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/2023.9/tutorials/phylogeny/rep-seqs.qza
Save as: rep-seqs.qza
wget \
-O "rep-seqs.qza" \
"https://data.qiime2.org/2023.9/tutorials/phylogeny/rep-seqs.qza"
curl -sL \
"https://data.qiime2.org/2023.9/tutorials/phylogeny/rep-seqs.qza" > \
"rep-seqs.qza"
Run MAFFT
qiime alignment mafft \
--i-sequences rep-seqs.qza \
--o-alignment aligned-rep-seqs.qza
Reducing alignment ambiguity: masking and reference alignments¶
Why mask an alignment?
Masking helps to eliminate alignment columns that are phylogenetically uninformative or misleading before phylogenetic analysis. Much of the time alignment errors can introduce noise and confound phylogenetic inference. It is common practice to mask (remove) these ambiguously aligned regions prior to performing phylogenetic inference. In particular, David Lane’s (1991) chapter 16S/23S rRNA sequencing proposed masking SSU data prior to phylogenetic analysis. However, knowing how to deal with ambiguously aligned regions and when to apply masks largely depends on the marker genes being analyzed and the question being asked of the data.
Note
Keep in mind that this is still an active area of discussion, as highlighted by the following non-exhaustive list of articles: Wu et al. 2012, Ashkenazy et al. 2018, Schloss 2010, Tan et al. 2015, Rajan 2015.
How to mask alignment.
For our purposes, we’ll assume that we have ambiguously aligned columns in the
MAFFT alignment we produced above. The default settings for the
--p-min-conservation of the
alignment mask approximates the
Lane mask filtering of QIIME 1. Keep an eye out for updates to the alignment
plugin.
qiime alignment mask \
--i-alignment aligned-rep-seqs.qza \
--o-masked-alignment masked-aligned-rep-seqs.qza
Reference based alignments
There are several tools that attempt to reduce the amount of ambiguously aligned regions by using curated reference alignments. Traditional, de novo alignment methods mututally align a set of unaligned sequences to create a multiple sequence alignment (MSA) from scratch. Re-running these methods with additional sequences will create MSAs with varying numbers of columns and assignments of bases to each column. These alignments is therefore incompatible with one another and may not be joined through concatenation.
Reference based alignments, on the other hand, are meant to add sequences to an existing alignment. Alignments computed using reference based alignment tools always have widths identical to the reference alignment and maintain the meaning of each column. Therefore, these alignments may be concatenated.
QIIME 2 currently does not wrap any methods for reference-based alignments, but alignments created using these methods can be imported into QIIME 2 as FeatureData[AlignedSequence] artifacts, provided that the alignments are standard FASTA formats. Some examples of tools for reference-based alignment include PyNAST (using NAST), Infernal, and SINA. SILVA Reference
alignments are particularly powerful for rRNA gene sequence data, as knowledge
of secondary structure is incorporated into the curation process, thus
increasing alignment quality.
Note
Alignments constructed using reference based alignment approaches can be masked too, just like the above MAFFT example. Also, the reference alignment approach we are discussing here is distinct from the reference phylogeny approach (i.e. q2-fragment-insertion) we mentioned earlier. That is, we are not inserting our data into an existing tree, but simply trying to create a more robust alignment for making a better de novo phylogeny.
Construct a phylogeny¶
As with MSA algorithms, phylogenetic inference tools are also legion. Fortunately, there are many great resources to learn about phylogentics. Below are just a few introductory resources to get you started:
There are several methods / pipelines available through the q2-phylogeny plugin of :qiime2:. These are based on the following tools:
Methods¶
fasttree¶
FastTree is able to construct phylogenies from large sequence alignments quite rapidly. It does this by using the using a CAT-like rate category approximation, which is also available through RAxML (discussed below). Check out the FastTree online manual for more information.
qiime phylogeny fasttree \
--i-alignment masked-aligned-rep-seqs.qza \
--o-tree fasttree-tree.qza
Tip
For an easy and direct way to view your tree.qza files, upload
them to iTOL. Here, you can interactively view and manipulate your
phylogeny. Even better, while viewing the tree topology in “Normal mode”,
you can drag and drop your associated alignment.qza (the one you used to
build the phylogeny) or a relevent taxonomy.qza file onto the iTOL tree
visualization. This will allow you to directly view the sequence alignment
or taxonomy alongside the phylogeny. 🕶️
raxml¶
Like fasttree, raxml will perform a single phylogentic inference and
return a tree. Note, the default model for raxml is
--p-substitution-model GTRGAMMA. If you’d like to construct a tree using
the CAT model like fasttree, simply replace GTRGAMMA with GTRCAT as
shown below:
qiime phylogeny raxml \
--i-alignment masked-aligned-rep-seqs.qza \
--p-substitution-model GTRCAT \
--o-tree raxml-cat-tree.qza \
--verbose
stdout:
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Sarah Lutteropp (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
Charlie Taylor (UF)
Alignment has 157 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 39.77%
RAxML rapid hill-climbing mode
Using 1 distinct models/data partitions with joint branch length optimization
Executing 1 inferences on the original alignment using 1 distinct randomized MP trees
All free model parameters will be estimated by RAxML
ML estimate of 25 per site rate categories
Likelihood of final tree will be evaluated and optimized under GAMMA
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 157
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
raxmlHPC -m GTRCAT -p 6193 -N 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -w /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp1mbn_au1 -n q2
Partition: 0 with name: No Name Provided
Base frequencies: 0.243 0.182 0.319 0.256
Inference[0]: Time 0.560795 CAT-based likelihood -1243.159856, best rearrangement setting 5
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -1387.921095 tree written to file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp1mbn_au1/RAxML_result.q2
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -1387.921095 ....
Final GAMMA-based Score of best tree -1387.244907
Program execution info written to /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp1mbn_au1/RAxML_info.q2
Best-scoring ML tree written to: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp1mbn_au1/RAxML_bestTree.q2
Overall execution time: 1.133656 secs or 0.000315 hours or 0.000013 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 6193 -N 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -w /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp1mbn_au1 -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/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -w /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp29dpg6al -n q2
Partition: 0 with name: No Name Provided
Base frequencies: 0.243 0.182 0.319 0.256
Inference[0]: Time 0.601734 CAT-based likelihood -1238.242991, best rearrangement setting 5
Inference[1]: Time 0.603768 CAT-based likelihood -1249.502284, best rearrangement setting 5
Inference[2]: Time 0.463911 CAT-based likelihood -1242.978035, best rearrangement setting 5
Inference[3]: Time 0.500115 CAT-based likelihood -1243.159855, best rearrangement setting 5
Inference[4]: Time 0.369468 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/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp29dpg6al/RAxML_result.q2.RUN.0
Inference[1] final GAMMA-based Likelihood: -1392.813982 tree written to file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp29dpg6al/RAxML_result.q2.RUN.1
Inference[2] final GAMMA-based Likelihood: -1388.073642 tree written to file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp29dpg6al/RAxML_result.q2.RUN.2
Inference[3] final GAMMA-based Likelihood: -1387.945266 tree written to file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp29dpg6al/RAxML_result.q2.RUN.3
Inference[4] final GAMMA-based Likelihood: -1387.557031 tree written to file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp29dpg6al/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/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp29dpg6al/RAxML_info.q2
Best-scoring ML tree written to: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp29dpg6al/RAxML_bestTree.q2
Overall execution time: 3.095985 secs or 0.000860 hours or 0.000036 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/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -w /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp29dpg6al -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/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -w /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp2wtf6xaz -n q2bootstrap
Time for BS model parameter optimization 0.041756
Bootstrap[0]: Time 0.142858 seconds, bootstrap likelihood -1199.758796, best rearrangement setting 12
Bootstrap[1]: Time 0.098568 seconds, bootstrap likelihood -1344.229251, best rearrangement setting 6
Bootstrap[2]: Time 0.089263 seconds, bootstrap likelihood -1295.343000, best rearrangement setting 8
Bootstrap[3]: Time 0.080156 seconds, bootstrap likelihood -1273.768320, best rearrangement setting 8
Bootstrap[4]: Time 0.085367 seconds, bootstrap likelihood -1253.402952, best rearrangement setting 6
Bootstrap[5]: Time 0.092213 seconds, bootstrap likelihood -1260.866113, best rearrangement setting 10
Bootstrap[6]: Time 0.093784 seconds, bootstrap likelihood -1293.636299, best rearrangement setting 14
Bootstrap[7]: Time 0.084976 seconds, bootstrap likelihood -1227.178693, best rearrangement setting 6
Bootstrap[8]: Time 0.096603 seconds, bootstrap likelihood -1321.820787, best rearrangement setting 13
Bootstrap[9]: Time 0.094339 seconds, bootstrap likelihood -1147.233446, best rearrangement setting 6
Bootstrap[10]: Time 0.066820 seconds, bootstrap likelihood -1220.766493, best rearrangement setting 13
Bootstrap[11]: Time 0.096941 seconds, bootstrap likelihood -1200.006355, best rearrangement setting 8
Bootstrap[12]: Time 0.106260 seconds, bootstrap likelihood -1346.392834, best rearrangement setting 14
Bootstrap[13]: Time 0.087336 seconds, bootstrap likelihood -1301.111096, best rearrangement setting 14
Bootstrap[14]: Time 0.093865 seconds, bootstrap likelihood -1262.253559, best rearrangement setting 11
Bootstrap[15]: Time 0.094338 seconds, bootstrap likelihood -1215.017551, best rearrangement setting 14
Bootstrap[16]: Time 0.078193 seconds, bootstrap likelihood -1238.832009, best rearrangement setting 7
Bootstrap[17]: Time 0.068992 seconds, bootstrap likelihood -1393.989732, best rearrangement setting 12
Bootstrap[18]: Time 0.070935 seconds, bootstrap likelihood -1173.921002, best rearrangement setting 15
Bootstrap[19]: Time 0.077066 seconds, bootstrap likelihood -1185.726976, best rearrangement setting 11
Bootstrap[20]: Time 0.070720 seconds, bootstrap likelihood -1158.491940, best rearrangement setting 6
Bootstrap[21]: Time 0.068553 seconds, bootstrap likelihood -1154.664272, best rearrangement setting 11
Bootstrap[22]: Time 0.076756 seconds, bootstrap likelihood -1244.159837, best rearrangement setting 10
Bootstrap[23]: Time 0.088874 seconds, bootstrap likelihood -1211.171036, best rearrangement setting 15
Bootstrap[24]: Time 0.075300 seconds, bootstrap likelihood -1261.440677, best rearrangement setting 12
Bootstrap[25]: Time 0.074686 seconds, bootstrap likelihood -1331.836715, best rearrangement setting 15
Bootstrap[26]: Time 0.077408 seconds, bootstrap likelihood -1129.144509, best rearrangement setting 5
Bootstrap[27]: Time 0.094202 seconds, bootstrap likelihood -1226.624056, best rearrangement setting 7
Bootstrap[28]: Time 0.094468 seconds, bootstrap likelihood -1221.046176, best rearrangement setting 12
Bootstrap[29]: Time 0.068129 seconds, bootstrap likelihood -1211.791204, best rearrangement setting 14
Bootstrap[30]: Time 0.085406 seconds, bootstrap likelihood -1389.442380, best rearrangement setting 5
Bootstrap[31]: Time 0.086026 seconds, bootstrap likelihood -1303.638592, best rearrangement setting 12
Bootstrap[32]: Time 0.089506 seconds, bootstrap likelihood -1172.859456, best rearrangement setting 12
Bootstrap[33]: Time 0.074756 seconds, bootstrap likelihood -1244.617135, best rearrangement setting 9
Bootstrap[34]: Time 0.071238 seconds, bootstrap likelihood -1211.871717, best rearrangement setting 15
Bootstrap[35]: Time 0.086106 seconds, bootstrap likelihood -1299.862912, best rearrangement setting 5
Bootstrap[36]: Time 0.066697 seconds, bootstrap likelihood -1141.967505, best rearrangement setting 5
Bootstrap[37]: Time 0.086854 seconds, bootstrap likelihood -1283.923198, best rearrangement setting 12
Bootstrap[38]: Time 0.067726 seconds, bootstrap likelihood -1304.250946, best rearrangement setting 5
Bootstrap[39]: Time 0.065663 seconds, bootstrap likelihood -1407.084376, best rearrangement setting 15
Bootstrap[40]: Time 0.077608 seconds, bootstrap likelihood -1277.946299, best rearrangement setting 13
Bootstrap[41]: Time 0.076321 seconds, bootstrap likelihood -1279.006200, best rearrangement setting 7
Bootstrap[42]: Time 0.073227 seconds, bootstrap likelihood -1160.274606, best rearrangement setting 6
Bootstrap[43]: Time 0.089519 seconds, bootstrap likelihood -1216.079259, best rearrangement setting 14
Bootstrap[44]: Time 0.069083 seconds, bootstrap likelihood -1382.278311, best rearrangement setting 8
Bootstrap[45]: Time 0.078914 seconds, bootstrap likelihood -1099.004439, best rearrangement setting 11
Bootstrap[46]: Time 0.062524 seconds, bootstrap likelihood -1296.527478, best rearrangement setting 8
Bootstrap[47]: Time 0.092570 seconds, bootstrap likelihood -1291.322658, best rearrangement setting 9
Bootstrap[48]: Time 0.062766 seconds, bootstrap likelihood -1161.908080, best rearrangement setting 6
Bootstrap[49]: Time 0.085277 seconds, bootstrap likelihood -1257.348428, best rearrangement setting 13
Bootstrap[50]: Time 0.095625 seconds, bootstrap likelihood -1309.422533, best rearrangement setting 13
Bootstrap[51]: Time 0.070469 seconds, bootstrap likelihood -1197.633097, best rearrangement setting 11
Bootstrap[52]: Time 0.079098 seconds, bootstrap likelihood -1347.123005, best rearrangement setting 8
Bootstrap[53]: Time 0.069565 seconds, bootstrap likelihood -1234.934890, best rearrangement setting 14
Bootstrap[54]: Time 0.083919 seconds, bootstrap likelihood -1227.092434, best rearrangement setting 6
Bootstrap[55]: Time 0.084724 seconds, bootstrap likelihood -1280.635747, best rearrangement setting 7
Bootstrap[56]: Time 0.070057 seconds, bootstrap likelihood -1225.911449, best rearrangement setting 6
Bootstrap[57]: Time 0.069331 seconds, bootstrap likelihood -1236.213347, best rearrangement setting 11
Bootstrap[58]: Time 0.101723 seconds, bootstrap likelihood -1393.245723, best rearrangement setting 14
Bootstrap[59]: Time 0.077167 seconds, bootstrap likelihood -1212.039371, best rearrangement setting 6
Bootstrap[60]: Time 0.067722 seconds, bootstrap likelihood -1248.692011, best rearrangement setting 10
Bootstrap[61]: Time 0.078876 seconds, bootstrap likelihood -1172.820979, best rearrangement setting 13
Bootstrap[62]: Time 0.090732 seconds, bootstrap likelihood -1126.745788, best rearrangement setting 14
Bootstrap[63]: Time 0.072222 seconds, bootstrap likelihood -1267.434444, best rearrangement setting 12
Bootstrap[64]: Time 0.070899 seconds, bootstrap likelihood -1340.680748, best rearrangement setting 5
Bootstrap[65]: Time 0.072692 seconds, bootstrap likelihood -1072.671059, best rearrangement setting 5
Bootstrap[66]: Time 0.088014 seconds, bootstrap likelihood -1234.294838, best rearrangement setting 8
Bootstrap[67]: Time 0.088848 seconds, bootstrap likelihood -1109.249439, best rearrangement setting 15
Bootstrap[68]: Time 0.067255 seconds, bootstrap likelihood -1314.493588, best rearrangement setting 8
Bootstrap[69]: Time 0.068437 seconds, bootstrap likelihood -1173.850035, best rearrangement setting 13
Bootstrap[70]: Time 0.071686 seconds, bootstrap likelihood -1231.066465, best rearrangement setting 10
Bootstrap[71]: Time 0.072364 seconds, bootstrap likelihood -1146.861379, best rearrangement setting 9
Bootstrap[72]: Time 0.071450 seconds, bootstrap likelihood -1148.753369, best rearrangement setting 8
Bootstrap[73]: Time 0.075534 seconds, bootstrap likelihood -1333.374056, best rearrangement setting 9
Bootstrap[74]: Time 0.066061 seconds, bootstrap likelihood -1259.382378, best rearrangement setting 5
Bootstrap[75]: Time 0.077102 seconds, bootstrap likelihood -1319.944496, best rearrangement setting 6
Bootstrap[76]: Time 0.084699 seconds, bootstrap likelihood -1309.042165, best rearrangement setting 14
Bootstrap[77]: Time 0.099674 seconds, bootstrap likelihood -1232.061289, best rearrangement setting 8
Bootstrap[78]: Time 0.080914 seconds, bootstrap likelihood -1261.333984, best rearrangement setting 9
Bootstrap[79]: Time 0.082087 seconds, bootstrap likelihood -1194.644341, best rearrangement setting 13
Bootstrap[80]: Time 0.073970 seconds, bootstrap likelihood -1214.037389, best rearrangement setting 9
Bootstrap[81]: Time 0.078814 seconds, bootstrap likelihood -1224.527657, best rearrangement setting 8
Bootstrap[82]: Time 0.094777 seconds, bootstrap likelihood -1241.464826, best rearrangement setting 11
Bootstrap[83]: Time 0.071318 seconds, bootstrap likelihood -1230.730558, best rearrangement setting 6
Bootstrap[84]: Time 0.078332 seconds, bootstrap likelihood -1219.034592, best rearrangement setting 10
Bootstrap[85]: Time 0.081425 seconds, bootstrap likelihood -1280.071994, best rearrangement setting 8
Bootstrap[86]: Time 0.069263 seconds, bootstrap likelihood -1444.747777, best rearrangement setting 9
Bootstrap[87]: Time 0.071189 seconds, bootstrap likelihood -1245.890035, best rearrangement setting 14
Bootstrap[88]: Time 0.080651 seconds, bootstrap likelihood -1287.832766, best rearrangement setting 7
Bootstrap[89]: Time 0.071598 seconds, bootstrap likelihood -1325.245976, best rearrangement setting 5
Bootstrap[90]: Time 0.081102 seconds, bootstrap likelihood -1227.883697, best rearrangement setting 5
Bootstrap[91]: Time 0.078872 seconds, bootstrap likelihood -1273.489392, best rearrangement setting 8
Bootstrap[92]: Time 0.029973 seconds, bootstrap likelihood -1234.725870, best rearrangement setting 7
Bootstrap[93]: Time 0.083925 seconds, bootstrap likelihood -1235.733064, best rearrangement setting 11
Bootstrap[94]: Time 0.070626 seconds, bootstrap likelihood -1204.319488, best rearrangement setting 15
Bootstrap[95]: Time 0.066394 seconds, bootstrap likelihood -1183.328582, best rearrangement setting 11
Bootstrap[96]: Time 0.078019 seconds, bootstrap likelihood -1196.298898, best rearrangement setting 13
Bootstrap[97]: Time 0.083404 seconds, bootstrap likelihood -1339.251746, best rearrangement setting 12
Bootstrap[98]: Time 0.031670 seconds, bootstrap likelihood -1404.363552, best rearrangement setting 7
Bootstrap[99]: Time 0.039689 seconds, bootstrap likelihood -1270.157811, best rearrangement setting 7
Overall Time for 100 Rapid Bootstraps 7.910136 seconds
Average Time per Rapid Bootstrap 0.079101 seconds
Starting ML Search ...
