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/2024.2/tutorials/phylogeny/rep-seqs.qza
Save as: rep-seqs.qza
wget \
-O "rep-seqs.qza" \
"https://data.qiime2.org/2024.2/tutorials/phylogeny/rep-seqs.qza"
curl -sL \
"https://data.qiime2.org/2024.2/tutorials/phylogeny/rep-seqs.qza" > \
"rep-seqs.qza"
Run MAFFT
qiime alignment mafft \
--i-sequences rep-seqs.qza \
--o-alignment aligned-rep-seqs.qza
Reducing alignment ambiguity: masking and reference alignments¶
Why mask an alignment?
Masking helps to eliminate alignment columns that are phylogenetically uninformative or misleading before phylogenetic analysis. Much of the time alignment errors can introduce noise and confound phylogenetic inference. It is common practice to mask (remove) these ambiguously aligned regions prior to performing phylogenetic inference. In particular, David Lane’s (1991) chapter 16S/23S rRNA sequencing proposed masking SSU data prior to phylogenetic analysis. However, knowing how to deal with ambiguously aligned regions and when to apply masks largely depends on the marker genes being analyzed and the question being asked of the data.
Note
Keep in mind that this is still an active area of discussion, as highlighted by the following non-exhaustive list of articles: Wu et al. 2012, Ashkenazy et al. 2018, Schloss 2010, Tan et al. 2015, Rajan 2015.
How to mask alignment.
For our purposes, we’ll assume that we have ambiguously aligned columns in the
MAFFT alignment we produced above. The default settings for the
--p-min-conservation of the
alignment mask approximates the
Lane mask filtering of QIIME 1. Keep an eye out for updates to the alignment
plugin.
qiime alignment mask \
--i-alignment aligned-rep-seqs.qza \
--o-masked-alignment masked-aligned-rep-seqs.qza
Reference based alignments
There are several tools that attempt to reduce the amount of ambiguously aligned regions by using curated reference alignments. Traditional, de novo alignment methods mututally align a set of unaligned sequences to create a multiple sequence alignment (MSA) from scratch. Re-running these methods with additional sequences will create MSAs with varying numbers of columns and assignments of bases to each column. These alignments is therefore incompatible with one another and may not be joined through concatenation.
Reference based alignments, on the other hand, are meant to add sequences to an existing alignment. Alignments computed using reference based alignment tools always have widths identical to the reference alignment and maintain the meaning of each column. Therefore, these alignments may be concatenated.
QIIME 2 currently does not wrap any methods for reference-based alignments, but alignments created using these methods can be imported into QIIME 2 as FeatureData[AlignedSequence] artifacts, provided that the alignments are standard FASTA formats. Some examples of tools for reference-based alignment include PyNAST (using NAST), Infernal, and SINA. SILVA Reference
alignments are particularly powerful for rRNA gene sequence data, as knowledge
of secondary structure is incorporated into the curation process, thus
increasing alignment quality.
Note
Alignments constructed using reference based alignment approaches can be masked too, just like the above MAFFT example. Also, the reference alignment approach we are discussing here is distinct from the reference phylogeny approach (i.e. q2-fragment-insertion) we mentioned earlier. That is, we are not inserting our data into an existing tree, but simply trying to create a more robust alignment for making a better de novo phylogeny.
Construct a phylogeny¶
As with MSA algorithms, phylogenetic inference tools are also legion. Fortunately, there are many great resources to learn about phylogentics. Below are just a few introductory resources to get you started:
There are several methods / pipelines available through the q2-phylogeny plugin of :qiime2:. These are based on the following tools:
Methods¶
fasttree¶
FastTree is able to construct phylogenies from large sequence alignments quite rapidly. It does this by using the using a CAT-like rate category approximation, which is also available through RAxML (discussed below). Check out the FastTree online manual for more information.
qiime phylogeny fasttree \
--i-alignment masked-aligned-rep-seqs.qza \
--o-tree fasttree-tree.qza
Tip
For an easy and direct way to view your tree.qza files, upload
them to iTOL. Here, you can interactively view and manipulate your
phylogeny. Even better, while viewing the tree topology in “Normal mode”,
you can drag and drop your associated alignment.qza (the one you used to
build the phylogeny) or a relevent taxonomy.qza file onto the iTOL tree
visualization. This will allow you to directly view the sequence alignment
or taxonomy alongside the phylogeny. 🕶️
raxml¶
Like fasttree, raxml will perform a single phylogentic inference and
return a tree. Note, the default model for raxml is
--p-substitution-model GTRGAMMA. If you’d like to construct a tree using
the CAT model like fasttree, simply replace GTRGAMMA with GTRCAT as
shown below:
qiime phylogeny raxml \
--i-alignment masked-aligned-rep-seqs.qza \
--p-substitution-model GTRCAT \
--o-tree raxml-cat-tree.qza \
--verbose
stdout:
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Sarah Lutteropp (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
Charlie Taylor (UF)
Alignment has 157 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 39.77%
RAxML rapid hill-climbing mode
Using 1 distinct models/data partitions with joint branch length optimization
Executing 1 inferences on the original alignment using 1 distinct randomized MP trees
All free model parameters will be estimated by RAxML
ML estimate of 25 per site rate categories
Likelihood of final tree will be evaluated and optimized under GAMMA
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 157
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
raxmlHPC -m GTRCAT -p 5172 -N 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -w /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp1ti15ful -n q2
Partition: 0 with name: No Name Provided
Base frequencies: 0.243 0.182 0.319 0.256
Inference[0]: Time 0.472023 CAT-based likelihood -1243.159859, best rearrangement setting 5
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -1387.902017 tree written to file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp1ti15ful/RAxML_result.q2
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -1387.902017 ....
