 TPM3u+F+R2 1411.509 44 2911.018 2934.450 3059.121
146 TPM3+G4 1409.920 40 2899.840 2918.800 3034.479
147 TPM3+I+G4 1410.222 41 2902.444 2922.468 3040.449
148 TPM3+R2 1409.475 41 2900.949 2920.973 3038.954
159 TPM2u+F+G4 1414.513 43 2915.027 2937.285 3059.764
160 TPM2u+F+I+G4 1414.706 44 2917.412 2940.844 3065.515
161 TPM2u+F+R2 1413.432 44 2914.865 2938.297 3062.968
172 TPM2+G4 1416.372 40 2912.744 2931.703 3047.383
173 TPM2+I+G4 1416.576 41 2915.151 2935.175 3053.156
174 TPM2+R2 1415.392 41 2912.785 2932.808 3050.790
185 K3Pu+F+G4 1410.801 43 2907.602 2929.861 3052.339
186 K3Pu+F+I+G4 1410.996 44 2909.992 2933.423 3058.094
187 K3Pu+F+R2 1409.746 44 2907.492 2930.924 3055.595
198 K3P+G4 1412.990 40 2905.980 2924.939 3040.619
199 K3P+I+G4 1413.209 41 2908.419 2928.442 3046.424
200 K3P+R2 1412.217 41 2906.434 2926.457 3044.439
211 TN+F+G4 1414.297 43 2914.594 2936.852 3059.330
212 TN+F+I+G4 1414.624 44 2917.247 2940.679 3065.350
213 TN+F+R2 1413.063 44 2914.127 2937.559 3062.230
224 TNe+G4 1416.377 40 2912.754 2931.713 3047.393
225 TNe+I+G4 1416.521 41 2915.042 2935.066 3053.047
226 TNe+R2 1415.337 41 2912.673 2932.697 3050.679
237 HKY+F+G4 1415.198 42 2914.396 2935.519 3055.767
238 HKY+F+I+G4 1415.411 43 2916.822 2939.080 3061.559
239 HKY+F+R2 1413.820 43 2913.641 2935.900 3058.378
250 K2P+G4 1416.427 39 2910.854 2928.785 3042.127
251 K2P+I+G4 1416.628 40 2913.255 2932.215 3047.894
252 K2P+R2 1415.391 40 2910.782 2929.741 3045.421
263 F81+F+G4 1424.177 41 2930.354 2950.377 3068.359
264 F81+F+I+G4 1424.331 42 2932.663 2953.785 3074.034
265 F81+F+R2 1423.107 42 2930.213 2951.336 3071.584
276 JC+G4 1425.391 38 2926.783 2943.720 3054.690
277 JC+I+G4 1425.387 39 2928.774 2946.705 3060.048
278 JC+R2 1424.585 39 2927.170 2945.101 3058.443
289 UNREST+FO+G4 1403.073 50 2906.146 2937.434 3074.444
290 UNREST+FO+I+G4 1403.350 51 2908.700 2941.441 3080.365
291 UNREST+FO+R2 1403.013 51 2908.026 2940.767 3079.691
Akaike Information Criterion: TVMe+G4
Corrected Akaike Information Criterion: TVMe+G4
Bayesian Information Criterion: TPM3+G4
Best-fit model: TPM3+G4 chosen according to BIC
All model information printed to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfdh4xk3s/q2iqtreeufboot.model.gz
CPU time for ModelFinder: 1.622 seconds (0h:0m:1s)
Wall-clock time for ModelFinder: 1.628 seconds (0h:0m:1s)
Generating 1000 samples for ultrafast bootstrap (seed: 42654)...