Fast ML optimization finished
Fast ML search Time: 3.202385 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: 1.619862 seconds
Thorough ML search Time: 0.436857 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 5.262061 secs or 0.001462 hours
Combined Bootstrap and ML search took 13.172523 secs or 0.003659 hours
Drawing Bootstrap Support Values on best-scoring ML tree ...
Found 1 tree in File /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp2wtf6xaz/RAxML_bestTree.q2bootstrap
Found 1 tree in File /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp2wtf6xaz/RAxML_bestTree.q2bootstrap
Program execution info written to /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp2wtf6xaz/RAxML_info.q2bootstrap
All 100 bootstrapped trees written to: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp2wtf6xaz/RAxML_bootstrap.q2bootstrap
Best-scoring ML tree written to: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp2wtf6xaz/RAxML_bestTree.q2bootstrap
Best-scoring ML tree with support values written to: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp2wtf6xaz/RAxML_bipartitions.q2bootstrap
Best-scoring ML tree with support values as branch labels written to: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp2wtf6xaz/RAxML_bipartitionsBranchLabels.q2bootstrap
Overall execution time for full ML analysis: 13.180730 secs or 0.003661 hours or 0.000153 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/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -w /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp2wtf6xaz -n q2bootstrap
Saved Phylogeny[Unrooted] to: raxml-cat-bootstrap-tree.qza
Tip
Optimizing RAxML Run Time.
You may gave noticed that we haven’t added the flag --p-raxml-version to
the RAxML methods. This parameter provides a means to access versions of
RAxML that have optimized vector instructions for various modern x86
processor architectures. Paraphrased from the RAxML manual and help
documentation: Firstly, most recent processors will support SSE3 vector
instructions (i.e. will likely support the faster AVX2 vector instructions).
Secondly, these instructions will substantially accelerate the likelihood
and parsimony computations. In general, SSE3 versions will run approximately
40% faster than the standard version. The AVX2 version will run 10-30%
faster than the SSE3 version. Additionally, keep in mind that using more
cores / threads will not necessarily decrease run time. The RAxML manual
suggests using 1 core per ~500 DNA alignment patterns. Alignment pattern
information is usually visible on screen, when the --verbose option is
used. Additionally, try using a rate category (CAT model; via
--p-substitution-model), which results in equally good trees as the
GAMMA models and is approximately 4 times faster. See the CAT paper. The
CAT approximation is also Ideal for alignments containing 10,000 or more
taxa, and is very much similar the CAT-like model of FastTree2.
iqtree¶
Similar to the raxml and raxml-rapid-bootstrap methods above, we
provide similar functionality for IQ-TREE: iqtree and
iqtree-ultrafast-bootstrap. IQ-TREE is unique compared to the fastree
and raxml options, in that it provides access to 286 models of nucleotide
substitution! IQ-TREE can also determine which of these models best fits your
dataset prior to constructing your tree via its built-in ModelFinder
algorithm. This is the default in QIIME 2, but do not worry, you can set any
one of the 286 models of nucleotide substitution via the
--p-substitution-model flag, e.g. you can set the model as HKY+I+G
instead of the default MFP (a basic short-hand for: “build a phylogeny
after determining the best fit model as determined by ModelFinder”). Keep in
mind the additional computational time required for model testing via
ModelFinder.
The simplest way to run the
iqtree command with default
settings and automatic model selection (MFP) is like so:
qiime phylogeny iqtree \
--i-alignment masked-aligned-rep-seqs.qza \
--o-tree iqt-tree.qza \
--verbose
stdout:
IQ-TREE multicore version 2.2.5 COVID-edition for Mac OS X 64-bit built Sep 15 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: Elizabeths-MacBook-Pro-2.local (AVX512, FMA3, 32 GB RAM)
Command: iqtree -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpma0q71zi/q2iqtree -nt 1
Seed: 932848 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Nov 16 16:36:12 2023
Kernel: AVX+FMA - 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/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000634909 secs using 20.63% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000233173 secs using 69.05% 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 1.19209e-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 6.50883e-05 secs using 55.31% 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 0.00929499 secs using 96.17% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1389.703
Optimal log-likelihood: -1388.843
Rate parameters: A-C: 0.35840 A-G: 2.36329 A-T: 2.12617 C-G: 1.22968 C-T: 3.29817 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.034
Gamma shape alpha: 1.424
Parameters optimization took 1 rounds (0.005 sec)
Time for fast ML tree search: 0.032 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 484 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1402.574 45 2895.147 2919.790 3046.616
2 GTR+F+I 1401.119 46 2894.238 2920.130 3049.072
3 GTR+F+G4 1387.362 46 2866.724 2892.616 3021.558
4 GTR+F+I+G4 1387.729 47 2869.457 2896.638 3027.658
5 GTR+F+R2 1382.368 47 2858.736 2885.917 3016.937
6 GTR+F+R3 1382.422 49 2862.845 2892.723 3027.777
14 GTR+F+I+R2 1382.420 48 2860.839 2889.349 3022.406
15 GTR+F+I+R3 1382.451 50 2864.902 2896.190 3033.201
25 SYM+G4 1387.133 43 2860.266 2882.525 3005.003
27 SYM+R2 1383.095 44 2854.190 2877.621 3002.292
36 SYM+I+R2 1383.227 45 2856.454 2881.097 3007.923
47 TVM+F+G4 1388.357 45 2866.713 2891.356 3018.182
49 TVM+F+R2 1383.790 46 2859.580 2885.472 3014.415
58 TVM+F+I+R2 1383.813 47 2861.626 2888.806 3019.826
69 TVMe+G4 1387.121 42 2858.243 2879.366 2999.614
71 TVMe+R2 1383.080 43 2852.159 2874.418 2996.896
80 TVMe+I+R2 1383.224 44 2854.449 2877.881 3002.552
91 TIM3+F+G4 1391.377 44 2870.754 2894.186 3018.857
93 TIM3+F+R2 1385.913 45 2861.826 2886.469 3013.295
102 TIM3+F+I+R2 1386.042 46 2864.083 2889.976 3018.918
113 TIM3e+G4 1390.357 41 2862.713 2882.736 3000.718
115 TIM3e+R2 1385.918 42 2855.835 2876.958 2997.206
124 TIM3e+I+R2 1386.072 43 2858.145 2880.404 3002.882
135 TIM2+F+G4 1393.635 44 2875.271 2898.703 3023.374
137 TIM2+F+R2 1387.682 45 2865.363 2890.006 3016.832
146 TIM2+F+I+R2 1387.782 46 2867.565 2893.457 3022.400
157 TIM2e+G4 1396.794 41 2875.588 2895.611 3013.593
159 TIM2e+R2 1391.573 42 2867.147 2888.270 3008.518
168 TIM2e+I+R2 1391.651 43 2869.302 2891.561 3014.039
179 TIM+F+G4 1390.364 44 2868.727 2892.159 3016.830
181 TIM+F+R2 1384.935 45 2859.870 2884.512 3011.338
190 TIM+F+I+R2 1385.017 46 2862.035 2887.927 3016.870
201 TIMe+G4 1394.002 41 2870.004 2890.027 3008.009
203 TIMe+R2 1389.000 42 2862.001 2883.123 3003.372
212 TIMe+I+R2 1389.095 43 2864.190 2886.449 3008.927
223 TPM3u+F+G4 1392.305 43 2870.611 2892.870 3015.348
225 TPM3u+F+R2 1387.330 44 2862.659 2886.091 3010.762
234 TPM3u+F+I+R2 1387.462 45 2864.924 2889.567 3016.393
245 TPM3+G4 1390.373 40 2860.746 2879.706 2995.385
247 TPM3+R2 1385.925 41 2853.850 2873.873 2991.855
256 TPM3+I+R2 1386.070 42 2856.140 2877.263 2997.511
267 TPM2u+F+G4 1394.533 43 2875.067 2897.326 3019.804
269 TPM2u+F+R2 1389.057 44 2866.114 2889.546 3014.217
278 TPM2u+F+I+R2 1389.101 45 2868.202 2892.845 3019.671
289 TPM2+G4 1396.823 40 2873.645 2892.605 3008.284
291 TPM2+R2 1391.577 41 2865.155 2885.178 3003.160
300 TPM2+I+R2 1391.649 42 2867.297 2888.420 3008.668
311 K3Pu+F+G4 1391.381 43 2868.762 2891.021 3013.499
313 K3Pu+F+R2 1386.372 44 2860.743 2884.175 3008.846
322 K3Pu+F+I+R2 1386.425 45 2862.851 2887.494 3014.320
333 K3P+G4 1394.015 40 2868.030 2886.989 3002.669
335 K3P+R2 1389.002 41 2860.005 2880.028 2998.010
344 K3P+I+R2 1389.099 42 2862.198 2883.320 3003.569
355 TN+F+G4 1394.039 43 2874.077 2896.336 3018.814
357 TN+F+R2 1388.242 44 2864.484 2887.916 3012.587
366 TN+F+I+R2 1388.289 45 2866.579 2891.221 3018.048
377 TNe+G4 1396.791 40 2873.581 2892.541 3008.220
379 TNe+R2 1391.586 41 2865.171 2885.195 3003.176
388 TNe+I+R2 1391.666 42 2867.332 2888.454 3008.703
399 HKY+F+G4 1394.951 42 2873.902 2895.024 3015.273
401 HKY+F+R2 1389.609 43 2865.218 2887.477 3009.955
410 HKY+F+I+R2 1389.664 44 2867.327 2890.759 3015.430
421 K2P+G4 1396.824 39 2871.648 2889.579 3002.921
423 K2P+R2 1391.594 40 2863.189 2882.148 2997.828
432 K2P+I+R2 1391.664 41 2865.327 2885.351 3003.332
443 F81+F+G4 1405.743 41 2893.487 2913.510 3031.492
445 F81+F+R2 1400.806 42 2885.613 2906.736 3026.984
454 F81+F+I+R2 1400.909 43 2887.818 2910.077 3032.555
465 JC+G4 1407.650 38 2891.300 2908.237 3019.207
467 JC+R2 1402.858 39 2883.716 2901.648 3014.990
476 JC+I+R2 1402.926 40 2885.852 2904.812 3020.491
Akaike Information Criterion: TVMe+R2
Corrected Akaike Information Criterion: TPM3+R2
Bayesian Information Criterion: TPM3+R2
Best-fit model: TPM3+R2 chosen according to BIC
All model information printed to /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpma0q71zi/q2iqtree.model.gz
CPU time for ModelFinder: 0.902 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.957 seconds (0h:0m:0s)
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1385.925
Optimal log-likelihood: -1385.924
Rate parameters: A-C: 0.40868 A-G: 1.56207 A-T: 1.00000 C-G: 0.40868 C-T: 1.56207 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.716,0.409) (0.284,2.491)
Parameters optimization took 1 rounds (0.002 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000628948 secs using 93.97% CPU
Computing ML distances took 0.000687 sec (of wall-clock time) 0.000631 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 2.88486e-05 secs using 79.73% CPU
Constructing RapidNJ tree: done in 5.31673e-05 secs using 103.4% CPU
Computing RapidNJ tree took 0.000127 sec (of wall-clock time) 0.000104 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.820
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.082 second
Computing log-likelihood of 98 initial trees ... 0.063 seconds
Current best score: -1385.924
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00324702 secs using 174.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.880
Optimizing NNI: done in 0.00790906 secs using 189.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1385.311
Optimizing NNI: done in 0.010155 secs using 138.4% CPU
Optimizing NNI: done in 0.00915003 secs using 178.6% CPU
Optimizing NNI: done in 0.00820994 secs using 185.8% CPU
Optimizing NNI: done in 0.00830603 secs using 97.65% CPU
Optimizing NNI: done in 0.00744581 secs using 95.23% CPU
Optimizing NNI: done in 0.00882483 secs using 97.36% CPU
Optimizing NNI: done in 0.00931621 secs using 98.75% CPU
Optimizing NNI: done in 0.0079 secs using 97.84% CPU
Iteration 10 / LogL: -1385.335 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00709701 secs using 96.56% CPU
Optimizing NNI: done in 0.00675821 secs using 97.53% CPU
Optimizing NNI: done in 0.00693512 secs using 98.9% CPU
Optimizing NNI: done in 0.00803614 secs using 96.74% CPU
Optimizing NNI: done in 0.0108089 secs using 97.97% CPU
Optimizing NNI: done in 0.00896502 secs using 95.74% CPU
Optimizing NNI: done in 0.00787187 secs using 96.43% CPU
Optimizing NNI: done in 0.00617099 secs using 99.97% CPU
Optimizing NNI: done in 0.00734591 secs using 92.91% CPU
Optimizing NNI: done in 0.00740004 secs using 98.12% CPU
Iteration 20 / LogL: -1385.345 / Time: 0h:0m:0s
Finish initializing candidate tree set (2)
Current best tree score: -1385.311 / CPU time: 0.319
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0130522 secs using 99.14% CPU
Optimizing NNI: done in 0.00945401 secs using 96.49% CPU
Optimizing NNI: done in 0.012037 secs using 97.05% CPU
Optimizing NNI: done in 0.0108941 secs using 96.05% CPU
Optimizing NNI: done in 0.0091958 secs using 96.04% CPU
Optimizing NNI: done in 0.00826597 secs using 98.58% CPU
Optimizing NNI: done in 0.00617814 secs using 99.17% CPU
Optimizing NNI: done in 0.00718212 secs using 98.13% CPU
Optimizing NNI: done in 0.00942278 secs using 99.84% CPU
Optimizing NNI: done in 0.0124421 secs using 99.73% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.311
Iteration 30 / LogL: -1385.311 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.00855112 secs using 97.99% CPU
Optimizing NNI: done in 0.0060811 secs using 99.29% CPU
Optimizing NNI: done in 0.00941181 secs using 99.87% CPU
Optimizing NNI: done in 0.00554085 secs using 99.77% CPU
Optimizing NNI: done in 0.00994205 secs using 99.86% CPU
Optimizing NNI: done in 0.00746393 secs using 98.49% CPU
Optimizing NNI: done in 0.00778699 secs using 99.91% CPU
Optimizing NNI: done in 0.00794697 secs using 99.84% CPU
Optimizing NNI: done in 0.00850487 secs using 99.51% CPU
Optimizing NNI: done in 0.0101709 secs using 98.72% CPU
Iteration 40 / LogL: -1385.871 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00786901 secs using 99.72% CPU
Optimizing NNI: done in 0.0086689 secs using 99.3% CPU
Optimizing NNI: done in 0.00480795 secs using 99.9% CPU
Optimizing NNI: done in 0.00841808 secs using 99.96% CPU
Optimizing NNI: done in 0.00627398 secs using 99.9% CPU
Optimizing NNI: done in 0.00565481 secs using 99.91% CPU
Optimizing NNI: done in 0.00835991 secs using 99.94% CPU
Optimizing NNI: done in 0.00711894 secs using 99.03% CPU
Optimizing NNI: done in 0.0103271 secs using 97.15% CPU
Optimizing NNI: done in 0.00669694 secs using 99.93% CPU
Iteration 50 / LogL: -1385.843 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00453806 secs using 99.73% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.311
Optimizing NNI: done in 0.00608087 secs using 99.82% CPU
Optimizing NNI: done in 0.00710297 secs using 98.71% CPU
Optimizing NNI: done in 0.0109499 secs using 99.94% CPU
Optimizing NNI: done in 0.0100899 secs using 99.93% CPU
Optimizing NNI: done in 0.0124059 secs using 99.48% CPU
Optimizing NNI: done in 0.00855184 secs using 97.49% CPU
Optimizing NNI: done in 0.00729012 secs using 99.92% CPU
Optimizing NNI: done in 0.00953007 secs using 99.29% CPU
Optimizing NNI: done in 0.00835395 secs using 99.47% CPU
Iteration 60 / LogL: -1385.929 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00910997 secs using 99.93% CPU
Optimizing NNI: done in 0.00758791 secs using 99.92% CPU
Optimizing NNI: done in 0.00631499 secs using 99.92% CPU
Optimizing NNI: done in 0.010323 secs using 99.51% CPU
Optimizing NNI: done in 0.00546193 secs using 99.85% CPU
Optimizing NNI: done in 0.0117581 secs using 99.45% CPU
Optimizing NNI: done in 0.00754213 secs using 99.92% CPU
Optimizing NNI: done in 0.00718021 secs using 99.91% CPU
Optimizing NNI: done in 0.00671101 secs using 99.93% CPU