Final GAMMA-based Score of best tree -1387.229193
Program execution info written to /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp1ti15ful/RAxML_info.q2
Best-scoring ML tree written to: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp1ti15ful/RAxML_bestTree.q2
Overall execution time: 0.971498 secs or 0.000270 hours or 0.000011 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 5172 -N 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -w /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp1ti15ful -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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -w /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpbsgdd0cf -n q2
Partition: 0 with name: No Name Provided
Base frequencies: 0.243 0.182 0.319 0.256
Inference[0]: Time 0.428249 CAT-based likelihood -1238.242991, best rearrangement setting 5
Inference[1]: Time 0.351028 CAT-based likelihood -1249.502284, best rearrangement setting 5
Inference[2]: Time 0.366055 CAT-based likelihood -1242.978035, best rearrangement setting 5
Inference[3]: Time 0.474151 CAT-based likelihood -1243.159855, best rearrangement setting 5
Inference[4]: Time 0.351225 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/tmpbsgdd0cf/RAxML_result.q2.RUN.0
Inference[1] final GAMMA-based Likelihood: -1392.813982 tree written to file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpbsgdd0cf/RAxML_result.q2.RUN.1
Inference[2] final GAMMA-based Likelihood: -1388.073642 tree written to file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpbsgdd0cf/RAxML_result.q2.RUN.2
Inference[3] final GAMMA-based Likelihood: -1387.945266 tree written to file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpbsgdd0cf/RAxML_result.q2.RUN.3
Inference[4] final GAMMA-based Likelihood: -1387.557031 tree written to file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpbsgdd0cf/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/tmpbsgdd0cf/RAxML_info.q2
Best-scoring ML tree written to: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpbsgdd0cf/RAxML_bestTree.q2
Overall execution time: 2.518388 secs or 0.000700 hours or 0.000029 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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -w /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpbsgdd0cf -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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -w /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpcjv5b5i5 -n q2bootstrap
Time for BS model parameter optimization 0.036868
Bootstrap[0]: Time 0.120482 seconds, bootstrap likelihood -1199.758796, best rearrangement setting 12
Bootstrap[1]: Time 0.080728 seconds, bootstrap likelihood -1344.229251, best rearrangement setting 6
Bootstrap[2]: Time 0.076798 seconds, bootstrap likelihood -1295.343000, best rearrangement setting 8
Bootstrap[3]: Time 0.063730 seconds, bootstrap likelihood -1273.768320, best rearrangement setting 8
Bootstrap[4]: Time 0.076849 seconds, bootstrap likelihood -1253.402952, best rearrangement setting 6
Bootstrap[5]: Time 0.079933 seconds, bootstrap likelihood -1260.866113, best rearrangement setting 10
Bootstrap[6]: Time 0.079295 seconds, bootstrap likelihood -1293.636299, best rearrangement setting 14
Bootstrap[7]: Time 0.069965 seconds, bootstrap likelihood -1227.178693, best rearrangement setting 6
Bootstrap[8]: Time 0.075968 seconds, bootstrap likelihood -1321.820787, best rearrangement setting 13
Bootstrap[9]: Time 0.084791 seconds, bootstrap likelihood -1147.233446, best rearrangement setting 6
Bootstrap[10]: Time 0.058059 seconds, bootstrap likelihood -1220.766493, best rearrangement setting 13
Bootstrap[11]: Time 0.082992 seconds, bootstrap likelihood -1200.006355, best rearrangement setting 8
Bootstrap[12]: Time 0.090462 seconds, bootstrap likelihood -1346.392834, best rearrangement setting 14
Bootstrap[13]: Time 0.074159 seconds, bootstrap likelihood -1301.111096, best rearrangement setting 14
Bootstrap[14]: Time 0.079054 seconds, bootstrap likelihood -1262.253559, best rearrangement setting 11
Bootstrap[15]: Time 0.079305 seconds, bootstrap likelihood -1215.017551, best rearrangement setting 14
Bootstrap[16]: Time 0.075725 seconds, bootstrap likelihood -1238.832009, best rearrangement setting 7
Bootstrap[17]: Time 0.069291 seconds, bootstrap likelihood -1393.989732, best rearrangement setting 12
Bootstrap[18]: Time 0.074917 seconds, bootstrap likelihood -1173.921002, best rearrangement setting 15
Bootstrap[19]: Time 0.085186 seconds, bootstrap likelihood -1185.726976, best rearrangement setting 11
Bootstrap[20]: Time 0.066581 seconds, bootstrap likelihood -1158.491940, best rearrangement setting 6
Bootstrap[21]: Time 0.064731 seconds, bootstrap likelihood -1154.664272, best rearrangement setting 11
Bootstrap[22]: Time 0.072235 seconds, bootstrap likelihood -1244.159837, best rearrangement setting 10
Bootstrap[23]: Time 0.086245 seconds, bootstrap likelihood -1211.171036, best rearrangement setting 15
Bootstrap[24]: Time 0.073353 seconds, bootstrap likelihood -1261.440677, best rearrangement setting 12
Bootstrap[25]: Time 0.074340 seconds, bootstrap likelihood -1331.836715, best rearrangement setting 15
Bootstrap[26]: Time 0.075668 seconds, bootstrap likelihood -1129.144509, best rearrangement setting 5
Bootstrap[27]: Time 0.094054 seconds, bootstrap likelihood -1226.624056, best rearrangement setting 7
Bootstrap[28]: Time 0.091694 seconds, bootstrap likelihood -1221.046176, best rearrangement setting 12
Bootstrap[29]: Time 0.061034 seconds, bootstrap likelihood -1211.791204, best rearrangement setting 14
Bootstrap[30]: Time 0.077501 seconds, bootstrap likelihood -1389.442380, best rearrangement setting 5
Bootstrap[31]: Time 0.078253 seconds, bootstrap likelihood -1303.638592, best rearrangement setting 12
Bootstrap[32]: Time 0.084987 seconds, bootstrap likelihood -1172.859456, best rearrangement setting 12
Bootstrap[33]: Time 0.073122 seconds, bootstrap likelihood -1244.617135, best rearrangement setting 9
Bootstrap[34]: Time 0.069891 seconds, bootstrap likelihood -1211.871717, best rearrangement setting 15
Bootstrap[35]: Time 0.084236 seconds, bootstrap likelihood -1299.862912, best rearrangement setting 5
Bootstrap[36]: Time 0.066865 seconds, bootstrap likelihood -1141.967505, best rearrangement setting 5
Bootstrap[37]: Time 0.085267 seconds, bootstrap likelihood -1283.923198, best rearrangement setting 12
Bootstrap[38]: Time 0.068473 seconds, bootstrap likelihood -1304.250946, best rearrangement setting 5
Bootstrap[39]: Time 0.064114 seconds, bootstrap likelihood -1407.084376, best rearrangement setting 15