NOTE: 1 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1409.920
Optimal log-likelihood: -1409.906
Rate parameters: A-C: 0.34522 A-G: 1.45352 A-T: 1.00000 C-G: 0.34522 C-T: 1.45352 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Gamma shape alpha: 0.891
Parameters optimization took 1 rounds (0.005 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00172615 secs using 98.77% CPU
Computing ML distances took 0.001822 sec (of wall-clock time) 0.001778 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 7.20024e-05 secs using 109.7% CPU
Constructing RapidNJ tree: done in 0.00012207 secs using 154.8% CPU
Computing RapidNJ tree took 0.000287 sec (of wall-clock time) 0.000351 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1406.537
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| INITIALIZING CANDIDATE TREE SET |
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Generating 98 parsimony trees... 0.034 second
Computing log-likelihood of 98 initial trees ... 0.141 seconds
Current best score: -1406.537
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.0421259 secs using 134.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1390.540
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 13: -1390.373
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Iteration 20 / LogL: -1569.674 / Time: 0h:0m:2s
Finish initializing candidate tree set (20)
Current best tree score: -1390.373 / CPU time: 2.035
Number of iterations: 20
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| OPTIMIZING CANDIDATE TREE SET |
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UPDATE BEST LOG-LIKELIHOOD: -1390.372
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Iteration 50 / LogL: -1390.373 / Time: 0h:0m:2s (0h:0m:9s left)
Log-likelihood cutoff on original alignment: -1413.674
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Iteration 100 / LogL: -1390.585 / Time: 0h:0m:4s (0h:0m:5s left)
Log-likelihood cutoff on original alignment: -1414.492
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.996
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UPDATE BEST LOG-LIKELIHOOD: -1390.370
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UPDATE BEST LOG-LIKELIHOOD: -1390.369
Iteration 130 / LogL: -1390.369 / Time: 0h:0m:5s (0h:0m:3s left)
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Iteration 150 / LogL: -1390.428 / Time: 0h:0m:6s (0h:0m:2s left)
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Iteration 200 / LogL: -1390.402 / Time: 0h:0m:7s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -1413.443
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.995
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Optimizing NNI: done in 0.0238101 secs using 99.96% CPU
Optimizing NNI: done in 0.0240021 secs using 99.97% CPU
Optimizing NNI: done in 0.0335569 secs using 99.97% CPU
Iteration 210 / LogL: -1390.426 / Time: 0h:0m:7s (0h:0m:3s left)
Optimizing NNI: done in 0.0260289 secs using 99.97% CPU
Optimizing NNI: done in 0.00982094 secs using 99.97% CPU
Optimizing NNI: done in 0.0170381 secs using 99.96% CPU
Optimizing NNI: done in 0.018856 secs using 99.97% CPU
TREE SEARCH COMPLETED AFTER 214 ITERATIONS / Time: 0h:0m:8s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1390.369
Optimal log-likelihood: -1390.359
Rate parameters: A-C: 0.38543 A-G: 1.52207 A-T: 1.00000 C-G: 0.38543 C-T: 1.52207 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Gamma shape alpha: 1.408
Parameters optimization took 1 rounds (0.003 sec)
BEST SCORE FOUND : -1390.359
Creating bootstrap support values...
Split supports printed to NEXUS file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfdh4xk3s/q2iqtreeufboot.splits.nex
Total tree length: 7.081
Total number of iterations: 214
CPU time used for tree search: 8.147 sec (0h:0m:8s)
Wall-clock time used for tree search: 7.985 sec (0h:0m:7s)
Total CPU time used: 8.256 sec (0h:0m:8s)
Total wall-clock time used: 8.091 sec (0h:0m:8s)
Computing bootstrap consensus tree...
Reading input file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfdh4xk3s/q2iqtreeufboot.splits.nex...
20 taxa and 163 splits.
Consensus tree written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfdh4xk3s/q2iqtreeufboot.contree
Reading input trees file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfdh4xk3s/q2iqtreeufboot.contree
Log-likelihood of consensus tree: -1390.371
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfdh4xk3s/q2iqtreeufboot.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfdh4xk3s/q2iqtreeufboot.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfdh4xk3s/q2iqtreeufboot.mldist
Ultrafast bootstrap approximation results written to:
Split support values: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfdh4xk3s/q2iqtreeufboot.splits.nex
Consensus tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfdh4xk3s/q2iqtreeufboot.contree
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfdh4xk3s/q2iqtreeufboot.log
Date and Time: Mon Feb 21 12:28:50 2022
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -bb 1000 -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-swijfhdn/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfdh4xk3s/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:
Plugin warning from phylogeny:
iqtree-ultrafast-bootstrap is deprecated and will be removed in a future version of this plugin.