Optimizing NNI: done in 0.00898981 secs using 99.95% CPU
Iteration 70 / LogL: -1385.935 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00786901 secs using 99.94% CPU
Optimizing NNI: done in 0.0114601 secs using 98.96% CPU
Optimizing NNI: done in 0.00747013 secs using 99.61% CPU
Optimizing NNI: done in 0.00689197 secs using 99.57% CPU
Optimizing NNI: done in 0.0119381 secs using 99.4% CPU
Optimizing NNI: done in 0.00750399 secs using 99.84% CPU
Optimizing NNI: done in 0.0106709 secs using 99.05% CPU
Optimizing NNI: done in 0.0106881 secs using 99.92% CPU
Optimizing NNI: done in 0.00805306 secs using 99.96% CPU
Optimizing NNI: done in 0.0107741 secs using 96.81% CPU
Iteration 80 / LogL: -1385.703 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00952816 secs using 99.07% CPU
Optimizing NNI: done in 0.00772595 secs using 99.64% CPU
Optimizing NNI: done in 0.00895095 secs using 99.91% CPU
Optimizing NNI: done in 0.0100121 secs using 99.93% CPU
Optimizing NNI: done in 0.0116889 secs using 99.95% CPU
Optimizing NNI: done in 0.00901198 secs using 99.72% CPU
Optimizing NNI: done in 0.010113 secs using 98.34% CPU
Optimizing NNI: done in 0.010334 secs using 99.52% CPU
Optimizing NNI: done in 0.00690198 secs using 99.93% CPU
Optimizing NNI: done in 0.0122731 secs using 99.76% CPU
Iteration 90 / LogL: -1385.931 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00906992 secs using 99.96% CPU
Optimizing NNI: done in 0.00720811 secs using 99.86% CPU
Optimizing NNI: done in 0.00927901 secs using 99.92% CPU
Optimizing NNI: done in 0.00618219 secs using 99.95% CPU
Optimizing NNI: done in 0.00991988 secs using 98.96% CPU
Optimizing NNI: done in 0.00837994 secs using 99.05% CPU
Optimizing NNI: done in 0.0100539 secs using 99.65% CPU
Optimizing NNI: done in 0.011126 secs using 99.8% CPU
Optimizing NNI: done in 0.00714087 secs using 99.92% CPU
Optimizing NNI: done in 0.00879812 secs using 99.25% CPU
Iteration 100 / LogL: -1385.951 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00929594 secs using 99.83% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.311
Optimizing NNI: done in 0.00619698 secs using 99.56% CPU
Optimizing NNI: done in 0.00911999 secs using 99.01% CPU
TREE SEARCH COMPLETED AFTER 103 ITERATIONS / Time: 0h:0m:1s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1385.311
Optimal log-likelihood: -1385.306
Rate parameters: A-C: 0.39448 A-G: 1.56666 A-T: 1.00000 C-G: 0.39448 C-T: 1.56666 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.721,0.402) (0.279,2.542)
Parameters optimization took 1 rounds (0.002 sec)
BEST SCORE FOUND : -1385.306
Total tree length: 6.846
Total number of iterations: 103
CPU time used for tree search: 1.212 sec (0h:0m:1s)
Wall-clock time used for tree search: 1.076 sec (0h:0m:1s)
Total CPU time used: 1.229 sec (0h:0m:1s)
Total wall-clock time used: 1.091 sec (0h:0m:1s)
Analysis results written to:
IQ-TREE report: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpma0q71zi/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpma0q71zi/q2iqtree.treefile
Likelihood distances: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpma0q71zi/q2iqtree.mldist
Screen log file: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpma0q71zi/q2iqtree.log
Date and Time: Thu Nov 16 16:36:14 2023
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpma0q71zi/q2iqtree -nt 1
Saved Phylogeny[Unrooted] to: iqt-tree.qza
Specifying a substitution model¶
We can also set a substitution model of our choosing. You may have noticed
while watching the onscreen output of the previous command that the best
fitting model selected by ModelFinder is noted. For the sake of argument, let’s
say the best selected model was shown as GTR+F+I+G4. The F is only a
notation to let us know that if a given model supports unequal base
frequencies, then the empirical base frequencies will be used by default.
Using empirical base frequencies (F), rather than estimating them, greatly
reduces computational time. The iqtree plugin will not accept F within
the model notation supplied at the command line, as this will always be implied
automatically for the appropriate model. Also, the iqtree plugin only
accepts G not G4 to be specified within the model notation. The 4
is simply another explicit notation to remind us that four rate categories are
being assumed by default. The notation approach used by the plugin simply helps
to retain simplicity and familiarity when supplying model notations on the
command line. So, in brief, we only have to type GTR+I+G as our input
model:
qiime phylogeny iqtree \
--i-alignment masked-aligned-rep-seqs.qza \
--p-substitution-model 'GTR+I+G' \
--o-tree iqt-gtrig-tree.qza \
--verbose
stdout:
IQ-TREE multicore version 2.2.5 COVID-edition for Mac OS X 64-bit built Sep 15 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: Elizabeths-MacBook-Pro-2.local (AVX512, FMA3, 32 GB RAM)
Command: iqtree -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpuyuvyt4f/q2iqtree -nt 1
Seed: 649482 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Nov 16 16:36:23 2023
Kernel: AVX+FMA - 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/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000159025 secs using 81.12% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000333071 secs using 53.44% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 1.09673e-05 secs using 82.06% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 3.8147e-05 secs using 68.16% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Thoroughly optimizing +I+G parameters from 10 start values...
Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 1.218 / LogL: -1394.499
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.008, 1.293 / LogL: -1394.744
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.008, 1.296 / LogL: -1394.739
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.008, 1.294 / LogL: -1394.737
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.008, 1.301 / LogL: -1394.766
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.007, 1.297 / LogL: -1394.718
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.008, 1.299 / LogL: -1394.735
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.008, 1.301 / LogL: -1394.747
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.008, 1.304 / LogL: -1394.750
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.008, 1.307 / LogL: -1394.761
Optimal pinv,alpha: 0.000, 1.218 / LogL: -1394.499
Parameters optimization took 0.335 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000892878 secs using 98.33% CPU
Computing ML distances took 0.000957 sec (of wall-clock time) 0.000923 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 2.88486e-05 secs using 79.73% CPU
Constructing RapidNJ tree: done in 5.48363e-05 secs using 147.7% CPU
Computing RapidNJ tree took 0.000129 sec (of wall-clock time) 0.000132 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.880
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.075 second
Computing log-likelihood of 98 initial trees ... 0.081 seconds
Current best score: -1392.880
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.013232 secs using 179.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.268
Optimizing NNI: done in 0.00571918 secs using 173.3% CPU
Optimizing NNI: done in 0.0089469 secs using 178.1% CPU
Optimizing NNI: done in 0.00766516 secs using 96.27% CPU
Optimizing NNI: done in 0.00728393 secs using 98.37% CPU
Optimizing NNI: done in 0.00750589 secs using 97.04% CPU
Optimizing NNI: done in 0.017123 secs using 96.81% CPU
Optimizing NNI: done in 0.0162199 secs using 96.47% CPU
Optimizing NNI: done in 0.013422 secs using 97.76% CPU
Optimizing NNI: done in 0.0150909 secs using 96.91% CPU
Iteration 10 / LogL: -1387.284 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0174851 secs using 95.46% CPU
Optimizing NNI: done in 0.0143161 secs using 96.51% CPU
Optimizing NNI: done in 0.015554 secs using 97.02% CPU
Optimizing NNI: done in 0.017592 secs using 98.18% CPU
Optimizing NNI: done in 0.014071 secs using 96.64% CPU
Optimizing NNI: done in 0.015187 secs using 96.92% CPU
Optimizing NNI: done in 0.0167792 secs using 95.74% CPU
Optimizing NNI: done in 0.0145309 secs using 96.02% CPU
Optimizing NNI: done in 0.013865 secs using 97.58% CPU
Optimizing NNI: done in 0.017241 secs using 95.37% CPU
Iteration 20 / LogL: -1387.284 / Time: 0h:0m:0s
Finish initializing candidate tree set (2)
Current best tree score: -1387.268 / CPU time: 0.443
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.006387 secs using 98.54% CPU
Optimizing NNI: done in 0.010524 secs using 93.99% CPU
Optimizing NNI: done in 0.013268 secs using 99.01% CPU
Optimizing NNI: done in 0.020314 secs using 97.49% CPU
Optimizing NNI: done in 0.021174 secs using 99.24% CPU
Optimizing NNI: done in 0.0204031 secs using 98.04% CPU
Optimizing NNI: done in 0.0156999 secs using 95.98% CPU
Optimizing NNI: done in 0.0230608 secs using 98.27% CPU
Optimizing NNI: done in 0.0140929 secs using 98.11% CPU
Optimizing NNI: done in 0.021003 secs using 96.85% CPU
Iteration 30 / LogL: -1387.374 / Time: 0h:0m:0s (0h:0m:2s left)
Optimizing NNI: done in 0.0122211 secs using 97.32% CPU
Optimizing NNI: done in 0.012929 secs using 97.94% CPU
Optimizing NNI: done in 0.025713 secs using 97.85% CPU
Optimizing NNI: done in 0.0143161 secs using 96.72% CPU
Optimizing NNI: done in 0.00482106 secs using 95.08% CPU
Optimizing NNI: done in 0.0127461 secs using 97.24% CPU
Optimizing NNI: done in 0.0133569 secs using 95.58% CPU
Optimizing NNI: done in 0.00879097 secs using 97.09% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.266
Optimizing NNI: done in 0.0209398 secs using 96.97% CPU
Optimizing NNI: done in 0.0157249 secs using 94.9% CPU
Iteration 40 / LogL: -1387.347 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.029624 secs using 95.83% CPU
Optimizing NNI: done in 0.021522 secs using 97.67% CPU
Optimizing NNI: done in 0.0337288 secs using 96.7% CPU
Optimizing NNI: done in 0.0405562 secs using 97.21% CPU
Optimizing NNI: done in 0.0106912 secs using 96.61% CPU
Optimizing NNI: done in 0.0158019 secs using 98.79% CPU
Optimizing NNI: done in 0.0182819 secs using 96.18% CPU
Optimizing NNI: done in 0.0183229 secs using 97.23% CPU
Optimizing NNI: done in 0.030093 secs using 94.4% CPU
Optimizing NNI: done in 0.0147948 secs using 98.62% CPU
Iteration 50 / LogL: -1387.376 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.023165 secs using 98.04% CPU
Optimizing NNI: done in 0.0193641 secs using 95.84% CPU
Optimizing NNI: done in 0.015826 secs using 96.77% CPU
Optimizing NNI: done in 0.0161669 secs using 95.45% CPU
Optimizing NNI: done in 0.0222461 secs using 96.86% CPU
Optimizing NNI: done in 0.024163 secs using 96.07% CPU
Optimizing NNI: done in 0.0218601 secs using 97.23% CPU
Optimizing NNI: done in 0.0191951 secs using 96.99% CPU
Optimizing NNI: done in 0.010927 secs using 98.91% CPU
Optimizing NNI: done in 0.00939298 secs using 99.19% CPU
Iteration 60 / LogL: -1387.312 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.00918818 secs using 98.5% CPU
Optimizing NNI: done in 0.0115268 secs using 99.81% CPU
Optimizing NNI: done in 0.0134561 secs using 98.75% CPU
Optimizing NNI: done in 0.034245 secs using 99.02% CPU
Optimizing NNI: done in 0.00999689 secs using 99.93% CPU
Optimizing NNI: done in 0.013387 secs using 99.4% CPU
Optimizing NNI: done in 0.0152318 secs using 99.95% CPU
Optimizing NNI: done in 0.0125339 secs using 99.83% CPU
Optimizing NNI: done in 0.0276551 secs using 99.29% CPU
Optimizing NNI: done in 0.0140901 secs using 99.62% CPU
Iteration 70 / LogL: -1387.557 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0411861 secs using 99.23% CPU
Optimizing NNI: done in 0.0149269 secs using 99.02% CPU
Optimizing NNI: done in 0.0163321 secs using 99.58% CPU
Optimizing NNI: done in 0.019871 secs using 99.39% CPU
Optimizing NNI: done in 0.022855 secs using 99.44% CPU
Optimizing NNI: done in 0.019335 secs using 98.9% CPU
Optimizing NNI: done in 0.0208759 secs using 99.62% CPU
Optimizing NNI: done in 0.0111392 secs using 99.94% CPU
Optimizing NNI: done in 0.0208309 secs using 99.67% CPU
Optimizing NNI: done in 0.015569 secs using 98.16% CPU
Iteration 80 / LogL: -1387.306 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0152481 secs using 99.36% CPU
Optimizing NNI: done in 0.013839 secs using 99.93% CPU
Optimizing NNI: done in 0.0102251 secs using 99.95% CPU
Optimizing NNI: done in 0.020071 secs using 98.34% CPU
Optimizing NNI: done in 0.0200641 secs using 99.61% CPU
Optimizing NNI: done in 0.00348997 secs using 99.94% CPU
Optimizing NNI: done in 0.019022 secs using 99.95% CPU
Optimizing NNI: done in 0.018827 secs using 96.6% CPU
Optimizing NNI: done in 0.0107191 secs using 99.11% CPU
Optimizing NNI: done in 0.0325599 secs using 99.94% CPU
Iteration 90 / LogL: -1387.400 / Time: 0h:0m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.0205078 secs using 99.25% CPU
Optimizing NNI: done in 0.013602 secs using 99.24% CPU
Optimizing NNI: done in 0.0108881 secs using 99.51% CPU
Optimizing NNI: done in 0.00352287 secs using 99.92% CPU
Optimizing NNI: done in 0.0111299 secs using 99.96% CPU
Optimizing NNI: done in 0.0100589 secs using 99.95% CPU
Optimizing NNI: done in 0.0108449 secs using 98.84% CPU
Optimizing NNI: done in 0.034508 secs using 99.43% CPU
Optimizing NNI: done in 0.0284419 secs using 99.65% CPU
Optimizing NNI: done in 0.0122809 secs using 99.68% CPU
Iteration 100 / LogL: -1387.303 / Time: 0h:0m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.0107739 secs using 99.23% CPU
Optimizing NNI: done in 0.0139132 secs using 99.73% CPU
TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:2s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.266
Optimal log-likelihood: -1387.255
Rate parameters: A-C: 0.33049 A-G: 2.27244 A-T: 2.15046 C-G: 1.17763 C-T: 3.30856 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.000
Gamma shape alpha: 1.313
Parameters optimization took 1 rounds (0.002 sec)
BEST SCORE FOUND : -1387.255
Total tree length: 6.777
Total number of iterations: 102
CPU time used for tree search: 2.037 sec (0h:0m:2s)
Wall-clock time used for tree search: 1.933 sec (0h:0m:1s)
Total CPU time used: 2.378 sec (0h:0m:2s)
Total wall-clock time used: 2.283 sec (0h:0m:2s)
Analysis results written to:
IQ-TREE report: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpuyuvyt4f/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpuyuvyt4f/q2iqtree.treefile
Likelihood distances: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpuyuvyt4f/q2iqtree.mldist
Screen log file: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpuyuvyt4f/q2iqtree.log
Date and Time: Thu Nov 16 16:36:25 2023
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpuyuvyt4f/q2iqtree -nt 1
Saved Phylogeny[Unrooted] to: iqt-gtrig-tree.qza