Bootstrap[40]: Time 0.076501 seconds, bootstrap likelihood -1277.946299, best rearrangement setting 13
Bootstrap[41]: Time 0.075458 seconds, bootstrap likelihood -1279.006200, best rearrangement setting 7
Bootstrap[42]: Time 0.072784 seconds, bootstrap likelihood -1160.274606, best rearrangement setting 6
Bootstrap[43]: Time 0.087997 seconds, bootstrap likelihood -1216.079259, best rearrangement setting 14
Bootstrap[44]: Time 0.069549 seconds, bootstrap likelihood -1382.278311, best rearrangement setting 8
Bootstrap[45]: Time 0.080095 seconds, bootstrap likelihood -1099.004439, best rearrangement setting 11
Bootstrap[46]: Time 0.061248 seconds, bootstrap likelihood -1296.527478, best rearrangement setting 8
Bootstrap[47]: Time 0.091361 seconds, bootstrap likelihood -1291.322658, best rearrangement setting 9
Bootstrap[48]: Time 0.059856 seconds, bootstrap likelihood -1161.908080, best rearrangement setting 6
Bootstrap[49]: Time 0.082722 seconds, bootstrap likelihood -1257.348428, best rearrangement setting 13
Bootstrap[50]: Time 0.094081 seconds, bootstrap likelihood -1309.422533, best rearrangement setting 13
Bootstrap[51]: Time 0.069112 seconds, bootstrap likelihood -1197.633097, best rearrangement setting 11
Bootstrap[52]: Time 0.077572 seconds, bootstrap likelihood -1347.123005, best rearrangement setting 8
Bootstrap[53]: Time 0.068698 seconds, bootstrap likelihood -1234.934890, best rearrangement setting 14
Bootstrap[54]: Time 0.079791 seconds, bootstrap likelihood -1227.092434, best rearrangement setting 6
Bootstrap[55]: Time 0.083447 seconds, bootstrap likelihood -1280.635747, best rearrangement setting 7
Bootstrap[56]: Time 0.068337 seconds, bootstrap likelihood -1225.911449, best rearrangement setting 6
Bootstrap[57]: Time 0.064744 seconds, bootstrap likelihood -1236.213347, best rearrangement setting 11
Bootstrap[58]: Time 0.094157 seconds, bootstrap likelihood -1393.245723, best rearrangement setting 14
Bootstrap[59]: Time 0.074448 seconds, bootstrap likelihood -1212.039371, best rearrangement setting 6
Bootstrap[60]: Time 0.063910 seconds, bootstrap likelihood -1248.692011, best rearrangement setting 10
Bootstrap[61]: Time 0.074866 seconds, bootstrap likelihood -1172.820979, best rearrangement setting 13
Bootstrap[62]: Time 0.087798 seconds, bootstrap likelihood -1126.745788, best rearrangement setting 14
Bootstrap[63]: Time 0.067982 seconds, bootstrap likelihood -1267.434444, best rearrangement setting 12
Bootstrap[64]: Time 0.065903 seconds, bootstrap likelihood -1340.680748, best rearrangement setting 5
Bootstrap[65]: Time 0.067832 seconds, bootstrap likelihood -1072.671059, best rearrangement setting 5
Bootstrap[66]: Time 0.082996 seconds, bootstrap likelihood -1234.294838, best rearrangement setting 8
Bootstrap[67]: Time 0.084415 seconds, bootstrap likelihood -1109.249439, best rearrangement setting 15
Bootstrap[68]: Time 0.063732 seconds, bootstrap likelihood -1314.493588, best rearrangement setting 8
Bootstrap[69]: Time 0.065657 seconds, bootstrap likelihood -1173.850035, best rearrangement setting 13
Bootstrap[70]: Time 0.070938 seconds, bootstrap likelihood -1231.066465, best rearrangement setting 10
Bootstrap[71]: Time 0.070131 seconds, bootstrap likelihood -1146.861379, best rearrangement setting 9
Bootstrap[72]: Time 0.060704 seconds, bootstrap likelihood -1148.753369, best rearrangement setting 8
Bootstrap[73]: Time 0.069789 seconds, bootstrap likelihood -1333.374056, best rearrangement setting 9
Bootstrap[74]: Time 0.062079 seconds, bootstrap likelihood -1259.382378, best rearrangement setting 5
Bootstrap[75]: Time 0.066806 seconds, bootstrap likelihood -1319.944496, best rearrangement setting 6
Bootstrap[76]: Time 0.080093 seconds, bootstrap likelihood -1309.042165, best rearrangement setting 14
Bootstrap[77]: Time 0.094027 seconds, bootstrap likelihood -1232.061289, best rearrangement setting 8
Bootstrap[78]: Time 0.076903 seconds, bootstrap likelihood -1261.333984, best rearrangement setting 9
Bootstrap[79]: Time 0.079917 seconds, bootstrap likelihood -1194.644341, best rearrangement setting 13
Bootstrap[80]: Time 0.071773 seconds, bootstrap likelihood -1214.037389, best rearrangement setting 9
Bootstrap[81]: Time 0.075060 seconds, bootstrap likelihood -1224.527657, best rearrangement setting 8
Bootstrap[82]: Time 0.089393 seconds, bootstrap likelihood -1241.464826, best rearrangement setting 11
Bootstrap[83]: Time 0.066754 seconds, bootstrap likelihood -1230.730558, best rearrangement setting 6
Bootstrap[84]: Time 0.071494 seconds, bootstrap likelihood -1219.034592, best rearrangement setting 10
Bootstrap[85]: Time 0.077478 seconds, bootstrap likelihood -1280.071994, best rearrangement setting 8
Bootstrap[86]: Time 0.067025 seconds, bootstrap likelihood -1444.747777, best rearrangement setting 9
Bootstrap[87]: Time 0.065468 seconds, bootstrap likelihood -1245.890035, best rearrangement setting 14
Bootstrap[88]: Time 0.076014 seconds, bootstrap likelihood -1287.832766, best rearrangement setting 7
Bootstrap[89]: Time 0.070617 seconds, bootstrap likelihood -1325.245976, best rearrangement setting 5
Bootstrap[90]: Time 0.078893 seconds, bootstrap likelihood -1227.883697, best rearrangement setting 5
Bootstrap[91]: Time 0.076641 seconds, bootstrap likelihood -1273.489392, best rearrangement setting 8
Bootstrap[92]: Time 0.031133 seconds, bootstrap likelihood -1234.725870, best rearrangement setting 7
Bootstrap[93]: Time 0.087267 seconds, bootstrap likelihood -1235.733064, best rearrangement setting 11
Bootstrap[94]: Time 0.067577 seconds, bootstrap likelihood -1204.319488, best rearrangement setting 15
Bootstrap[95]: Time 0.065300 seconds, bootstrap likelihood -1183.328582, best rearrangement setting 11
Bootstrap[96]: Time 0.077503 seconds, bootstrap likelihood -1196.298898, best rearrangement setting 13
Bootstrap[97]: Time 0.082222 seconds, bootstrap likelihood -1339.251746, best rearrangement setting 12
Bootstrap[98]: Time 0.029972 seconds, bootstrap likelihood -1404.363552, best rearrangement setting 7
Bootstrap[99]: Time 0.039911 seconds, bootstrap likelihood -1270.157811, best rearrangement setting 7
Overall Time for 100 Rapid Bootstraps 7.455652 seconds
Average Time per Rapid Bootstrap 0.074557 seconds
Starting ML Search ...
Fast ML optimization finished
Fast ML search Time: 3.132830 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: 1.605503 seconds
Thorough ML search Time: 0.449633 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 5.192315 secs or 0.001442 hours
Combined Bootstrap and ML search took 12.648165 secs or 0.003513 hours
Drawing Bootstrap Support Values on best-scoring ML tree ...