IQ-TREE multicore version 2.2.0-beta COVID-edition for Mac OS X 64-bit built Dec 21 2021 built Dec 21 2021
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-archive-lnml3hrr/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfcpmvo7j/q2iqtreeufboot -nt 1 -alrt 1000 -abayes -lbp 1000 -nstop 200 -pers 0.200000
Seed: 645505 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Mon Feb 21 12:29:00 2022
Kernel: AVX - 1 threads (8 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-lnml3hrr/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.00022912 secs using 85.11% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000463009 secs using 78.62% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 1.90735e-05 secs using 83.89% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 7.39098e-05 secs using 75.77% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
Generating 1000 samples for ultrafast bootstrap (seed: 645505)...
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, 0.411 / LogL: -1956.473
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.020, 0.466 / LogL: -1956.320
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.028, 0.479 / LogL: -1955.766
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.030, 0.476 / LogL: -1954.993
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.029, 0.469 / LogL: -1954.124
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.034, 0.474 / LogL: -1953.466
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.036, 0.470 / LogL: -1952.629
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.037, 0.466 / LogL: -1951.816
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.038, 0.462 / LogL: -1950.914
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.039, 0.457 / LogL: -1950.061
Optimal pinv,alpha: 0.039, 0.457 / LogL: -1950.061
Parameters optimization took 0.849 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00243115 secs using 99.25% CPU
Computing ML distances took 0.002507 sec (of wall-clock time) 0.002469 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 6.00815e-05 secs using 88.21% CPU
Constructing RapidNJ tree: done in 0.000101089 secs using 146.4% CPU
Computing RapidNJ tree took 0.000233 sec (of wall-clock time) 0.000275 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1416.742
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.034 second
Computing log-likelihood of 98 initial trees ... 0.145 seconds
Current best score: -1416.742
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.01845 secs using 158.6% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.665
Optimizing NNI: done in 0.0964019 secs using 99.97% CPU
Optimizing NNI: done in 0.0871301 secs using 99.97% CPU
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Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 7: -1387.353
Optimizing NNI: done in 0.109731 secs using 99.97% CPU
WARNING: NNI search needs unusual large number of steps (20) to converge!
Optimizing NNI: done in 0.107748 secs using 99.97% CPU
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Iteration 10 / LogL: -1689.748 / Time: 0h:0m:2s
Optimizing NNI: done in 0.122629 secs using 99.9% CPU
WARNING: NNI search needs unusual large number of steps (20) to converge!
Optimizing NNI: done in 0.131087 secs using 99.93% CPU
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WARNING: NNI search needs unusual large number of steps (20) to converge!
Optimizing NNI: done in 0.132074 secs using 99.81% CPU
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WARNING: NNI search needs unusual large number of steps (20) to converge!
Iteration 20 / LogL: -1393.064 / Time: 0h:0m:3s
Finish initializing candidate tree set (19)
Current best tree score: -1387.353 / CPU time: 2.373
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0509739 secs using 99.89% CPU
Optimizing NNI: done in 0.0585711 secs using 99.95% CPU
Optimizing NNI: done in 0.02564 secs using 99.97% CPU
BETTER TREE FOUND at iteration 23: -1387.353
Optimizing NNI: done in 0.05546 secs using 99.87% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.351
Optimizing NNI: done in 0.013247 secs using 99.62% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 25: -1387.298
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UPDATE BEST LOG-LIKELIHOOD: -1387.298
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UPDATE BEST LOG-LIKELIHOOD: -1387.298
Iteration 30 / LogL: -1387.298 / Time: 0h:0m:3s (0h:0m:24s left)
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Iteration 40 / LogL: -1387.298 / Time: 0h:0m:4s (0h:0m:19s left)
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Iteration 50 / LogL: -1389.649 / Time: 0h:0m:4s (0h:0m:15s left)
Log-likelihood cutoff on original alignment: -1415.849
Optimizing NNI: done in 0.0121369 secs using 99.95% CPU
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Iteration 60 / LogL: -1387.509 / Time: 0h:0m:4s (0h:0m:12s left)
Optimizing NNI: done in 0.0219378 secs using 99.96% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.297
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UPDATE BEST LOG-LIKELIHOOD: -1387.297
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UPDATE BEST LOG-LIKELIHOOD: -1387.297