Let’s rerun the command above and add the --p-fast option. This option,
only compatible with the iqtree method, resembles the fast search performed
by fasttree. 🏎️ Secondly, let’s also perform multiple tree searches and
keep the best of those trees (as we did earlier with the
raxml --p-n-searches ... command):
qiime phylogeny iqtree \
--i-alignment masked-aligned-rep-seqs.qza \
--p-substitution-model 'GTR+I+G' \
--p-fast \
--p-n-runs 10 \
--o-tree iqt-gtrig-fast-ms-tree.qza \
--verbose
stdout:
IQ-TREE multicore version 2.2.5 COVID-edition for Mac OS X 64-bit built Sep 15 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: Elizabeths-MacBook-Pro-2.local (AVX512, FMA3, 32 GB RAM)
Command: iqtree -st DNA --runs 10 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp_tyl4biv/q2iqtree -nt 1 -fast
Seed: 463772 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Nov 16 16:36:34 2023
Kernel: AVX+FMA - 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/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000102997 secs using 86.41% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000213861 secs using 70.14% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Analyzing sequences: done in 2.40803e-05 secs using 74.75% CPU
Checking for duplicate sequences: done in 4.81606e-05 secs using 64.37% CPU
---> START RUN NUMBER 1 (seed: 463772)
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: -1493.17
2. Current log-likelihood: -1403.04
3. Current log-likelihood: -1398.31
4. Current log-likelihood: -1396.96
5. Current log-likelihood: -1396.23
Optimal log-likelihood: -1395.71
Rate parameters: A-C: 0.23146 A-G: 2.06956 A-T: 1.96268 C-G: 1.07937 C-T: 2.84175 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.322
Parameters optimization took 5 rounds (0.026 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00111389 secs using 98.21% CPU
Computing ML distances took 0.001257 sec (of wall-clock time) 0.001166 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 5.10216e-05 secs using 72.52% CPU
Constructing RapidNJ tree: done in 0.000137091 secs using 138.6% CPU
Computing RapidNJ tree took 0.000273 sec (of wall-clock time) 0.000278 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.184
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0114431 secs using 188.8% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.955
Optimizing NNI: done in 0.00921106 secs using 152.2% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.955 / CPU time: 0.031
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1387.955
2. Current log-likelihood: -1387.798
3. Current log-likelihood: -1387.680
4. Current log-likelihood: -1387.590
5. Current log-likelihood: -1387.521
6. Current log-likelihood: -1387.467
Optimal log-likelihood: -1387.423
Rate parameters: A-C: 0.33566 A-G: 2.27095 A-T: 2.14605 C-G: 1.17829 C-T: 3.29012 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.352
Parameters optimization took 6 rounds (0.015 sec)
BEST SCORE FOUND : -1387.423
Total tree length: 6.744
Total number of iterations: 2
CPU time used for tree search: 0.055 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.031 sec (0h:0m:0s)
Total CPU time used: 0.122 sec (0h:0m:0s)
Total wall-clock time used: 0.087 sec (0h:0m:0s)
---> START RUN NUMBER 2 (seed: 464772)
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: -1496.306
2. Current log-likelihood: -1403.641
3. Current log-likelihood: -1398.531
4. Current log-likelihood: -1397.067
5. Current log-likelihood: -1396.244
6. Current log-likelihood: -1395.736
Optimal log-likelihood: -1395.357
Rate parameters: A-C: 0.22740 A-G: 2.00038 A-T: 1.90797 C-G: 1.02878 C-T: 2.75984 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.021
Gamma shape alpha: 1.340
Parameters optimization took 6 rounds (0.028 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00166583 secs using 116.8% CPU
Computing ML distances took 0.001765 sec (of wall-clock time) 0.002083 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 4.29153e-05 secs using 142.1% CPU
Constructing RapidNJ tree: done in 8.2016e-05 secs using 151.2% CPU
Computing RapidNJ tree took 0.000184 sec (of wall-clock time) 0.000243 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.949
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0126069 secs using 185.1% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.982
Optimizing NNI: done in 0.015507 secs using 180.2% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.982 / CPU time: 0.036
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: -1387.982
2. Current log-likelihood: -1387.819
3. Current log-likelihood: -1387.693
4. Current log-likelihood: -1387.600
5. Current log-likelihood: -1387.528
6. Current log-likelihood: -1387.473
Optimal log-likelihood: -1387.428
Rate parameters: A-C: 0.32622 A-G: 2.24716 A-T: 2.12097 C-G: 1.16448 C-T: 3.24964 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: 1.355
Parameters optimization took 6 rounds (0.017 sec)
BEST SCORE FOUND : -1387.428
Total tree length: 6.738
Total number of iterations: 2
CPU time used for tree search: 0.066 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.037 sec (0h:0m:0s)
Total CPU time used: 0.167 sec (0h:0m:0s)
Total wall-clock time used: 0.097 sec (0h:0m:0s)
---> START RUN NUMBER 3 (seed: 465772)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1493.550
2. Current log-likelihood: -1403.090
3. Current log-likelihood: -1398.358
4. Current log-likelihood: -1396.975
5. Current log-likelihood: -1396.257
Optimal log-likelihood: -1395.748
Rate parameters: A-C: 0.23785 A-G: 2.06889 A-T: 1.95307 C-G: 1.06292 C-T: 2.77329 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.358
Parameters optimization took 5 rounds (0.026 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00133801 secs using 165.9% CPU
Computing ML distances took 0.001435 sec (of wall-clock time) 0.002367 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 0.000102997 secs using 33.98% CPU
Constructing RapidNJ tree: done in 8.79765e-05 secs using 106.8% CPU
Computing RapidNJ tree took 0.000269 sec (of wall-clock time) 0.000200 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.197
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.010576 secs using 186.1% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.961
Optimizing NNI: done in 0.0295539 secs using 161% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.961 / CPU time: 0.050
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1387.961
2. Current log-likelihood: -1387.803
3. Current log-likelihood: -1387.684
4. Current log-likelihood: -1387.593
5. Current log-likelihood: -1387.523
6. Current log-likelihood: -1387.469
Optimal log-likelihood: -1387.424
Rate parameters: A-C: 0.33442 A-G: 2.26003 A-T: 2.13495 C-G: 1.17227 C-T: 3.27212 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.353
Parameters optimization took 6 rounds (0.014 sec)
BEST SCORE FOUND : -1387.424
Total tree length: 6.742
Total number of iterations: 2
CPU time used for tree search: 0.085 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.051 sec (0h:0m:0s)
Total CPU time used: 0.181 sec (0h:0m:0s)
Total wall-clock time used: 0.105 sec (0h:0m:0s)
---> START RUN NUMBER 4 (seed: 466772)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1493.167
2. Current log-likelihood: -1403.041
3. Current log-likelihood: -1398.313
4. Current log-likelihood: -1396.957
5. Current log-likelihood: -1396.228
Optimal log-likelihood: -1395.709
Rate parameters: A-C: 0.23146 A-G: 2.06957 A-T: 1.96268 C-G: 1.07937 C-T: 2.84174 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.322
Parameters optimization took 5 rounds (0.028 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000928164 secs using 197.2% CPU
Computing ML distances took 0.000995 sec (of wall-clock time) 0.001922 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 2.71797e-05 secs using 80.94% CPU
Constructing RapidNJ tree: done in 7.00951e-05 secs using 89.88% CPU
Computing RapidNJ tree took 0.000140 sec (of wall-clock time) 0.000105 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.184
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0129979 secs using 190.3% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.955
Optimizing NNI: done in 0.00684595 secs using 179.7% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.955 / CPU time: 0.031
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1387.955
2. Current log-likelihood: -1387.798
3. Current log-likelihood: -1387.680
4. Current log-likelihood: -1387.590
5. Current log-likelihood: -1387.521
6. Current log-likelihood: -1387.467
Optimal log-likelihood: -1387.423
Rate parameters: A-C: 0.33566 A-G: 2.27095 A-T: 2.14605 C-G: 1.17829 C-T: 3.29012 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.352
Parameters optimization took 6 rounds (0.018 sec)
BEST SCORE FOUND : -1387.423
Total tree length: 6.744
Total number of iterations: 2
CPU time used for tree search: 0.057 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.031 sec (0h:0m:0s)
Total CPU time used: 0.156 sec (0h:0m:0s)
Total wall-clock time used: 0.089 sec (0h:0m:0s)
---> START RUN NUMBER 5 (seed: 467772)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1492.097
2. Current log-likelihood: -1401.816
3. Current log-likelihood: -1396.523
4. Current log-likelihood: -1395.122
5. Current log-likelihood: -1394.389
Optimal log-likelihood: -1393.818
Rate parameters: A-C: 0.27163 A-G: 2.41073 A-T: 2.17144 C-G: 1.24911 C-T: 3.27679 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.416
Parameters optimization took 5 rounds (0.028 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00134921 secs using 174% CPU
Computing ML distances took 0.016524 sec (of wall-clock time) 0.016701 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 4.50611e-05 secs using 79.89% CPU
Constructing RapidNJ tree: done in 6.19888e-05 secs using 103.2% CPU
Computing RapidNJ tree took 0.005356 sec (of wall-clock time) 0.000146 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.794
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0121341 secs using 190.4% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.214
Optimizing NNI: done in 0.013602 secs using 174.4% CPU
Finish initializing candidate tree set (3)
Current best tree score: -1388.214 / CPU time: 0.032
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.214
2. Current log-likelihood: -1388.015
3. Current log-likelihood: -1387.868
4. Current log-likelihood: -1387.760
5. Current log-likelihood: -1387.676
6. Current log-likelihood: -1387.611
7. Current log-likelihood: -1387.560
Optimal log-likelihood: -1387.519
Rate parameters: A-C: 0.35522 A-G: 2.35151 A-T: 2.13874 C-G: 1.20261 C-T: 3.36909 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.362
Parameters optimization took 7 rounds (0.016 sec)
BEST SCORE FOUND : -1387.519
Total tree length: 6.815
Total number of iterations: 2
CPU time used for tree search: 0.058 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.032 sec (0h:0m:0s)
Total CPU time used: 0.175 sec (0h:0m:0s)
Total wall-clock time used: 0.111 sec (0h:0m:0s)
---> START RUN NUMBER 6 (seed: 468772)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1493.459
2. Current log-likelihood: -1403.057
3. Current log-likelihood: -1398.315
4. Current log-likelihood: -1396.957
5. Current log-likelihood: -1396.224
Optimal log-likelihood: -1395.705
Rate parameters: A-C: 0.23667 A-G: 2.08551 A-T: 1.97696 C-G: 1.07651 C-T: 2.86648 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.322
Parameters optimization took 5 rounds (0.026 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000941992 secs using 194% CPU
Computing ML distances took 0.001024 sec (of wall-clock time) 0.001936 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 2.81334e-05 secs using 74.64% CPU
Constructing RapidNJ tree: done in 5.60284e-05 secs using 89.24% CPU
Computing RapidNJ tree took 0.000126 sec (of wall-clock time) 0.000088 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.170
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0125899 secs using 183.3% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.175
Optimizing NNI: done in 0.00560188 secs using 189.9% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1388.175 / CPU time: 0.026
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.175
2. Current log-likelihood: -1387.959
3. Current log-likelihood: -1387.799
4. Current log-likelihood: -1387.681
5. Current log-likelihood: -1387.591
6. Current log-likelihood: -1387.521
7. Current log-likelihood: -1387.467
Optimal log-likelihood: -1387.423
Rate parameters: A-C: 0.33681 A-G: 2.27128 A-T: 2.14654 C-G: 1.17860 C-T: 3.29078 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.351
Parameters optimization took 7 rounds (0.020 sec)
BEST SCORE FOUND : -1387.423
Total tree length: 6.745
Total number of iterations: 2
CPU time used for tree search: 0.048 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.026 sec (0h:0m:0s)
Total CPU time used: 0.149 sec (0h:0m:0s)
Total wall-clock time used: 0.085 sec (0h:0m:0s)
---> START RUN NUMBER 7 (seed: 469772)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1493.259
2. Current log-likelihood: -1403.078
3. Current log-likelihood: -1398.354
4. Current log-likelihood: -1396.979
5. Current log-likelihood: -1396.262
Optimal log-likelihood: -1395.753
Rate parameters: A-C: 0.24339 A-G: 2.10097 A-T: 1.98595 C-G: 1.09180 C-T: 2.82193 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.355
Parameters optimization took 5 rounds (0.024 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00137711 secs using 160.9% CPU
Computing ML distances took 0.001511 sec (of wall-clock time) 0.002481 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 3.60012e-05 secs using 75% CPU
Constructing RapidNJ tree: done in 0.000141144 secs using 131.1% CPU
Computing RapidNJ tree took 0.000243 sec (of wall-clock time) 0.000269 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.173
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0118542 secs using 179.9% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.961
Optimizing NNI: done in 0.029408 secs using 179.5% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.961 / CPU time: 0.052
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1387.961
2. Current log-likelihood: -1387.803
3. Current log-likelihood: -1387.684
4. Current log-likelihood: -1387.593
5. Current log-likelihood: -1387.523
6. Current log-likelihood: -1387.468
Optimal log-likelihood: -1387.424
Rate parameters: A-C: 0.33414 A-G: 2.26635 A-T: 2.14117 C-G: 1.17550 C-T: 3.28158 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.353
Parameters optimization took 6 rounds (0.016 sec)
BEST SCORE FOUND : -1387.424
Total tree length: 6.743
Total number of iterations: 2
CPU time used for tree search: 0.094 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.052 sec (0h:0m:0s)
Total CPU time used: 0.188 sec (0h:0m:0s)