Found 1 tree in File /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpcjv5b5i5/RAxML_bestTree.q2bootstrap
Found 1 tree in File /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpcjv5b5i5/RAxML_bestTree.q2bootstrap
Program execution info written to /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpcjv5b5i5/RAxML_info.q2bootstrap
All 100 bootstrapped trees written to: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpcjv5b5i5/RAxML_bootstrap.q2bootstrap
Best-scoring ML tree written to: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpcjv5b5i5/RAxML_bestTree.q2bootstrap
Best-scoring ML tree with support values written to: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpcjv5b5i5/RAxML_bipartitions.q2bootstrap
Best-scoring ML tree with support values as branch labels written to: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpcjv5b5i5/RAxML_bipartitionsBranchLabels.q2bootstrap
Overall execution time for full ML analysis: 12.657861 secs or 0.003516 hours or 0.000147 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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -w /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpcjv5b5i5 -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 2.2.6 COVID-edition for Mac OS X 64-bit built Dec 8 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: eduroam-lfx-dock-1-371.intern.ethz.ch (AVX512, FMA3, 32 GB RAM)
Command: iqtree -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp_83u2b1s/q2iqtree -nt 1
Seed: 668348 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Apr 4 14:00:13 2024
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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000112057 secs using 86.56% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000208855 secs using 70.38% 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 3.40939e-05 secs using 70.39% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.0113599 secs using 99.11% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1396.575
2. Current log-likelihood: -1395.213
Optimal log-likelihood: -1394.464
Rate parameters: A-C: 0.21819 A-G: 2.03593 A-T: 1.93394 C-G: 1.05109 C-T: 2.56337 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.033
Gamma shape alpha: 1.322
Parameters optimization took 2 rounds (0.007 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 1411.054 45 2912.108 2936.751 3063.577
2 GTR+F+I 1409.135 46 2910.270 2936.162 3065.105
3 GTR+F+G4 1392.992 46 2877.983 2903.876 3032.818
4 GTR+F+I+G4 1393.280 47 2880.561 2907.741 3038.762
5 GTR+F+R2 1387.712 47 2869.423 2896.604 3027.624
6 GTR+F+R3 1387.747 49 2873.494 2903.372 3038.427
14 GTR+F+I+R2 1387.798 48 2871.597 2900.106 3033.164
15 GTR+F+I+R3 1387.816 50 2875.631 2906.920 3043.930
25 SYM+G4 1393.506 43 2873.012 2895.271 3017.749
27 SYM+R2 1389.901 44 2867.802 2891.234 3015.905
36 SYM+I+R2 1390.056 45 2870.112 2894.755 3021.581
47 TVM+F+G4 1393.474 45 2876.947 2901.590 3028.416
49 TVM+F+R2 1388.475 46 2868.950 2894.842 3023.785
58 TVM+F+I+R2 1388.497 47 2870.994 2898.175 3029.195
69 TVMe+G4 1393.632 42 2871.264 2892.387 3012.635
71 TVMe+R2 1389.912 43 2865.824 2888.083 3010.561
80 TVMe+I+R2 1390.032 44 2868.063 2891.495 3016.166
91 TIM3+F+G4 1396.957 44 2881.914 2905.346 3030.017
93 TIM3+F+R2 1391.441 45 2872.881 2897.524 3024.350
102 TIM3+F+I+R2 1391.573 46 2875.146 2901.038 3029.981
113 TIM3e+G4 1397.005 41 2876.010 2896.033 3014.015
115 TIM3e+R2 1393.195 42 2870.390 2891.513 3011.761
124 TIM3e+I+R2 1393.369 43 2872.737 2894.996 3017.474
135 TIM2+F+G4 1401.480 44 2890.961 2914.393 3039.064
137 TIM2+F+R2 1395.762 45 2881.524 2906.167 3032.993
146 TIM2+F+I+R2 1395.853 46 2883.706 2909.598 3038.540
157 TIM2e+G4 1406.407 41 2894.815 2914.838 3032.820
159 TIM2e+R2 1402.269 42 2888.539 2909.662 3029.910
168 TIM2e+I+R2 1402.374 43 2890.749 2913.007 3035.486
179 TIM+F+G4 1397.972 44 2883.943 2907.375 3032.046
181 TIM+F+R2 1392.182 45 2874.365 2899.008 3025.834
190 TIM+F+I+R2 1392.255 46 2876.511 2902.403 3031.346
201 TIMe+G4 1403.787 41 2889.575 2909.598 3027.580
203 TIMe+R2 1399.417 42 2882.835 2903.958 3024.206
212 TIMe+I+R2 1399.551 43 2885.102 2907.361 3029.839
223 TPM3u+F+G4 1397.423 43 2880.846 2903.105 3025.583
225 TPM3u+F+R2 1392.257 44 2872.514 2895.946 3020.617
234 TPM3u+F+I+R2 1392.403 45 2874.805 2899.448 3026.274
245 TPM3+G4 1397.145 40 2874.290 2893.250 3008.929
247 TPM3+R2 1393.233 41 2868.465 2888.489 3006.471
256 TPM3+I+R2 1393.402 42 2870.804 2891.927 3012.175
267 TPM2u+F+G4 1401.931 43 2889.862 2912.120 3034.599
269 TPM2u+F+R2 1396.514 44 2881.029 2904.461 3029.132
278 TPM2u+F+I+R2 1396.609 45 2883.218 2907.861 3034.687
289 TPM2+G4 1406.566 40 2893.132 2912.092 3027.771
291 TPM2+R2 1402.312 41 2886.624 2906.647 3024.629
300 TPM2+I+R2 1402.426 42 2888.852 2909.975 3030.223
311 K3Pu+F+G4 1398.551 43 2883.101 2905.360 3027.838
313 K3Pu+F+R2 1393.054 44 2874.109 2897.541 3022.212
322 K3Pu+F+I+R2 1393.149 45 2876.299 2900.942 3027.768
333 K3P+G4 1403.892 40 2887.785 2906.744 3022.424
335 K3P+R2 1399.422 41 2880.844 2900.867 3018.849
344 K3P+I+R2 1399.575 42 2883.151 2904.274 3024.522
355 TN+F+G4 1401.586 43 2889.173 2911.432 3033.910
357 TN+F+R2 1395.969 44 2879.938 2903.370 3028.041
366 TN+F+I+R2 1396.066 45 2882.132 2906.775 3033.601
377 TNe+G4 1406.460 40 2892.919 2911.879 3027.558
379 TNe+R2 1402.304 41 2886.608 2906.631 3024.613
388 TNe+I+R2 1402.407 42 2888.814 2909.937 3030.185