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Iteration 70 / LogL: -1387.474 / Time: 0h:0m:4s (0h:0m:10s left)
Optimizing NNI: done in 0.006356 secs using 99.97% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.297
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UPDATE BEST LOG-LIKELIHOOD: -1387.297
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Iteration 80 / LogL: -1387.301 / Time: 0h:0m:5s (0h:0m:9s left)
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Iteration 90 / LogL: -1387.297 / Time: 0h:0m:5s (0h:0m:8s left)
Optimizing NNI: done in 0.0232949 secs using 99.97% CPU
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Optimizing NNI: done in 0.047823 secs using 99.97% CPU
Iteration 100 / LogL: -1387.309 / Time: 0h:0m:5s (0h:0m:7s left)
Log-likelihood cutoff on original alignment: -1415.849
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.987
NOTE: UFBoot does not converge, continue at least 100 more iterations
Optimizing NNI: done in 0.0187011 secs using 99.96% CPU
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Iteration 110 / LogL: -1387.316 / Time: 0h:0m:6s (0h:0m:6s left)
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Iteration 120 / LogL: -1387.297 / Time: 0h:0m:6s (0h:0m:5s left)
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Iteration 130 / LogL: -1387.297 / Time: 0h:0m:6s (0h:0m:4s left)
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Iteration 140 / LogL: -1387.299 / Time: 0h:0m:6s (0h:0m:4s left)
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Iteration 150 / LogL: -1387.322 / Time: 0h:0m:7s (0h:0m:3s left)
Log-likelihood cutoff on original alignment: -1415.849
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Iteration 160 / LogL: -1387.298 / Time: 0h:0m:7s (0h:0m:3s left)
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Iteration 170 / LogL: -1387.307 / Time: 0h:0m:7s (0h:0m:2s left)
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UPDATE BEST LOG-LIKELIHOOD: -1387.297
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Iteration 180 / LogL: -1387.298 / Time: 0h:0m:8s (0h:0m:2s left)
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Iteration 190 / LogL: -1387.297 / Time: 0h:0m:8s (0h:0m:1s left)
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Iteration 200 / LogL: -1387.297 / Time: 0h:0m:8s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -1415.849
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.998
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Iteration 210 / LogL: -1387.297 / Time: 0h:0m:9s (0h:0m:3s left)
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Iteration 220 / LogL: -1387.297 / Time: 0h:0m:9s (0h:0m:3s left)
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TREE SEARCH COMPLETED AFTER 226 ITERATIONS / Time: 0h:0m:9s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.297
2. Current log-likelihood: -1387.275
3. Current log-likelihood: -1387.258
4. Current log-likelihood: -1387.243
5. Current log-likelihood: -1387.231
6. Current log-likelihood: -1387.221
Optimal log-likelihood: -1387.212
Rate parameters: A-C: 0.34657 A-G: 2.30026 A-T: 2.12337 C-G: 1.22217 C-T: 3.18610 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.001
Gamma shape alpha: 1.290
Parameters optimization took 6 rounds (0.020 sec)
BEST SCORE FOUND : -1387.212
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/tmpfcpmvo7j/q2iqtreeufboot.splits.nex
Total tree length: 7.604
Total number of iterations: 226
CPU time used for tree search: 8.889 sec (0h:0m:8s)
Wall-clock time used for tree search: 8.728 sec (0h:0m:8s)
Total CPU time used: 9.916 sec (0h:0m:9s)
Total wall-clock time used: 9.756 sec (0h:0m:9s)
Computing bootstrap consensus tree...
Reading input file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfcpmvo7j/q2iqtreeufboot.splits.nex...
20 taxa and 173 splits.
Consensus tree written to /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfcpmvo7j/q2iqtreeufboot.contree
Reading input trees file /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfcpmvo7j/q2iqtreeufboot.contree
Log-likelihood of consensus tree: -1387.213
Analysis results written to:
IQ-TREE report: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfcpmvo7j/q2iqtreeufboot.iqtree
Maximum-likelihood tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfcpmvo7j/q2iqtreeufboot.treefile
Likelihood distances: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfcpmvo7j/q2iqtreeufboot.mldist
Ultrafast bootstrap approximation results written to:
Split support values: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfcpmvo7j/q2iqtreeufboot.splits.nex
Consensus tree: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfcpmvo7j/q2iqtreeufboot.contree
Screen log file: /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfcpmvo7j/q2iqtreeufboot.log
Date and Time: Mon Feb 21 12:29:10 2022
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -bb 1000 -st DNA --runs 1 -s /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/qiime2-archive-lnml3hrr/d8ca197e-74a6-4812-bb37-1ce969a79906/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/9h/268zfwl56h37jwt5qv866jcr0000gp/T/tmpfcpmvo7j/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!