Total wall-clock time used: 0.106 sec (0h:0m:0s)
---> START RUN NUMBER 8 (seed: 470772)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1493.550
2. Current log-likelihood: -1403.090
3. Current log-likelihood: -1398.358
4. Current log-likelihood: -1396.975
5. Current log-likelihood: -1396.257
Optimal log-likelihood: -1395.748
Rate parameters: A-C: 0.23785 A-G: 2.06889 A-T: 1.95307 C-G: 1.06292 C-T: 2.77329 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.358
Parameters optimization took 5 rounds (0.025 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000983953 secs using 190.9% CPU
Computing ML distances took 0.001063 sec (of wall-clock time) 0.001971 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 3.50475e-05 secs using 77.04% CPU
Constructing RapidNJ tree: done in 8.67844e-05 secs using 89.88% CPU
Computing RapidNJ tree took 0.000177 sec (of wall-clock time) 0.000140 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.197
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.0101571 secs using 186.6% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.961
Optimizing NNI: done in 0.028748 secs using 185% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.961 / CPU time: 0.051
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1387.961
2. Current log-likelihood: -1387.803
3. Current log-likelihood: -1387.684
4. Current log-likelihood: -1387.593
5. Current log-likelihood: -1387.523
6. Current log-likelihood: -1387.469
Optimal log-likelihood: -1387.424
Rate parameters: A-C: 0.33442 A-G: 2.26003 A-T: 2.13495 C-G: 1.17227 C-T: 3.27212 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.353
Parameters optimization took 6 rounds (0.013 sec)
BEST SCORE FOUND : -1387.424
Total tree length: 6.742
Total number of iterations: 2
CPU time used for tree search: 0.094 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.051 sec (0h:0m:0s)
Total CPU time used: 0.188 sec (0h:0m:0s)
Total wall-clock time used: 0.103 sec (0h:0m:0s)
---> START RUN NUMBER 9 (seed: 471772)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1493.259
2. Current log-likelihood: -1403.078
3. Current log-likelihood: -1398.354
4. Current log-likelihood: -1396.979
5. Current log-likelihood: -1396.262
Optimal log-likelihood: -1395.753
Rate parameters: A-C: 0.24339 A-G: 2.10097 A-T: 1.98595 C-G: 1.09180 C-T: 2.82193 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.355
Parameters optimization took 5 rounds (0.027 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00115418 secs using 161.8% CPU
Computing ML distances took 0.001240 sec (of wall-clock time) 0.002004 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 2.71797e-05 secs using 80.94% CPU
Constructing RapidNJ tree: done in 5.50747e-05 secs using 90.79% CPU
Computing RapidNJ tree took 0.000120 sec (of wall-clock time) 0.000089 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.173
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.00970507 secs using 185.9% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.961
Optimizing NNI: done in 0.0314541 secs using 164.9% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.961 / CPU time: 0.068
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1387.961
2. Current log-likelihood: -1387.803
3. Current log-likelihood: -1387.684
4. Current log-likelihood: -1387.593
5. Current log-likelihood: -1387.523
6. Current log-likelihood: -1387.468
Optimal log-likelihood: -1387.424
Rate parameters: A-C: 0.33414 A-G: 2.26635 A-T: 2.14117 C-G: 1.17550 C-T: 3.28158 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.353
Parameters optimization took 6 rounds (0.014 sec)
BEST SCORE FOUND : -1387.424
Total tree length: 6.743
Total number of iterations: 2
CPU time used for tree search: 0.105 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.068 sec (0h:0m:0s)
Total CPU time used: 0.199 sec (0h:0m:0s)
Total wall-clock time used: 0.122 sec (0h:0m:0s)
---> START RUN NUMBER 10 (seed: 472772)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.500)
1. Initial log-likelihood: -1495.571
2. Current log-likelihood: -1402.008
3. Current log-likelihood: -1396.794
4. Current log-likelihood: -1395.393
5. Current log-likelihood: -1394.655
Optimal log-likelihood: -1394.081
Rate parameters: A-C: 0.27755 A-G: 2.37595 A-T: 2.10647 C-G: 1.20302 C-T: 3.28732 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.386
Parameters optimization took 5 rounds (0.024 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000895023 secs using 188.7% CPU
Computing ML distances took 0.000951 sec (of wall-clock time) 0.001789 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 2.69413e-05 secs using 81.66% CPU
Constructing RapidNJ tree: done in 0.00010705 secs using 93.41% CPU
Computing RapidNJ tree took 0.000174 sec (of wall-clock time) 0.000140 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.809
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.010951 secs using 187.1% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.217
Optimizing NNI: done in 0.0184801 secs using 182.8% CPU
BETTER TREE FOUND at iteration 2: -1388.188
Finish initializing candidate tree set (4)
Current best tree score: -1388.188 / CPU time: 0.037
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.188
2. Current log-likelihood: -1387.973
3. Current log-likelihood: -1387.830
4. Current log-likelihood: -1387.725
5. Current log-likelihood: -1387.645
6. Current log-likelihood: -1387.584
Optimal log-likelihood: -1387.534
Rate parameters: A-C: 0.36987 A-G: 2.31020 A-T: 2.11745 C-G: 1.22270 C-T: 3.27880 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.006
Gamma shape alpha: 1.332
Parameters optimization took 6 rounds (0.014 sec)
BEST SCORE FOUND : -1387.534
Total tree length: 7.502
Total number of iterations: 2
CPU time used for tree search: 0.067 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.037 sec (0h:0m:0s)
Total CPU time used: 0.163 sec (0h:0m:0s)
Total wall-clock time used: 0.090 sec (0h:0m:0s)
---> SUMMARIZE RESULTS FROM 10 RUNS
Run 6 gave best log-likelihood: -1387.423
Total CPU time for 10 runs: 1.715 seconds.
Total wall-clock time for 10 runs: 1.013 seconds.
Analysis results written to:
IQ-TREE report: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp_tyl4biv/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp_tyl4biv/q2iqtree.treefile
Trees from independent runs: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp_tyl4biv/q2iqtree.runtrees
Likelihood distances: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp_tyl4biv/q2iqtree.mldist
Screen log file: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp_tyl4biv/q2iqtree.log
Date and Time: Thu Nov 16 16:36:35 2023
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 10 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp_tyl4biv/q2iqtree -nt 1 -fast
Saved Phylogeny[Unrooted] to: iqt-gtrig-fast-ms-tree.qza
Single branch tests¶
IQ-TREE provides access to a few single branch testing methods
SH-aLRT via
--p-alrt [INT >= 1000]aBayes via
--p-abayes [TRUE | FALSE]local bootstrap test via
--p-lbp [INT >= 1000]
Single branch tests are commonly used as an alternative to the bootstrapping
approach we’ve discussed above, as they are substantially faster and often
recommended when constructing large phylogenies (e.g. >10,000 taxa). All
three of these methods can be applied simultaneously and viewed within iTOL
as separate bootstrap support values. These values are always in listed in the
following order of alrt / lbp / abayes. We’ll go ahead and apply all of the
branch tests in our next command, while specifying the same substitution model
as above. Feel free to combine this with the --p-fast option. 😉
qiime phylogeny iqtree \
--i-alignment masked-aligned-rep-seqs.qza \
--p-alrt 1000 \
--p-abayes \
--p-lbp 1000 \
--p-substitution-model 'GTR+I+G' \
--o-tree iqt-sbt-tree.qza \
--verbose
stdout:
IQ-TREE multicore version 2.2.5 COVID-edition for Mac OS X 64-bit built Sep 15 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: Elizabeths-MacBook-Pro-2.local (AVX512, FMA3, 32 GB RAM)
Command: iqtree -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpvyndmkuy/q2iqtree -nt 1 -alrt 1000 -abayes -lbp 1000
Seed: 142492 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Nov 16 16:36:44 2023
Kernel: AVX+FMA - 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/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000141859 secs using 88.12% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.00027895 secs using 70.62% 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 1.09673e-05 secs using 91.18% 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 3.71933e-05 secs using 69.91% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Thoroughly optimizing +I+G parameters from 10 start values...
Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 1.261 / LogL: -1392.812
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.008, 1.354 / LogL: -1393.088
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.009, 1.366 / LogL: -1393.159
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.009, 1.362 / LogL: -1393.150
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.008, 1.357 / LogL: -1393.112
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.009, 1.361 / LogL: -1393.138
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.009, 1.364 / LogL: -1393.160
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.008, 1.358 / LogL: -1393.102
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.008, 1.359 / LogL: -1393.108
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.008, 1.361 / LogL: -1393.119
Optimal pinv,alpha: 0.000, 1.261 / LogL: -1392.812
Parameters optimization took 0.337 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000965118 secs using 97.6% CPU
Computing ML distances took 0.001037 sec (of wall-clock time) 0.000994 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 2.90871e-05 secs using 89.39% CPU
Constructing RapidNJ tree: done in 5.91278e-05 secs using 157.3% CPU
Computing RapidNJ tree took 0.000134 sec (of wall-clock time) 0.000153 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.727
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.080 second
Computing log-likelihood of 98 initial trees ... 0.079 seconds
Current best score: -1392.727
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.0118439 secs using 185% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.357
Optimizing NNI: done in 0.009022 secs using 117.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1387.266
Optimizing NNI: done in 0.00858498 secs using 95.97% CPU
Optimizing NNI: done in 0.00904799 secs using 93.81% CPU
Optimizing NNI: done in 0.00793409 secs using 95.64% CPU
Optimizing NNI: done in 0.007339 secs using 98.65% CPU
Optimizing NNI: done in 0.0075779 secs using 97.68% CPU
Optimizing NNI: done in 0.00808787 secs using 97.03% CPU
Optimizing NNI: done in 0.015239 secs using 96.38% CPU
Optimizing NNI: done in 0.0154071 secs using 96.58% CPU
Iteration 10 / LogL: -1387.280 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0153151 secs using 98.37% CPU
Optimizing NNI: done in 0.0143499 secs using 96.17% CPU
Optimizing NNI: done in 0.0143759 secs using 95.6% CPU
Optimizing NNI: done in 0.012933 secs using 98.37% CPU
Optimizing NNI: done in 0.0153949 secs using 97.49% CPU
Optimizing NNI: done in 0.014236 secs using 96.79% CPU
Optimizing NNI: done in 0.0144169 secs using 95.29% CPU
Optimizing NNI: done in 0.0133128 secs using 98.48% CPU
Optimizing NNI: done in 0.0142539 secs using 97.45% CPU
Optimizing NNI: done in 0.014468 secs using 97.84% CPU
Iteration 20 / LogL: -1387.280 / Time: 0h:0m:0s
Finish initializing candidate tree set (2)
Current best tree score: -1387.266 / CPU time: 0.418
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0171208 secs using 98.07% CPU
Optimizing NNI: done in 0.021004 secs using 94.73% CPU
Optimizing NNI: done in 0.023886 secs using 95.4% CPU
Optimizing NNI: done in 0.00907588 secs using 95.48% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.266
Optimizing NNI: done in 0.0185859 secs using 95.86% CPU
Optimizing NNI: done in 0.0228751 secs using 97.17% CPU
Optimizing NNI: done in 0.0234759 secs using 95.99% CPU
Optimizing NNI: done in 0.0129709 secs using 96.86% CPU
Optimizing NNI: done in 0.0279272 secs using 97.24% CPU
Optimizing NNI: done in 0.0368271 secs using 96.48% CPU
Iteration 30 / LogL: -1387.587 / Time: 0h:0m:1s (0h:0m:2s left)
Optimizing NNI: done in 0.019274 secs using 95.84% CPU
Optimizing NNI: done in 0.0312569 secs using 96.09% CPU
Optimizing NNI: done in 0.0151279 secs using 96.35% CPU
Optimizing NNI: done in 0.0195608 secs using 97.32% CPU
Optimizing NNI: done in 0.0191221 secs using 93.44% CPU
Optimizing NNI: done in 0.01547 secs using 95.25% CPU
Optimizing NNI: done in 0.0172932 secs using 95.34% CPU
Optimizing NNI: done in 0.0121169 secs using 95.36% CPU
Optimizing NNI: done in 0.00915813 secs using 96.23% CPU
Optimizing NNI: done in 0.0156579 secs using 97.5% CPU
Iteration 40 / LogL: -1387.385 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.0256369 secs using 95.99% CPU
Optimizing NNI: done in 0.0147591 secs using 95.39% CPU
Optimizing NNI: done in 0.019722 secs using 96.03% CPU
Optimizing NNI: done in 0.014147 secs using 95.99% CPU
Optimizing NNI: done in 0.00475001 secs using 94.23% CPU
Optimizing NNI: done in 0.0150378 secs using 97.77% CPU
Optimizing NNI: done in 0.017509 secs using 96.32% CPU
Optimizing NNI: done in 0.0123889 secs using 94.38% CPU
Optimizing NNI: done in 0.01882 secs using 96.07% CPU
Optimizing NNI: done in 0.0281188 secs using 96.9% CPU
Iteration 50 / LogL: -1387.351 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.013272 secs using 95.94% CPU
Optimizing NNI: done in 0.0208559 secs using 94.52% CPU
Optimizing NNI: done in 0.017755 secs using 96.72% CPU
Optimizing NNI: done in 0.02232 secs using 94.92% CPU
Optimizing NNI: done in 0.0214691 secs using 97.29% CPU
Optimizing NNI: done in 0.0313289 secs using 96.73% CPU
Optimizing NNI: done in 0.021975 secs using 96.4% CPU
Optimizing NNI: done in 0.0140688 secs using 97.91% CPU
Optimizing NNI: done in 0.0140781 secs using 99.59% CPU
Optimizing NNI: done in 0.0118861 secs using 99.24% CPU
Iteration 60 / LogL: -1387.272 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.023217 secs using 99.43% CPU
Optimizing NNI: done in 0.0115008 secs using 98.84% CPU
Optimizing NNI: done in 0.0110631 secs using 99% CPU
Optimizing NNI: done in 0.023284 secs using 97.71% CPU
Optimizing NNI: done in 0.0201778 secs using 99.36% CPU
Optimizing NNI: done in 0.0156779 secs using 97.79% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.264
Optimizing NNI: done in 0.015563 secs using 99.3% CPU
Optimizing NNI: done in 0.00977802 secs using 99.57% CPU
Optimizing NNI: done in 0.0382609 secs using 97.51% CPU
WARNING: NNI search needs unusual large number of steps (20) to converge!