399 HKY+F+G4 1402.059 42 2888.117 2909.240 3029.488
401 HKY+F+R2 1396.722 43 2879.445 2901.704 3024.182
410 HKY+F+I+R2 1396.828 44 2881.656 2905.088 3029.759
421 K2P+G4 1406.634 39 2891.268 2909.199 3022.541
423 K2P+R2 1402.339 40 2884.677 2903.637 3019.316
432 K2P+I+R2 1402.460 41 2886.919 2906.943 3024.924
443 F81+F+G4 1410.287 41 2902.575 2922.598 3040.580
445 F81+F+R2 1405.897 42 2895.793 2916.916 3037.164
454 F81+F+I+R2 1405.928 43 2897.857 2920.116 3042.594
465 JC+G4 1414.943 38 2905.887 2922.824 3033.794
467 JC+R2 1411.518 39 2901.035 2918.966 3032.308
476 JC+I+R2 1411.519 40 2903.039 2921.998 3037.678
Akaike Information Criterion: TVMe+R2
Corrected Akaike Information Criterion: TVMe+R2
Bayesian Information Criterion: TPM3+R2
Best-fit model: TPM3+R2 chosen according to BIC
All model information printed to /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp_83u2b1s/q2iqtree.model.gz
CPU time for ModelFinder: 0.795 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.808 seconds (0h:0m:0s)
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1393.233
Optimal log-likelihood: -1393.222
Rate parameters: A-C: 0.30881 A-G: 1.35555 A-T: 1.00000 C-G: 0.30881 C-T: 1.35555 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.687,0.341) (0.313,2.448)
Parameters optimization took 1 rounds (0.003 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000586033 secs using 97.61% CPU
Computing ML distances took 0.000634 sec (of wall-clock time) 0.000610 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 5.6982e-05 secs using 96.52% CPU
Constructing RapidNJ tree: done in 8.79765e-05 secs using 140.9% CPU
Computing RapidNJ tree took 0.000208 sec (of wall-clock time) 0.000247 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1394.436
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.064 second
Computing log-likelihood of 98 initial trees ... 0.049 seconds
Current best score: -1393.222
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00246787 secs using 195.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1392.059
Optimizing NNI: done in 0.0080719 secs using 188% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1385.324
Optimizing NNI: done in 0.00697899 secs using 194.4% CPU
Optimizing NNI: done in 0.00644398 secs using 194.4% CPU
Optimizing NNI: done in 0.00681186 secs using 197.4% CPU
Optimizing NNI: done in 0.00634193 secs using 196.4% CPU
Optimizing NNI: done in 0.00633907 secs using 195.6% CPU
Optimizing NNI: done in 0.00720596 secs using 189.4% CPU
Optimizing NNI: done in 0.00674582 secs using 193.7% CPU
Optimizing NNI: done in 0.00718498 secs using 192.3% CPU
Iteration 10 / LogL: -1385.354 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00633502 secs using 164% CPU
Optimizing NNI: done in 0.006109 secs using 99.97% CPU
Optimizing NNI: done in 0.00622201 secs using 99.84% CPU
Optimizing NNI: done in 0.00630498 secs using 99.87% CPU
Optimizing NNI: done in 0.00638008 secs using 98.98% CPU
Optimizing NNI: done in 0.00641704 secs using 99.52% CPU
Optimizing NNI: done in 0.00887203 secs using 99.13% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.324
Optimizing NNI: done in 0.00877094 secs using 99.81% CPU
Optimizing NNI: done in 0.00857019 secs using 99.94% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.324
Optimizing NNI: done in 0.00632 secs using 99.73% CPU
Iteration 20 / LogL: -1385.355 / Time: 0h:0m:0s
Finish initializing candidate tree set (3)
Current best tree score: -1385.324 / CPU time: 0.263
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0118659 secs using 98.14% CPU
Optimizing NNI: done in 0.009866 secs using 95.66% CPU
Optimizing NNI: done in 0.00575709 secs using 94.08% CPU
Optimizing NNI: done in 0.00602388 secs using 97.33% CPU
Optimizing NNI: done in 0.010644 secs using 95.74% CPU
Optimizing NNI: done in 0.00919509 secs using 97.38% CPU
Optimizing NNI: done in 0.00910711 secs using 96.35% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.321
Optimizing NNI: done in 0.00756288 secs using 99.94% CPU
Optimizing NNI: done in 0.00998783 secs using 95.91% CPU
Optimizing NNI: done in 0.00831199 secs using 97.75% CPU
Iteration 30 / LogL: -1387.710 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00550795 secs using 98.78% CPU
Optimizing NNI: done in 0.00776505 secs using 97.53% CPU
Optimizing NNI: done in 0.0102079 secs using 94.21% CPU
Optimizing NNI: done in 0.00752592 secs using 96.6% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.321
Optimizing NNI: done in 0.00790691 secs using 98.7% CPU
Optimizing NNI: done in 0.0129199 secs using 95.91% CPU
Optimizing NNI: done in 0.00568318 secs using 99.91% CPU
Optimizing NNI: done in 0.008672 secs using 95.13% CPU
Optimizing NNI: done in 0.00678301 secs using 99.93% CPU
Optimizing NNI: done in 0.00471711 secs using 94.95% CPU
Iteration 40 / LogL: -1385.906 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00876093 secs using 98.14% CPU
Optimizing NNI: done in 0.00739694 secs using 99.76% CPU
Optimizing NNI: done in 0.00924206 secs using 99.78% CPU
Optimizing NNI: done in 0.00403404 secs using 99.55% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.320
Optimizing NNI: done in 0.00813317 secs using 98.44% CPU
Optimizing NNI: done in 0.013442 secs using 99.59% CPU
Optimizing NNI: done in 0.0077641 secs using 99.93% CPU
Optimizing NNI: done in 0.0114069 secs using 98.44% CPU
Optimizing NNI: done in 0.00869799 secs using 98.43% CPU