Optimizing NNI: done in 0.0114119 secs using 96.88% CPU
Iteration 70 / LogL: -1387.349 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.019264 secs using 96.78% CPU
Optimizing NNI: done in 0.0149021 secs using 97.56% CPU
Optimizing NNI: done in 0.0112121 secs using 98.81% CPU
Optimizing NNI: done in 0.014307 secs using 96.92% CPU
Optimizing NNI: done in 0.0127771 secs using 96.57% CPU
Optimizing NNI: done in 0.027097 secs using 96.66% CPU
Optimizing NNI: done in 0.025069 secs using 97.65% CPU
Optimizing NNI: done in 0.0176032 secs using 97.11% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 78: -1387.168
Optimizing NNI: done in 0.00793791 secs using 99.08% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.168
Optimizing NNI: done in 0.013916 secs using 96.14% CPU
Iteration 80 / LogL: -1387.336 / Time: 0h:0m:1s (0h:0m:2s left)
Optimizing NNI: done in 0.00980401 secs using 96.04% CPU
Optimizing NNI: done in 0.01246 secs using 97.87% CPU
Optimizing NNI: done in 0.0123169 secs using 98.23% CPU
Optimizing NNI: done in 0.0144379 secs using 96.42% CPU
Optimizing NNI: done in 0.0155771 secs using 96.91% CPU
Optimizing NNI: done in 0.0130589 secs using 96.49% CPU
Optimizing NNI: done in 0.010216 secs using 97.15% CPU
Optimizing NNI: done in 0.017725 secs using 98.28% CPU
Optimizing NNI: done in 0.014679 secs using 98.37% CPU
Optimizing NNI: done in 0.0154161 secs using 98.54% CPU
Iteration 90 / LogL: -1387.343 / Time: 0h:0m:2s (0h:0m:2s left)
Optimizing NNI: done in 0.0173149 secs using 98.8% CPU
Optimizing NNI: done in 0.00987506 secs using 98.46% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.168
Optimizing NNI: done in 0.016047 secs using 97.61% CPU
Optimizing NNI: done in 0.0193112 secs using 97.94% CPU
Optimizing NNI: done in 0.0238371 secs using 99.17% CPU
Optimizing NNI: done in 0.013072 secs using 98.71% CPU
Optimizing NNI: done in 0.0205441 secs using 98.87% CPU
Optimizing NNI: done in 0.00869989 secs using 98.09% CPU
Optimizing NNI: done in 0.0164671 secs using 98.91% CPU
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Iteration 100 / LogL: -1387.348 / Time: 0h:0m:2s (0h:0m:1s left)
Optimizing NNI: done in 0.0246549 secs using 99.21% CPU
Optimizing NNI: done in 0.00841403 secs using 98.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.168
Optimizing NNI: done in 0.00950217 secs using 98.92% CPU
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Iteration 110 / LogL: -1387.202 / Time: 0h:0m:2s (0h:0m:1s left)
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Iteration 120 / LogL: -1387.342 / Time: 0h:0m:2s (0h:0m:1s left)
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Iteration 130 / LogL: -1387.168 / Time: 0h:0m:2s (0h:0m:1s left)
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Iteration 140 / LogL: -1387.168 / Time: 0h:0m:2s (0h:0m:0s left)
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Iteration 150 / LogL: -1396.648 / Time: 0h:0m:3s (0h:0m:0s left)
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Iteration 160 / LogL: -1387.168 / Time: 0h:0m:3s (0h:0m:0s left)
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Iteration 170 / LogL: -1387.168 / Time: 0h:0m:3s (0h:0m:0s left)
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Optimizing NNI: done in 0.00627708 secs using 98.87% CPU
TREE SEARCH COMPLETED AFTER 179 ITERATIONS / Time: 0h:0m:3s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.168
Optimal log-likelihood: -1387.167
Rate parameters: A-C: 0.34721 A-G: 2.33346 A-T: 2.15402 C-G: 1.24060 C-T: 3.23440 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.000
Gamma shape alpha: 1.284
Parameters optimization took 1 rounds (0.003 sec)
BEST SCORE FOUND : -1387.167
Testing tree branches by SH-like aLRT with 1000 replicates...
Testing tree branches by local-BP test with 1000 replicates...
Testing tree branches by aBayes parametric test...
0.046 sec.
Total tree length: 7.606
Total number of iterations: 179
CPU time used for tree search: 3.184 sec (0h:0m:3s)
Wall-clock time used for tree search: 3.149 sec (0h:0m:3s)
Total CPU time used: 3.569 sec (0h:0m:3s)
Total wall-clock time used: 3.548 sec (0h:0m:3s)
Analysis results written to:
IQ-TREE report: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpvyndmkuy/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpvyndmkuy/q2iqtree.treefile
Likelihood distances: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpvyndmkuy/q2iqtree.mldist
Screen log file: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpvyndmkuy/q2iqtree.log
Date and Time: Thu Nov 16 16:36:47 2023
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpvyndmkuy/q2iqtree -nt 1 -alrt 1000 -abayes -lbp 1000
Saved Phylogeny[Unrooted] to: iqt-sbt-tree.qza
Tip
IQ-TREE search settings.
There are quite a few adjustable parameters available for iqtree that
can be modified improve searches through “tree space” and prevent the search
algorithms from getting stuck in local optima. One particular best
practice to aid in this regard, is to adjust the following parameters:
--p-perturb-nni-strength and --p-stop-iter (each respectively maps
to the -pers and -nstop flags of iqtree ). In brief, the larger
the value for NNI (nearest-neighbor interchange) perturbation, the larger
the jumps in “tree space”. This value should be set high enough to allow the
search algorithm to avoid being trapped in local optima, but not to high
that the search is haphazardly jumping around “tree space”. That is, like
Goldilocks and the three 🐻s you need to find a setting that is “just
right”, or at least within a set of reasonable bounds. One way of assessing
this, is to do a few short trial runs using the --verbose flag. If you
see that the likelihood values are jumping around to much, then lowering the
value for --p-perturb-nni-strength may be warranted. As for the stopping
criteria, i.e. --p-stop-iter, the higher this value, the more thorough
your search in “tree space”. Be aware, increasing this value may also
increase the run time. That is, the search will continue until it has
sampled a number of trees, say 100 (default), without finding a better
scoring tree. If a better tree is found, then the counter resets, and the
search continues. These two parameters deserve special consideration when a
given data set contains many short sequences, quite common for microbiome
survey data. We can modify our original command to include these extra
parameters with the recommended modifications for short sequences, i.e. a
lower value for perturbation strength (shorter reads do not contain as much
phylogenetic information, thus we should limit how far we jump around in
“tree space”) and a larger number of stop iterations. See the IQ-TREE
command reference for more details about default parameter settings.
Finally, we’ll let iqtree perform the model testing, and automatically
determine the optimal number of CPU cores to use.
qiime phylogeny iqtree \
--i-alignment masked-aligned-rep-seqs.qza \
--p-perturb-nni-strength 0.2 \
--p-stop-iter 200 \
--p-n-cores 1 \
--o-tree iqt-nnisi-fast-tree.qza \
--verbose
stdout:
IQ-TREE multicore version 2.2.5 COVID-edition for Mac OS X 64-bit built Sep 15 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: Elizabeths-MacBook-Pro-2.local (AVX512, FMA3, 32 GB RAM)
Command: iqtree -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpqbljc6t_/q2iqtree -nt 1 -nstop 200 -pers 0.200000
Seed: 63698 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Nov 16 16:36:56 2023
Kernel: AVX+FMA - 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/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000101089 secs using 88.04% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000258923 secs using 68.75% 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 1.00136e-05 secs using 79.89% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 7.20024e-05 secs using 34.72% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.019872 secs using 94.66% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1389.605
Optimal log-likelihood: -1388.791
Rate parameters: A-C: 0.37331 A-G: 2.35436 A-T: 2.13670 C-G: 1.23381 C-T: 3.29661 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.034
Gamma shape alpha: 1.400
Parameters optimization took 1 rounds (0.004 sec)
Time for fast ML tree search: 0.045 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 484 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1402.600 45 2895.200 2919.842 3046.668
2 GTR+F+I 1401.121 46 2894.242 2920.134 3049.077
3 GTR+F+G4 1387.358 46 2866.716 2892.608 3021.551
4 GTR+F+I+G4 1387.726 47 2869.452 2896.633 3027.653
5 GTR+F+R2 1382.364 47 2858.729 2885.910 3016.930
6 GTR+F+R3 1382.420 49 2862.840 2892.718 3027.773
14 GTR+F+I+R2 1382.418 48 2860.837 2889.346 3022.403
15 GTR+F+I+R3 1382.449 50 2864.899 2896.187 3033.197
25 SYM+G4 1387.134 43 2860.269 2882.528 3005.006
27 SYM+R2 1383.095 44 2854.189 2877.621 3002.292
36 SYM+I+R2 1383.227 45 2856.454 2881.097 3007.923
47 TVM+F+G4 1388.357 45 2866.713 2891.356 3018.182
49 TVM+F+R2 1383.789 46 2859.578 2885.470 3014.413
58 TVM+F+I+R2 1383.812 47 2861.625 2888.805 3019.826
69 TVMe+G4 1387.122 42 2858.245 2879.368 2999.616
71 TVMe+R2 1383.079 43 2852.159 2874.418 2996.896
80 TVMe+I+R2 1383.224 44 2854.449 2877.881 3002.552
91 TIM3+F+G4 1391.377 44 2870.754 2894.186 3018.857
93 TIM3+F+R2 1385.912 45 2861.825 2886.468 3013.294
102 TIM3+F+I+R2 1386.041 46 2864.082 2889.975 3018.917
113 TIM3e+G4 1390.358 41 2862.715 2882.738 3000.720
115 TIM3e+R2 1385.918 42 2855.836 2876.959 2997.207
124 TIM3e+I+R2 1386.073 43 2858.145 2880.404 3002.882
135 TIM2+F+G4 1393.635 44 2875.270 2898.702 3023.373
137 TIM2+F+R2 1387.681 45 2865.362 2890.005 3016.831
146 TIM2+F+I+R2 1387.782 46 2867.564 2893.456 3022.399
157 TIM2e+G4 1396.795 41 2875.589 2895.613 3013.594
159 TIM2e+R2 1391.574 42 2867.148 2888.270 3008.519
168 TIM2e+I+R2 1391.651 43 2869.302 2891.561 3014.039
179 TIM+F+G4 1390.363 44 2868.726 2892.158 3016.829
181 TIM+F+R2 1384.933 45 2859.866 2884.509 3011.335
190 TIM+F+I+R2 1385.016 46 2862.032 2887.925 3016.867
201 TIMe+G4 1394.002 41 2870.005 2890.028 3008.010
203 TIMe+R2 1389.000 42 2862.000 2883.123 3003.371
212 TIMe+I+R2 1389.095 43 2864.190 2886.449 3008.927
223 TPM3u+F+G4 1392.306 43 2870.611 2892.870 3015.348
225 TPM3u+F+R2 1387.329 44 2862.659 2886.091 3010.762
234 TPM3u+F+I+R2 1387.462 45 2864.923 2889.566 3016.392
245 TPM3+G4 1390.374 40 2860.748 2879.708 2995.387
247 TPM3+R2 1385.925 41 2853.851 2873.874 2991.856
256 TPM3+I+R2 1386.070 42 2856.140 2877.263 2997.511
267 TPM2u+F+G4 1394.533 43 2875.067 2897.325 3019.804
269 TPM2u+F+R2 1389.057 44 2866.113 2889.545 3014.216
278 TPM2u+F+I+R2 1389.101 45 2868.201 2892.844 3019.670
289 TPM2+G4 1396.823 40 2873.646 2892.605 3008.285
291 TPM2+R2 1391.578 41 2865.155 2885.178 3003.160
300 TPM2+I+R2 1391.649 42 2867.297 2888.420 3008.668
311 K3Pu+F+G4 1391.381 43 2868.762 2891.021 3013.499
313 K3Pu+F+R2 1386.371 44 2860.742 2884.174 3008.845
322 K3Pu+F+I+R2 1386.425 45 2862.850 2887.493 3014.319
333 K3P+G4 1394.015 40 2868.030 2886.989 3002.669
335 K3P+R2 1389.002 41 2860.004 2880.028 2998.009
344 K3P+I+R2 1389.099 42 2862.197 2883.320 3003.568
355 TN+F+G4 1394.038 43 2874.077 2896.336 3018.814
357 TN+F+R2 1388.241 44 2864.483 2887.915 3012.586
366 TN+F+I+R2 1388.289 45 2866.578 2891.221 3018.047
377 TNe+G4 1396.791 40 2873.582 2892.542 3008.221
379 TNe+R2 1391.586 41 2865.172 2885.195 3003.177
388 TNe+I+R2 1391.666 42 2867.332 2888.454 3008.703
399 HKY+F+G4 1394.951 42 2873.902 2895.024 3015.273
401 HKY+F+R2 1389.609 43 2865.217 2887.476 3009.954
410 HKY+F+I+R2 1389.663 44 2867.327 2890.759 3015.430
421 K2P+G4 1396.825 39 2871.649 2889.580 3002.922
423 K2P+R2 1391.594 40 2863.189 2882.148 2997.828
432 K2P+I+R2 1391.664 41 2865.327 2885.351 3003.332
443 F81+F+G4 1405.743 41 2893.486 2913.509 3031.491
445 F81+F+R2 1400.805 42 2885.611 2906.733 3026.982
454 F81+F+I+R2 1400.908 43 2887.816 2910.075 3032.553
465 JC+G4 1407.650 38 2891.299 2908.236 3019.206
467 JC+R2 1402.858 39 2883.715 2901.646 3014.988
476 JC+I+R2 1402.926 40 2885.851 2904.811 3020.490
Akaike Information Criterion: TVMe+R2
Corrected Akaike Information Criterion: TPM3+R2
Bayesian Information Criterion: TPM3+R2
Best-fit model: TPM3+R2 chosen according to BIC
All model information printed to /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpqbljc6t_/q2iqtree.model.gz
CPU time for ModelFinder: 0.925 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.976 seconds (0h:0m:0s)
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1385.925
Optimal log-likelihood: -1385.924
Rate parameters: A-C: 0.40868 A-G: 1.56206 A-T: 1.00000 C-G: 0.40868 C-T: 1.56206 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.716,0.409) (0.284,2.490)
Parameters optimization took 1 rounds (0.003 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000634193 secs using 93.82% CPU
Computing ML distances took 0.000696 sec (of wall-clock time) 0.000641 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 3.00407e-05 secs using 89.88% CPU
Constructing RapidNJ tree: done in 5.50747e-05 secs using 152.5% CPU
Computing RapidNJ tree took 0.000130 sec (of wall-clock time) 0.000150 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.820
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.070 second
Computing log-likelihood of 98 initial trees ... 0.062 seconds
Current best score: -1385.924
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00359893 secs using 158.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.880
Optimizing NNI: done in 0.00816083 secs using 185.4% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1385.311
Optimizing NNI: done in 0.0074389 secs using 172.7% CPU
Optimizing NNI: done in 0.00941586 secs using 185.2% CPU
Optimizing NNI: done in 0.0119178 secs using 119.8% CPU
Optimizing NNI: done in 0.0154111 secs using 171.2% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.310
Optimizing NNI: done in 0.00984716 secs using 97.75% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.309
Optimizing NNI: done in 0.00757694 secs using 97.49% CPU
Optimizing NNI: done in 0.00862098 secs using 98.67% CPU
Optimizing NNI: done in 0.00917411 secs using 97.39% CPU
Iteration 10 / LogL: -1385.344 / Time: 0h:0m:0s
Optimizing NNI: done in 0.008214 secs using 96.66% CPU
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Iteration 20 / LogL: -1385.343 / Time: 0h:0m:0s
Finish initializing candidate tree set (2)
Current best tree score: -1385.309 / CPU time: 0.327
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
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Iteration 30 / LogL: -1385.930 / Time: 0h:0m:0s (0h:0m:2s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.309
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Iteration 40 / LogL: -1385.754 / Time: 0h:0m:0s (0h:0m:1s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.309
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Iteration 50 / LogL: -1385.559 / Time: 0h:0m:0s (0h:0m:1s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.309
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Optimizing NNI: done in 0.00525284 secs using 98.54% CPU
Iteration 60 / LogL: -1385.838 / Time: 0h:0m:0s (0h:0m:1s left)
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Iteration 70 / LogL: -1385.507 / Time: 0h:0m:0s (0h:0m:1s left)
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Iteration 80 / LogL: -1385.309 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.00557494 secs using 99.93% CPU
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Iteration 90 / LogL: -1385.518 / Time: 0h:0m:0s (0h:0m:0s left)
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Iteration 100 / LogL: -1385.839 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.010313 secs using 98.22% CPU
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Iteration 110 / LogL: -1385.636 / Time: 0h:0m:0s (0h:0m:0s left)
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Iteration 120 / LogL: -1385.355 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.007447 secs using 99.83% CPU
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Iteration 130 / LogL: -1385.516 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00391412 secs using 99.66% CPU
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Iteration 140 / LogL: -1385.310 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00791907 secs using 98.07% CPU
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Optimizing NNI: done in 0.00283289 secs using 99.9% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.309
Optimizing NNI: done in 0.00746894 secs using 99.92% CPU
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Iteration 150 / LogL: -1385.310 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00867915 secs using 97.73% CPU
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Iteration 160 / LogL: -1385.546 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.006078 secs using 99.44% CPU
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Iteration 170 / LogL: -1385.311 / Time: 0h:0m:1s (0h:0m:0s left)
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Iteration 180 / LogL: -1385.532 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00584602 secs using 99.73% CPU
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Optimizing NNI: done in 0.00158191 secs using 99.94% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.309
Optimizing NNI: done in 0.00381303 secs using 98.56% CPU
Optimizing NNI: done in 0.00166297 secs using 99.64% CPU
Iteration 190 / LogL: -1385.506 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00250888 secs using 99.73% CPU
Optimizing NNI: done in 0.0084939 secs using 94.83% CPU
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Iteration 200 / LogL: -1385.641 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00270605 secs using 98.7% CPU
Optimizing NNI: done in 0.00231004 secs using 99.91% CPU
Optimizing NNI: done in 0.00347304 secs using 99.85% CPU
TREE SEARCH COMPLETED AFTER 203 ITERATIONS / Time: 0h:0m:1s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1385.309
Optimal log-likelihood: -1385.305
Rate parameters: A-C: 0.39448 A-G: 1.56669 A-T: 1.00000 C-G: 0.39448 C-T: 1.56669 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.721,0.402) (0.279,2.542)
Parameters optimization took 1 rounds (0.002 sec)
BEST SCORE FOUND : -1385.305
Total tree length: 6.847
Total number of iterations: 203
CPU time used for tree search: 1.557 sec (0h:0m:1s)
Wall-clock time used for tree search: 1.438 sec (0h:0m:1s)
Total CPU time used: 1.576 sec (0h:0m:1s)
Total wall-clock time used: 1.456 sec (0h:0m:1s)
Analysis results written to:
IQ-TREE report: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpqbljc6t_/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpqbljc6t_/q2iqtree.treefile
Likelihood distances: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpqbljc6t_/q2iqtree.mldist
Screen log file: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpqbljc6t_/q2iqtree.log
Date and Time: Thu Nov 16 16:36:58 2023
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpqbljc6t_/q2iqtree -nt 1 -nstop 200 -pers 0.200000
Saved Phylogeny[Unrooted] to: iqt-nnisi-fast-tree.qza
iqtree-ultrafast-bootstrap¶
As per our discussion in the raxml-rapid-bootstrap section above, we can
also use IQ-TREE to evaluate how well our splits / bipartitions are supported
within our phylogeny via the ultrafast bootstrap algorithm. Below, we’ll
apply the plugin’s
ultrafast bootstrap command:
automatic model selection (MFP), perform 1000 bootstrap replicates
(minimum required), set the same generally suggested parameters for
constructing a phylogeny from short sequences, and automatically determine the
optimal number of CPU cores to use:
qiime phylogeny iqtree-ultrafast-bootstrap \
--i-alignment masked-aligned-rep-seqs.qza \
--p-perturb-nni-strength 0.2 \
--p-stop-iter 200 \
--p-n-cores 1 \
--o-tree iqt-nnisi-bootstrap-tree.qza \
--verbose
stdout:
IQ-TREE multicore version 2.2.5 COVID-edition for Mac OS X 64-bit built Sep 15 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: Elizabeths-MacBook-Pro-2.local (AVX512, FMA3, 32 GB RAM)
Command: iqtree -bb 1000 -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpi6oh821h/q2iqtreeufboot -nt 1 -nstop 200 -pers 0.200000
Seed: 84815 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Nov 16 16:37:07 2023
Kernel: AVX+FMA - 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/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000104904 secs using 88.65% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000219107 secs using 69.83% 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 1.50204e-05 secs using 86.55% 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 3.50475e-05 secs using 71.33% 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 0.017736 secs using 97.54% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1390.589
Optimal log-likelihood: -1389.805
Rate parameters: A-C: 0.32695 A-G: 2.17649 A-T: 2.01742 C-G: 1.14417 C-T: 3.04932 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.035
Gamma shape alpha: 1.401
Parameters optimization took 1 rounds (0.004 sec)
Time for fast ML tree search: 0.041 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 484 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1405.417 45 2900.834 2925.477 3052.303
2 GTR+F+I 1403.836 46 2899.673 2925.565 3054.508
3 GTR+F+G4 1388.331 46 2868.663 2894.555 3023.498
4 GTR+F+I+G4 1388.709 47 2871.418 2898.598 3029.618
5 GTR+F+R2 1382.562 47 2859.124 2886.305 3017.325
6 GTR+F+R3 1382.602 49 2863.203 2893.081 3028.136
14 GTR+F+I+R2 1382.708 48 2861.416 2889.925 3022.983
15 GTR+F+I+R3 1382.679 50 2865.358 2896.647 3033.657
25 SYM+G4 1388.448 43 2862.897 2885.156 3007.634
27 SYM+R2 1384.041 44 2856.081 2879.513 3004.184
36 SYM+I+R2 1384.179 45 2858.357 2883.000 3009.826
47 TVM+F+G4 1389.408 45 2868.815 2893.458 3020.284
49 TVM+F+R2 1384.278 46 2860.555 2886.448 3015.390
58 TVM+F+I+R2 1384.278 47 2862.557 2889.737 3020.758
69 TVMe+G4 1388.431 42 2860.861 2881.984 3002.232
71 TVMe+R2 1384.070 43 2854.141 2876.400 2998.878
80 TVMe+I+R2 1384.207 44 2856.414 2879.846 3004.517
91 TIM3+F+G4 1392.277 44 2872.555 2895.987 3020.658
93 TIM3+F+R2 1385.911 45 2861.822 2886.465 3013.291
102 TIM3+F+I+R2 1386.045 46 2864.089 2889.981 3018.924
113 TIM3e+G4 1391.664 41 2865.328 2885.351 3003.333
115 TIM3e+R2 1386.836 42 2857.673 2878.795 2999.044
124 TIM3e+I+R2 1386.991 43 2859.982 2882.241 3004.719
135 TIM2+F+G4 1395.130 44 2878.260 2901.692 3026.363
137 TIM2+F+R2 1388.182 45 2866.364 2891.007 3017.833
146 TIM2+F+I+R2 1388.319 46 2868.637 2894.529 3023.472
157 TIM2e+G4 1398.824 41 2879.647 2899.671 3017.652
159 TIM2e+R2 1393.017 42 2870.033 2891.156 3011.404
168 TIM2e+I+R2 1393.107 43 2872.215 2894.474 3016.952
179 TIM+F+G4 1391.782 44 2871.563 2894.995 3019.666
181 TIM+F+R2 1385.369 45 2860.738 2885.381 3012.207
190 TIM+F+I+R2 1385.497 46 2862.994 2888.887 3017.829
201 TIMe+G4 1396.021 41 2874.043 2894.066 3012.048
203 TIMe+R2 1390.461 42 2864.922 2886.044 3006.293
212 TIMe+I+R2 1390.568 43 2867.136 2889.394 3011.872
223 TPM3u+F+G4 1393.267 43 2872.534 2894.793 3017.271
225 TPM3u+F+R2 1387.637 44 2863.275 2886.706 3011.377
234 TPM3u+F+I+R2 1387.756 45 2865.513 2890.156 3016.982
245 TPM3+G4 1391.670 40 2863.340 2882.300 2997.980
247 TPM3+R2 1386.891 41 2855.783 2875.806 2993.788
256 TPM3+I+R2 1387.026 42 2858.051 2879.174 2999.422
267 TPM2u+F+G4 1396.100 43 2878.200 2900.459 3022.937
269 TPM2u+F+R2 1389.793 44 2867.586 2891.018 3015.689
278 TPM2u+F+I+R2 1389.878 45 2869.756 2894.399 3021.225
289 TPM2+G4 1398.841 40 2877.682 2896.641 3012.321
291 TPM2+R2 1393.061 41 2868.123 2888.146 3006.128
300 TPM2+I+R2 1393.137 42 2870.275 2891.398 3011.646
311 K3Pu+F+G4 1392.937 43 2871.874 2894.133 3016.611
313 K3Pu+F+R2 1387.034 44 2862.068 2885.500 3010.171
322 K3Pu+F+I+R2 1387.111 45 2864.221 2888.864 3015.690
333 K3P+G4 1396.021 40 2872.041 2891.001 3006.680
335 K3P+R2 1390.496 41 2862.992 2883.015 3000.997
344 K3P+I+R2 1390.601 42 2865.202 2886.325 3006.573
355 TN+F+G4 1395.486 43 2876.972 2899.231 3021.709
357 TN+F+R2 1388.575 44 2865.151 2888.583 3013.254
366 TN+F+I+R2 1388.715 45 2867.429 2892.072 3018.898
377 TNe+G4 1398.826 40 2877.651 2896.611 3012.290
379 TNe+R2 1393.014 41 2868.027 2888.051 3006.032
388 TNe+I+R2 1393.104 42 2870.208 2891.331 3011.579
399 HKY+F+G4 1396.476 42 2876.951 2898.074 3018.322
401 HKY+F+R2 1390.188 43 2866.375 2888.634 3011.112
410 HKY+F+I+R2 1390.281 44 2868.561 2891.993 3016.664
421 K2P+G4 1398.841 39 2875.683 2893.614 3006.956
423 K2P+R2 1393.061 40 2866.123 2885.082 3000.762
432 K2P+I+R2 1393.137 41 2868.274 2888.297 3006.279
443 F81+F+G4 1406.476 41 2894.952 2914.975 3032.957
445 F81+F+R2 1401.149 42 2886.297 2907.420 3027.668
454 F81+F+I+R2 1401.264 43 2888.528 2910.787 3033.265
465 JC+G4 1408.763 38 2893.527 2910.464 3021.434
467 JC+R2 1403.897 39 2885.793 2903.724 3017.066
476 JC+I+R2 1403.935 40 2887.870 2906.829 3022.509
Akaike Information Criterion: TVMe+R2
Corrected Akaike Information Criterion: TPM3+R2
Bayesian Information Criterion: TPM3+R2
Best-fit model: TPM3+R2 chosen according to BIC
All model information printed to /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpi6oh821h/q2iqtreeufboot.model.gz
CPU time for ModelFinder: 0.922 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.982 seconds (0h:0m:0s)
Generating 1000 samples for ultrafast bootstrap (seed: 84815)...
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1386.891
Optimal log-likelihood: -1386.887
Rate parameters: A-C: 0.39145 A-G: 1.51425 A-T: 1.00000 C-G: 0.39145 C-T: 1.51425 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.718,0.396) (0.282,2.538)
Parameters optimization took 1 rounds (0.003 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00108504 secs using 97.88% CPU
Computing ML distances took 0.001185 sec (of wall-clock time) 0.001133 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 4.1008e-05 secs using 78.03% CPU
Constructing RapidNJ tree: done in 8.2016e-05 secs using 130.5% CPU
Computing RapidNJ tree took 0.000190 sec (of wall-clock time) 0.000191 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.864
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| INITIALIZING CANDIDATE TREE SET |
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Generating 98 parsimony trees... 0.081 second
Computing log-likelihood of 97 initial trees ... 0.062 seconds
Current best score: -1386.887
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00922799 secs using 175.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.310
Optimizing NNI: done in 0.015718 secs using 181% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.308
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Iteration 10 / LogL: -1385.340 / Time: 0h:0m:0s
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Iteration 20 / LogL: -1385.339 / Time: 0h:0m:0s
Finish initializing candidate tree set (3)
Current best tree score: -1385.308 / CPU time: 0.453
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
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Optimizing NNI: done in 0.011986 secs using 94.76% CPU
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BETTER TREE FOUND at iteration 22: -1385.306
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UPDATE BEST LOG-LIKELIHOOD: -1385.306
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Iteration 30 / LogL: -1390.426 / Time: 0h:0m:0s (0h:0m:3s left)
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Iteration 40 / LogL: -1385.308 / Time: 0h:0m:0s (0h:0m:3s left)
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Iteration 50 / LogL: -1385.306 / Time: 0h:0m:0s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -1417.328
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Iteration 90 / LogL: -1385.316 / Time: 0h:0m:1s (0h:0m:1s left)
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Iteration 100 / LogL: -1385.817 / Time: 0h:0m:1s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -1417.722
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.993
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Iteration 150 / LogL: -1385.307 / Time: 0h:0m:2s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -1417.689
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Iteration 190 / LogL: -1394.214 / Time: 0h:0m:2s (0h:0m:0s left)
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Iteration 200 / LogL: -1385.358 / Time: 0h:0m:2s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -1417.689
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.996
Optimizing NNI: done in 0.0207391 secs using 97.53% CPU
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Optimizing NNI: done in 0.00783587 secs using 97.81% CPU
Iteration 210 / LogL: -1385.512 / Time: 0h:0m:3s (0h:0m:1s left)
Optimizing NNI: done in 0.0111129 secs using 97.43% CPU
Optimizing NNI: done in 0.0142131 secs using 94.72% CPU
Optimizing NNI: done in 0.0103979 secs using 97.76% CPU
Optimizing NNI: done in 0.0145359 secs using 96% CPU
Optimizing NNI: done in 0.0106959 secs using 97.62% CPU
Optimizing NNI: done in 0.00670099 secs using 99.57% CPU
Optimizing NNI: done in 0.01491 secs using 96.47% CPU
Optimizing NNI: done in 0.01122 secs using 97.07% CPU
Optimizing NNI: done in 0.0120418 secs using 95.6% CPU
Optimizing NNI: done in 0.00319505 secs using 94.87% CPU
Iteration 220 / LogL: -1388.875 / Time: 0h:0m:3s (0h:0m:1s left)
Optimizing NNI: done in 0.00939918 secs using 97.46% CPU
Optimizing NNI: done in 0.0117571 secs using 97.69% CPU
Optimizing NNI: done in 0.011441 secs using 97.22% CPU
TREE SEARCH COMPLETED AFTER 223 ITERATIONS / Time: 0h:0m:3s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1385.306
Optimal log-likelihood: -1385.305
Rate parameters: A-C: 0.39606 A-G: 1.57582 A-T: 1.00000 C-G: 0.39606 C-T: 1.57582 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.722,0.400) (0.278,2.554)
Parameters optimization took 1 rounds (0.003 sec)
BEST SCORE FOUND : -1385.305
Creating bootstrap support values...
Split supports printed to NEXUS file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpi6oh821h/q2iqtreeufboot.splits.nex
Total tree length: 6.876
Total number of iterations: 223
CPU time used for tree search: 3.277 sec (0h:0m:3s)
Wall-clock time used for tree search: 3.233 sec (0h:0m:3s)
Total CPU time used: 3.342 sec (0h:0m:3s)
Total wall-clock time used: 3.299 sec (0h:0m:3s)
Computing bootstrap consensus tree...
Reading input file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpi6oh821h/q2iqtreeufboot.splits.nex...
20 taxa and 167 splits.
Consensus tree written to /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpi6oh821h/q2iqtreeufboot.contree
Reading input trees file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpi6oh821h/q2iqtreeufboot.contree
Log-likelihood of consensus tree: -1385.305
Analysis results written to:
IQ-TREE report: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpi6oh821h/q2iqtreeufboot.iqtree
Maximum-likelihood tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpi6oh821h/q2iqtreeufboot.treefile
Likelihood distances: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpi6oh821h/q2iqtreeufboot.mldist
Ultrafast bootstrap approximation results written to:
Split support values: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpi6oh821h/q2iqtreeufboot.splits.nex
Consensus tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpi6oh821h/q2iqtreeufboot.contree
Screen log file: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpi6oh821h/q2iqtreeufboot.log
Date and Time: Thu Nov 16 16:37:11 2023
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -bb 1000 -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpi6oh821h/q2iqtreeufboot -nt 1 -nstop 200 -pers 0.200000
Saved Phylogeny[Unrooted] to: iqt-nnisi-bootstrap-tree.qza
Perform single branch tests alongside ufboot¶
We can also apply single branch test methods concurrently with ultrafast bootstrapping. The support values will always be represented in the following order: alrt / lbp / abayes / ufboot. Again, these values can be seen as separately listed bootstrap values in iTOL. We’ll also specify a model as we did earlier.
qiime phylogeny iqtree-ultrafast-bootstrap \
--i-alignment masked-aligned-rep-seqs.qza \
--p-perturb-nni-strength 0.2 \
--p-stop-iter 200 \
--p-n-cores 1 \
--p-alrt 1000 \
--p-abayes \
--p-lbp 1000 \
--p-substitution-model 'GTR+I+G' \
--o-tree iqt-nnisi-bootstrap-sbt-gtrig-tree.qza \
--verbose
stdout:
IQ-TREE multicore version 2.2.5 COVID-edition for Mac OS X 64-bit built Sep 15 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: Elizabeths-MacBook-Pro-2.local (AVX512, FMA3, 32 GB RAM)
Command: iqtree -bb 1000 -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmps0yit2kf/q2iqtreeufboot -nt 1 -alrt 1000 -abayes -lbp 1000 -nstop 200 -pers 0.200000
Seed: 514297 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Nov 16 16:37:20 2023
Kernel: AVX+FMA - 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/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000123978 secs using 84.69% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000259876 secs using 69.65% 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 1.00136e-05 secs using 79.89% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 4.19617e-05 secs using 73.88% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
Generating 1000 samples for ultrafast bootstrap (seed: 514297)...