Optimizing NNI: done in 0.00971389 secs using 97.79% CPU
Iteration 50 / LogL: -1385.866 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00928593 secs using 99.31% CPU
Optimizing NNI: done in 0.010416 secs using 98.45% CPU
Optimizing NNI: done in 0.00901699 secs using 99.78% CPU
Optimizing NNI: done in 0.00770497 secs using 99.68% CPU
Optimizing NNI: done in 0.00590014 secs using 96.68% CPU
Optimizing NNI: done in 0.00970101 secs using 98.74% CPU
Optimizing NNI: done in 0.011543 secs using 99.92% CPU
Optimizing NNI: done in 0.00606608 secs using 99.97% CPU
Optimizing NNI: done in 0.012656 secs using 99.13% CPU
Optimizing NNI: done in 0.00771093 secs using 98.61% CPU
Iteration 60 / LogL: -1385.323 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00669193 secs using 99.94% CPU
Optimizing NNI: done in 0.00768089 secs using 97.75% CPU
Optimizing NNI: done in 0.00630999 secs using 99.56% CPU
Optimizing NNI: done in 0.010015 secs using 99.64% CPU
Optimizing NNI: done in 0.00611281 secs using 96.98% CPU
Optimizing NNI: done in 0.0133522 secs using 99.06% CPU
Optimizing NNI: done in 0.00850701 secs using 99.93% CPU
Optimizing NNI: done in 0.00767994 secs using 99.71% CPU
Optimizing NNI: done in 0.0118561 secs using 99.06% CPU
Optimizing NNI: done in 0.014122 secs using 99.61% CPU
Iteration 70 / LogL: -1385.883 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00675011 secs using 99.87% CPU
Optimizing NNI: done in 0.0101061 secs using 97.83% CPU
Optimizing NNI: done in 0.00602794 secs using 99.3% CPU
Optimizing NNI: done in 0.00763202 secs using 99.91% CPU
Optimizing NNI: done in 0.00907516 secs using 99.58% CPU
Optimizing NNI: done in 0.00592399 secs using 98.48% CPU
Optimizing NNI: done in 0.00944901 secs using 98.56% CPU
Optimizing NNI: done in 0.00933409 secs using 98.5% CPU
Optimizing NNI: done in 0.00608897 secs using 99.93% CPU
Optimizing NNI: done in 0.00548387 secs using 97.34% CPU
Iteration 80 / LogL: -1385.642 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00851917 secs using 98.7% CPU
Optimizing NNI: done in 0.00775313 secs using 99.57% CPU
Optimizing NNI: done in 0.010541 secs using 97.66% CPU
Optimizing NNI: done in 0.010684 secs using 98.49% CPU
Optimizing NNI: done in 0.00701094 secs using 98.63% CPU
Optimizing NNI: done in 0.00418901 secs using 99.28% CPU
Optimizing NNI: done in 0.0110869 secs using 97.48% CPU
Optimizing NNI: done in 0.00867701 secs using 99.22% CPU
Optimizing NNI: done in 0.00673413 secs using 99.34% CPU
Optimizing NNI: done in 0.0062952 secs using 99.42% CPU
Iteration 90 / LogL: -1385.892 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00934601 secs using 99.59% CPU
Optimizing NNI: done in 0.00724792 secs using 99.85% CPU
Optimizing NNI: done in 0.00902987 secs using 98.85% CPU
Optimizing NNI: done in 0.00857615 secs using 99.63% CPU
Optimizing NNI: done in 0.00941491 secs using 98.57% CPU
Optimizing NNI: done in 0.00960898 secs using 99.9% CPU
Optimizing NNI: done in 0.00662994 secs using 99.14% CPU
Optimizing NNI: done in 0.0107691 secs using 99.91% CPU
Optimizing NNI: done in 0.0111511 secs using 98.46% CPU
Optimizing NNI: done in 0.00496197 secs using 98.17% CPU
Iteration 100 / LogL: -1385.787 / Time: 0h:0m:0s (0h:0m:0s left)
Optimizing NNI: done in 0.00660014 secs using 98.12% CPU
Optimizing NNI: done in 0.00758815 secs using 96.35% CPU
Optimizing NNI: done in 0.0089941 secs using 99.79% 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: -1385.320
Optimal log-likelihood: -1385.310
Rate parameters: A-C: 0.39424 A-G: 1.57283 A-T: 1.00000 C-G: 0.39424 C-T: 1.57283 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.717,0.394) (0.283,2.535)
Parameters optimization took 1 rounds (0.002 sec)
BEST SCORE FOUND : -1385.310
Total tree length: 6.953
Total number of iterations: 103
CPU time used for tree search: 1.169 sec (0h:0m:1s)
Wall-clock time used for tree search: 1.006 sec (0h:0m:1s)
Total CPU time used: 1.187 sec (0h:0m:1s)
Total wall-clock time used: 1.023 sec (0h:0m:1s)
Analysis results written to:
IQ-TREE report: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp_83u2b1s/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp_83u2b1s/q2iqtree.treefile
Likelihood distances: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp_83u2b1s/q2iqtree.mldist
Screen log file: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp_83u2b1s/q2iqtree.log
Date and Time: Thu Apr 4 14:00:15 2024
n cores 1
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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp_83u2b1s/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 2.2.6 COVID-edition for Mac OS X 64-bit built Dec 8 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: eduroam-lfx-dock-1-371.intern.ethz.ch (AVX512, FMA3, 32 GB RAM)
Command: iqtree -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp5ughae1i/q2iqtree -nt 1
Seed: 221406 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Apr 4 14:00:24 2024
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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000129938 secs using 69.26% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000272036 secs using 65.8% 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 89.88% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 3.50475e-05 secs using 71.33% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Thoroughly optimizing +I+G parameters from 10 start values...
Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 1.239 / LogL: -1394.544
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.010, 1.340 / LogL: -1394.887
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.010, 1.353 / LogL: -1394.887
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.009, 1.352 / LogL: -1394.871
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.009, 1.348 / LogL: -1394.836
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.009, 1.351 / LogL: -1394.862
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.010, 1.352 / LogL: -1394.884
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.008, 1.346 / LogL: -1394.826
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.009, 1.347 / LogL: -1394.838
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.009, 1.348 / LogL: -1394.841
Optimal pinv,alpha: 0.000, 1.239 / LogL: -1394.544
Parameters optimization took 0.299 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000900984 secs using 95.01% CPU
Computing ML distances took 0.000959 sec (of wall-clock time) 0.000899 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 3.21865e-05 secs using 74.57% CPU
Constructing RapidNJ tree: done in 9.01222e-05 secs using 149.8% CPU
Computing RapidNJ tree took 0.000199 sec (of wall-clock time) 0.000193 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.870
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.063 second
Computing log-likelihood of 98 initial trees ... 0.063 seconds
Current best score: -1392.870
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.010602 secs using 186% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.265
Optimizing NNI: done in 0.0112469 secs using 193.3% CPU
Optimizing NNI: done in 0.00665021 secs using 197.1% CPU
Optimizing NNI: done in 0.00702906 secs using 194.2% CPU
Optimizing NNI: done in 0.00737596 secs using 191.4% CPU
Optimizing NNI: done in 0.00693107 secs using 193.3% CPU
Optimizing NNI: done in 0.00754189 secs using 187.3% CPU
Optimizing NNI: done in 0.00667691 secs using 151.5% CPU
Optimizing NNI: done in 0.00687408 secs using 98.47% CPU
Optimizing NNI: done in 0.0126081 secs using 98.56% CPU
Iteration 10 / LogL: -1387.282 / Time: 0h:0m:0s
Optimizing NNI: done in 0.012944 secs using 99.21% CPU
Optimizing NNI: done in 0.0128331 secs using 99.41% CPU
Optimizing NNI: done in 0.0127041 secs using 99.79% CPU
Optimizing NNI: done in 0.0122108 secs using 99.85% CPU
Optimizing NNI: done in 0.0125661 secs using 99.77% CPU
Optimizing NNI: done in 0.012455 secs using 99.15% CPU
Optimizing NNI: done in 0.012444 secs using 99.62% CPU
Optimizing NNI: done in 0.013767 secs using 97.31% CPU
Optimizing NNI: done in 0.012605 secs using 98.33% CPU
Optimizing NNI: done in 0.00964522 secs using 99.26% CPU
Iteration 20 / LogL: -1387.267 / Time: 0h:0m:0s
Finish initializing candidate tree set (1)
Current best tree score: -1387.265 / CPU time: 0.350
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0151041 secs using 97.69% CPU
Optimizing NNI: done in 0.00999689 secs using 99.85% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.257
Optimizing NNI: done in 0.017611 secs using 96.33% CPU
Optimizing NNI: done in 0.0118289 secs using 99.77% CPU
Optimizing NNI: done in 0.014997 secs using 97.93% CPU
Optimizing NNI: done in 0.0180099 secs using 97.96% CPU
Optimizing NNI: done in 0.025594 secs using 97.3% CPU
Optimizing NNI: done in 0.0177741 secs using 96.72% CPU
Optimizing NNI: done in 0.0166781 secs using 97.89% CPU
Optimizing NNI: done in 0.0113301 secs using 99.04% CPU
Iteration 30 / LogL: -1387.306 / Time: 0h:0m:0s (0h:0m:2s left)
Optimizing NNI: done in 0.0210271 secs using 98.63% CPU
Optimizing NNI: done in 0.00664997 secs using 99.34% CPU
Optimizing NNI: done in 0.0229499 secs using 99.87% CPU
Optimizing NNI: done in 0.016968 secs using 99.23% CPU
Optimizing NNI: done in 0.0145898 secs using 99.78% CPU
Optimizing NNI: done in 0.01265 secs using 99.86% CPU
Optimizing NNI: done in 0.018955 secs using 96.25% CPU
Optimizing NNI: done in 0.0154948 secs using 97.68% CPU
Optimizing NNI: done in 0.0141361 secs using 98.87% CPU
Optimizing NNI: done in 0.0254831 secs using 97.3% CPU
Iteration 40 / LogL: -1387.348 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.00374413 secs using 99.92% CPU
Optimizing NNI: done in 0.01124 secs using 97.88% CPU
Optimizing NNI: done in 0.013293 secs using 97.68% CPU
Optimizing NNI: done in 0.0130839 secs using 97.72% CPU
Optimizing NNI: done in 0.0141609 secs using 96.35% CPU
Optimizing NNI: done in 0.0176899 secs using 99.2% CPU
Optimizing NNI: done in 0.0130851 secs using 97.62% CPU
Optimizing NNI: done in 0.011178 secs using 99.39% CPU
Optimizing NNI: done in 0.0109971 secs using 92.73% CPU
Optimizing NNI: done in 0.0197279 secs using 97.5% CPU
Iteration 50 / LogL: -1387.423 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.0179222 secs using 95.76% CPU
Optimizing NNI: done in 0.0116949 secs using 99.04% CPU
Optimizing NNI: done in 0.00642395 secs using 98.71% CPU
Optimizing NNI: done in 0.039556 secs using 96.76% CPU
Optimizing NNI: done in 0.0297868 secs using 98.45% CPU
Optimizing NNI: done in 0.0183601 secs using 96.01% CPU
Optimizing NNI: done in 0.021874 secs using 96.11% CPU
Optimizing NNI: done in 0.0190709 secs using 95.38% CPU
Optimizing NNI: done in 0.0144958 secs using 99.07% CPU
Optimizing NNI: done in 0.026444 secs using 97.19% CPU
Iteration 60 / LogL: -1387.348 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0197251 secs using 97.13% CPU
Optimizing NNI: done in 0.026772 secs using 96.94% CPU
Optimizing NNI: done in 0.016588 secs using 97.58% CPU
Optimizing NNI: done in 0.0152769 secs using 97.68% CPU
Optimizing NNI: done in 0.0175219 secs using 99.56% CPU
Optimizing NNI: done in 0.009763 secs using 98.99% CPU
Optimizing NNI: done in 0.022764 secs using 99.27% CPU
Optimizing NNI: done in 0.0110011 secs using 98.65% CPU
Optimizing NNI: done in 0.0136569 secs using 95.44% CPU
Optimizing NNI: done in 0.010778 secs using 98.8% CPU
Iteration 70 / LogL: -1387.314 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0173869 secs using 99.62% CPU
Optimizing NNI: done in 0.0247471 secs using 99.19% CPU
Optimizing NNI: done in 0.0150731 secs using 99.46% CPU
Optimizing NNI: done in 0.034024 secs using 99.48% CPU
Optimizing NNI: done in 0.013855 secs using 99.6% CPU
Optimizing NNI: done in 0.00469804 secs using 96.38% CPU
Optimizing NNI: done in 0.0120859 secs using 98.17% CPU
Optimizing NNI: done in 0.026546 secs using 98.36% CPU
Optimizing NNI: done in 0.0105889 secs using 98.35% CPU
Optimizing NNI: done in 0.00703406 secs using 98.8% CPU
Iteration 80 / LogL: -1387.265 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0213161 secs using 97.89% CPU
Optimizing NNI: done in 0.0246742 secs using 98.83% CPU
Optimizing NNI: done in 0.00966096 secs using 97.76% CPU
Optimizing NNI: done in 0.016566 secs using 98.74% CPU
Optimizing NNI: done in 0.011354 secs using 99.86% CPU
Optimizing NNI: done in 0.0150762 secs using 99.16% CPU
Optimizing NNI: done in 0.011137 secs using 98.56% CPU
Optimizing NNI: done in 0.0276251 secs using 99.87% CPU
Optimizing NNI: done in 0.014076 secs using 99.4% CPU
Optimizing NNI: done in 0.0124211 secs using 98.93% CPU
Iteration 90 / LogL: -1387.351 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.010601 secs using 99.24% CPU
Optimizing NNI: done in 0.0232279 secs using 99.49% CPU
Optimizing NNI: done in 0.01209 secs using 98.55% CPU
Optimizing NNI: done in 0.0303249 secs using 97.8% CPU
Optimizing NNI: done in 0.020947 secs using 98.63% CPU
Optimizing NNI: done in 0.0406551 secs using 95.52% CPU