NOTE: 1 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Thoroughly optimizing +I+G parameters from 10 start values...
Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 1.263 / LogL: -1392.811
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.008, 1.354 / LogL: -1393.088
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.009, 1.365 / LogL: -1393.160
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.009, 1.361 / LogL: -1393.150
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.008, 1.357 / LogL: -1393.113
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.009, 1.364 / LogL: -1393.141
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.007, 1.355 / LogL: -1393.088
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.008, 1.355 / LogL: -1393.102
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.008, 1.358 / LogL: -1393.108
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.008, 1.360 / LogL: -1393.118
Optimal pinv,alpha: 0.000, 1.263 / LogL: -1392.811
Parameters optimization took 0.349 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000955105 secs using 95.28% CPU
Computing ML distances took 0.001033 sec (of wall-clock time) 0.000960 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 7.10487e-05 secs using 67.56% CPU
Constructing RapidNJ tree: done in 8.60691e-05 secs using 153.4% CPU
Computing RapidNJ tree took 0.000221 sec (of wall-clock time) 0.000250 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.723
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.079 second
Computing log-likelihood of 98 initial trees ... 0.080 seconds
Current best score: -1392.723
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.0198309 secs using 186.1% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.358
Optimizing NNI: done in 0.014523 secs using 158.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1387.262
Optimizing NNI: done in 0.0129471 secs using 98.67% CPU
Optimizing NNI: done in 0.010942 secs using 98.76% CPU
Optimizing NNI: done in 0.011045 secs using 98% CPU
Optimizing NNI: done in 0.012557 secs using 96.14% CPU
Optimizing NNI: done in 0.0120659 secs using 97.78% CPU
Optimizing NNI: done in 0.010824 secs using 99.09% CPU
Optimizing NNI: done in 0.0112681 secs using 96.25% CPU
Optimizing NNI: done in 0.0116401 secs using 97.26% CPU
Iteration 10 / LogL: -1387.740 / Time: 0h:0m:0s
Optimizing NNI: done in 0.028255 secs using 95.18% CPU
Optimizing NNI: done in 0.0241241 secs using 96.51% CPU
Optimizing NNI: done in 0.0220869 secs using 97.9% CPU
Optimizing NNI: done in 0.0236912 secs using 96.91% CPU
Optimizing NNI: done in 0.024009 secs using 95.66% CPU
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Optimizing NNI: done in 0.0237231 secs using 94.63% CPU
Optimizing NNI: done in 0.0268371 secs using 94.25% CPU
Optimizing NNI: done in 0.0240271 secs using 94.17% CPU
Iteration 20 / LogL: -1387.281 / Time: 0h:0m:0s
Finish initializing candidate tree set (2)
Current best tree score: -1387.262 / CPU time: 0.562
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.014571 secs using 94.31% CPU
Optimizing NNI: done in 0.0133049 secs using 95.48% CPU
Optimizing NNI: done in 0.020364 secs using 97.11% CPU
Optimizing NNI: done in 0.0310569 secs using 96.16% CPU
Optimizing NNI: done in 0.033196 secs using 95.46% CPU
Optimizing NNI: done in 0.014446 secs using 98.15% CPU
Optimizing NNI: done in 0.038604 secs using 96.69% CPU
Optimizing NNI: done in 0.0311248 secs using 97.59% CPU
Optimizing NNI: done in 0.0243759 secs using 96.98% CPU
Optimizing NNI: done in 0.0164042 secs using 96.3% CPU
Iteration 30 / LogL: -1387.371 / Time: 0h:0m:1s (0h:0m:7s left)
Optimizing NNI: done in 0.0337842 secs using 97.22% CPU
Optimizing NNI: done in 0.0222249 secs using 92.08% CPU
Optimizing NNI: done in 0.015388 secs using 96.01% CPU
Optimizing NNI: done in 0.0277951 secs using 95.87% CPU
Optimizing NNI: done in 0.0210121 secs using 95.63% CPU
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Optimizing NNI: done in 0.00530291 secs using 99.02% CPU
Optimizing NNI: done in 0.010128 secs using 92.76% CPU
Optimizing NNI: done in 0.0201769 secs using 97.3% CPU
Optimizing NNI: done in 0.0270929 secs using 95.86% CPU
Iteration 40 / LogL: -1387.369 / Time: 0h:0m:1s (0h:0m:5s left)
Optimizing NNI: done in 0.0179098 secs using 95.38% CPU
Optimizing NNI: done in 0.02598 secs using 97.18% CPU
Optimizing NNI: done in 0.0135331 secs using 98.56% CPU
Optimizing NNI: done in 0.012471 secs using 95.88% CPU
Optimizing NNI: done in 0.0103381 secs using 97.4% CPU
Optimizing NNI: done in 0.0260069 secs using 95.82% CPU
Optimizing NNI: done in 0.00693393 secs using 97.85% CPU
Optimizing NNI: done in 0.026721 secs using 95.12% CPU
Optimizing NNI: done in 0.013001 secs using 95.1% CPU
Optimizing NNI: done in 0.013685 secs using 95.45% CPU
Iteration 50 / LogL: -1387.495 / Time: 0h:0m:1s (0h:0m:4s left)
Log-likelihood cutoff on original alignment: -1407.550
Optimizing NNI: done in 0.00372505 secs using 99.49% CPU
Optimizing NNI: done in 0.0054419 secs using 99.17% CPU
Optimizing NNI: done in 0.00676823 secs using 99.95% CPU
Optimizing NNI: done in 0.0190878 secs using 98.23% CPU
Optimizing NNI: done in 0.0154581 secs using 98.12% CPU
Optimizing NNI: done in 0.0041461 secs using 99.8% CPU
Optimizing NNI: done in 0.00943589 secs using 98.87% CPU
Optimizing NNI: done in 0.010191 secs using 98.08% CPU
Optimizing NNI: done in 0.013633 secs using 98.64% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.256
Optimizing NNI: done in 0.00579 secs using 99.08% CPU
Iteration 60 / LogL: -1387.366 / Time: 0h:0m:1s (0h:0m:4s left)
Optimizing NNI: done in 0.00915289 secs using 98.46% CPU
Optimizing NNI: done in 0.019592 secs using 99.3% CPU
Optimizing NNI: done in 0.00413609 secs using 99.83% CPU
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Optimizing NNI: done in 0.0221889 secs using 98.54% CPU
Optimizing NNI: done in 0.0158482 secs using 97.68% CPU
Iteration 70 / LogL: -1387.357 / Time: 0h:0m:1s (0h:0m:3s left)
Optimizing NNI: done in 0.017019 secs using 98.03% CPU
Optimizing NNI: done in 0.011796 secs using 97.31% CPU
Optimizing NNI: done in 0.0297911 secs using 94.65% CPU
Optimizing NNI: done in 0.00331998 secs using 99.64% CPU
Optimizing NNI: done in 0.030659 secs using 96.01% CPU
Optimizing NNI: done in 0.00373697 secs using 99.92% CPU
Optimizing NNI: done in 0.00500798 secs using 99.7% CPU
Optimizing NNI: done in 0.024394 secs using 96.27% CPU
Optimizing NNI: done in 0.0181079 secs using 98.29% CPU
Optimizing NNI: done in 0.012605 secs using 98.53% CPU
Iteration 80 / LogL: -1387.358 / Time: 0h:0m:2s (0h:0m:3s left)
Optimizing NNI: done in 0.00654697 secs using 99.59% CPU
Optimizing NNI: done in 0.0310509 secs using 98.57% CPU
Optimizing NNI: done in 0.00950098 secs using 99.88% CPU
Optimizing NNI: done in 0.015949 secs using 97.01% CPU
Optimizing NNI: done in 0.0106869 secs using 98.63% CPU
Optimizing NNI: done in 0.0492542 secs using 98.2% CPU
Optimizing NNI: done in 0.0126262 secs using 97.63% CPU
Optimizing NNI: done in 0.021194 secs using 97% CPU
Optimizing NNI: done in 0.0215468 secs using 97.68% CPU
Optimizing NNI: done in 0.0167069 secs using 97.35% CPU
Iteration 90 / LogL: -1387.355 / Time: 0h:0m:2s (0h:0m:3s left)
Optimizing NNI: done in 0.0114019 secs using 97.01% CPU
Optimizing NNI: done in 0.01721 secs using 97.43% CPU
Optimizing NNI: done in 0.00632405 secs using 96.81% CPU
Optimizing NNI: done in 0.0118041 secs using 97.2% CPU
Optimizing NNI: done in 0.0177181 secs using 97.08% CPU
Optimizing NNI: done in 0.0125151 secs using 96.97% CPU
Optimizing NNI: done in 0.0190599 secs using 97.88% CPU
Optimizing NNI: done in 0.00576401 secs using 99.57% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.255
Optimizing NNI: done in 0.017442 secs using 97.92% CPU
Optimizing NNI: done in 0.0135 secs using 98.87% CPU
Iteration 100 / LogL: -1387.354 / Time: 0h:0m:2s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -1406.502
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.993
Optimizing NNI: done in 0.00787997 secs using 98.53% CPU
Optimizing NNI: done in 0.00804901 secs using 97.15% CPU
Optimizing NNI: done in 0.0212169 secs using 98.03% CPU
Optimizing NNI: done in 0.0207181 secs using 97.36% CPU
Optimizing NNI: done in 0.0106969 secs using 99.08% CPU
Optimizing NNI: done in 0.0128622 secs using 99.66% CPU
Optimizing NNI: done in 0.0191081 secs using 97.2% CPU
Optimizing NNI: done in 0.00707197 secs using 98.67% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.255
Optimizing NNI: done in 0.00887012 secs using 98.43% CPU
Optimizing NNI: done in 0.00771308 secs using 99.79% CPU
Iteration 110 / LogL: -1387.282 / Time: 0h:0m:2s (0h:0m:2s left)
Optimizing NNI: done in 0.0214629 secs using 97.99% CPU
Optimizing NNI: done in 0.00486493 secs using 99.69% CPU
Optimizing NNI: done in 0.0147021 secs using 97.25% CPU
Optimizing NNI: done in 0.034843 secs using 98.32% CPU
Optimizing NNI: done in 0.0114119 secs using 98.68% CPU
Optimizing NNI: done in 0.0136368 secs using 98.28% CPU
Optimizing NNI: done in 0.0183139 secs using 99.07% CPU
Optimizing NNI: done in 0.018636 secs using 96.94% CPU
Optimizing NNI: done in 0.0162978 secs using 98.45% CPU
Optimizing NNI: done in 0.0126379 secs using 99.92% CPU
Iteration 120 / LogL: -1387.274 / Time: 0h:0m:2s (0h:0m:2s left)
Optimizing NNI: done in 0.00521111 secs using 99.98% CPU
Optimizing NNI: done in 0.0159822 secs using 97.06% CPU
Optimizing NNI: done in 0.014287 secs using 98.98% CPU
Optimizing NNI: done in 0.023109 secs using 99.05% CPU
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Optimizing NNI: done in 0.00913095 secs using 98.93% CPU
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Optimizing NNI: done in 0.00389194 secs using 99.23% CPU
Optimizing NNI: done in 0.0131121 secs using 97.59% CPU
Iteration 130 / LogL: -1387.354 / Time: 0h:0m:3s (0h:0m:1s left)
Optimizing NNI: done in 0.00973606 secs using 98.04% CPU
Optimizing NNI: done in 0.011797 secs using 98.68% CPU
Optimizing NNI: done in 0.00571513 secs using 95.76% CPU
Optimizing NNI: done in 0.0522082 secs using 93.8% CPU
Optimizing NNI: done in 0.0349052 secs using 99.56% CPU
Optimizing NNI: done in 0.037236 secs using 98.94% CPU
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Optimizing NNI: done in 0.016928 secs using 98.59% CPU
Optimizing NNI: done in 0.0160961 secs using 99.94% CPU
Iteration 140 / LogL: -1387.359 / Time: 0h:0m:3s (0h:0m:1s left)
Optimizing NNI: done in 0.0101051 secs using 96.44% CPU
Optimizing NNI: done in 0.0182569 secs using 99.17% CPU
Optimizing NNI: done in 0.00881195 secs using 99.93% CPU
Optimizing NNI: done in 0.00469494 secs using 99.94% CPU
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Optimizing NNI: done in 0.010644 secs using 99.94% CPU
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Optimizing NNI: done in 0.0393469 secs using 99.47% CPU
Optimizing NNI: done in 0.018904 secs using 99.87% CPU
Optimizing NNI: done in 0.00894308 secs using 99.18% CPU
Iteration 150 / LogL: -1387.306 / Time: 0h:0m:3s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -1406.925
Optimizing NNI: done in 0.00525713 secs using 99.52% CPU
Optimizing NNI: done in 0.00973892 secs using 98.05% CPU
Optimizing NNI: done in 0.0119491 secs using 99.27% CPU
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Iteration 160 / LogL: -1387.355 / Time: 0h:0m:3s (0h:0m:0s left)
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Iteration 170 / LogL: -1387.355 / Time: 0h:0m:3s (0h:0m:0s left)
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Iteration 180 / LogL: -1389.342 / Time: 0h:0m:4s (0h:0m:0s left)
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Iteration 190 / LogL: -1387.266 / Time: 0h:0m:4s (0h:0m:0s left)
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Iteration 200 / LogL: -1387.276 / Time: 0h:0m:4s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -1407.440
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.997
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TREE SEARCH COMPLETED AFTER 203 ITERATIONS / Time: 0h:0m:4s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.255
Optimal log-likelihood: -1387.253
Rate parameters: A-C: 0.33358 A-G: 2.30275 A-T: 2.18353 C-G: 1.19632 C-T: 3.35252 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.000
Gamma shape alpha: 1.318
Parameters optimization took 1 rounds (0.002 sec)
BEST SCORE FOUND : -1387.253
Testing tree branches by SH-like aLRT with 1000 replicates...
Testing tree branches by local-BP test with 1000 replicates...
Testing tree branches by aBayes parametric test...
0.047 sec.
Creating bootstrap support values...
Split supports printed to NEXUS file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmps0yit2kf/q2iqtreeufboot.splits.nex
Total tree length: 6.742
Total number of iterations: 203
CPU time used for tree search: 4.132 sec (0h:0m:4s)
Wall-clock time used for tree search: 4.110 sec (0h:0m:4s)
Total CPU time used: 4.570 sec (0h:0m:4s)
Total wall-clock time used: 4.566 sec (0h:0m:4s)
Computing bootstrap consensus tree...
Reading input file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmps0yit2kf/q2iqtreeufboot.splits.nex...
20 taxa and 150 splits.
Consensus tree written to /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmps0yit2kf/q2iqtreeufboot.contree
Reading input trees file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmps0yit2kf/q2iqtreeufboot.contree
Log-likelihood of consensus tree: -1387.434
Analysis results written to:
IQ-TREE report: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmps0yit2kf/q2iqtreeufboot.iqtree
Maximum-likelihood tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmps0yit2kf/q2iqtreeufboot.treefile
Likelihood distances: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmps0yit2kf/q2iqtreeufboot.mldist
Ultrafast bootstrap approximation results written to:
Split support values: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmps0yit2kf/q2iqtreeufboot.splits.nex
Consensus tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmps0yit2kf/q2iqtreeufboot.contree
Screen log file: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmps0yit2kf/q2iqtreeufboot.log
Date and Time: Thu Nov 16 16:37:25 2023
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: iqtree -bb 1000 -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/5118ee3a-886d-4d08-8466-bee4790c7177/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmps0yit2kf/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!