Optimizing NNI: done in 0.013396 secs using 96.29% CPU
Optimizing NNI: done in 0.0238211 secs using 98.03% CPU
Optimizing NNI: done in 0.0390751 secs using 97.31% CPU
Optimizing NNI: done in 0.017956 secs using 98.5% CPU
Iteration 100 / LogL: -1396.568 / Time: 0h:0m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.0227909 secs using 98.46% CPU
Optimizing NNI: done in 0.0160081 secs using 98.54% 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: -1387.257
Optimal log-likelihood: -1387.253
Rate parameters: A-C: 0.32885 A-G: 2.26144 A-T: 2.13969 C-G: 1.17291 C-T: 3.29064 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: 1.317
Parameters optimization took 1 rounds (0.002 sec)
BEST SCORE FOUND : -1387.253
Total tree length: 6.762
Total number of iterations: 102
CPU time used for tree search: 1.966 sec (0h:0m:1s)
Wall-clock time used for tree search: 1.820 sec (0h:0m:1s)
Total CPU time used: 2.261 sec (0h:0m:2s)
Total wall-clock time used: 2.135 sec (0h:0m:2s)
Analysis results written to:
IQ-TREE report: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp5ughae1i/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp5ughae1i/q2iqtree.treefile
Likelihood distances: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp5ughae1i/q2iqtree.mldist
Screen log file: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp5ughae1i/q2iqtree.log
Date and Time: Thu Apr 4 14:00:26 2024
n cores 1
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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp5ughae1i/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 2.2.6 COVID-edition for Mac OS X 64-bit built Dec 8 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: eduroam-lfx-dock-1-371.intern.ethz.ch (AVX512, FMA3, 32 GB RAM)
Command: iqtree -st DNA --runs 10 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpoxagra72/q2iqtree -nt 1 -fast
Seed: 615344 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Apr 4 14:00:34 2024
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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000112772 secs using 86.9% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000241041 secs using 69.7% CPU
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
Analyzing sequences: done in 2.69413e-05 secs using 55.68% CPU
Checking for duplicate sequences: done in 4.69685e-05 secs using 66% CPU
---> START RUN NUMBER 1 (seed: 615344)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.00 seconds
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.50)
1. Initial log-likelihood: -1492.20
2. Current log-likelihood: -1404.59
3. Current log-likelihood: -1399.23
4. Current log-likelihood: -1397.83
5. Current log-likelihood: -1397.07
Optimal log-likelihood: -1396.49
Rate parameters: A-C: 0.24620 A-G: 2.08306 A-T: 1.99580 C-G: 1.06240 C-T: 2.85598 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.432
Parameters optimization took 5 rounds (0.023 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00090003 secs using 98.33% CPU
Computing ML distances took 0.000988 sec (of wall-clock time) 0.000958 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 3.40939e-05 secs using 70.39% CPU
Constructing RapidNJ tree: done in 5.88894e-05 secs using 156.2% CPU
Computing RapidNJ tree took 0.000180 sec (of wall-clock time) 0.000169 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.972
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.00961804 secs using 185.4% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.188
Optimizing NNI: done in 0.0138299 secs using 182.9% CPU
UPDATE BEST LOG-LIKELIHOOD: -1388.187
Finish initializing candidate tree set (3)
Current best tree score: -1388.187 / CPU time: 0.030
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: -1388.187
2. Current log-likelihood: -1387.966
3. Current log-likelihood: -1387.806
4. Current log-likelihood: -1387.687
5. Current log-likelihood: -1387.596
6. Current log-likelihood: -1387.525
7. Current log-likelihood: -1387.471
Optimal log-likelihood: -1387.426
Rate parameters: A-C: 0.33228 A-G: 2.23741 A-T: 2.11202 C-G: 1.16006 C-T: 3.23503 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.356
Parameters optimization took 7 rounds (0.015 sec)
BEST SCORE FOUND : -1387.426
Total tree length: 6.737
Total number of iterations: 2
CPU time used for tree search: 0.054 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.030 sec (0h:0m:0s)
Total CPU time used: 0.118 sec (0h:0m:0s)
Total wall-clock time used: 0.080 sec (0h:0m:0s)
---> START RUN NUMBER 2 (seed: 616344)
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 (0.023 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000986099 secs using 198.6% CPU
Computing ML distances took 0.001049 sec (of wall-clock time) 0.002024 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 114.1% CPU
Constructing RapidNJ tree: done in 5.98431e-05 secs using 152.1% CPU
Computing RapidNJ tree took 0.000182 sec (of wall-clock time) 0.000190 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 0.0102639 secs using 183.5% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.961
Optimizing NNI: done in 0.024271 secs using 186.5% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.961 / CPU time: 0.045
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 (0.012 sec)
BEST SCORE FOUND : -1387.424
Total tree length: 6.743
Total number of iterations: 2
CPU time used for tree search: 0.083 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.045 sec (0h:0m:0s)
Total CPU time used: 0.168 sec (0h:0m:0s)
Total wall-clock time used: 0.092 sec (0h:0m:0s)
---> START RUN NUMBER 3 (seed: 617344)
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: -1492.199
2. Current log-likelihood: -1404.591
3. Current log-likelihood: -1399.228
4. Current log-likelihood: -1397.831
5. Current log-likelihood: -1397.074
Optimal log-likelihood: -1396.495
Rate parameters: A-C: 0.24620 A-G: 2.08306 A-T: 1.99581 C-G: 1.06240 C-T: 2.85598 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.432
Parameters optimization took 5 rounds (0.025 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000869036 secs using 198.6% CPU
Computing ML distances took 0.000930 sec (of wall-clock time) 0.001798 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 2.7895e-05 secs using 78.87% CPU
Constructing RapidNJ tree: done in 6.91414e-05 secs using 85.33% CPU
Computing RapidNJ tree took 0.000140 sec (of wall-clock time) 0.000098 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.972
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.00901699 secs using 197.3% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.188
Optimizing NNI: done in 0.0139019 secs using 194.4% CPU
UPDATE BEST LOG-LIKELIHOOD: -1388.187
Finish initializing candidate tree set (3)
Current best tree score: -1388.187 / CPU time: 0.029
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: -1388.187
2. Current log-likelihood: -1387.966
3. Current log-likelihood: -1387.806
4. Current log-likelihood: -1387.687
5. Current log-likelihood: -1387.596
6. Current log-likelihood: -1387.525
7. Current log-likelihood: -1387.471
Optimal log-likelihood: -1387.426
Rate parameters: A-C: 0.33228 A-G: 2.23741 A-T: 2.11202 C-G: 1.16006 C-T: 3.23503 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.356
Parameters optimization took 7 rounds (0.016 sec)
BEST SCORE FOUND : -1387.426
Total tree length: 6.737
Total number of iterations: 2
CPU time used for tree search: 0.056 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.029 sec (0h:0m:0s)
Total CPU time used: 0.149 sec (0h:0m:0s)
Total wall-clock time used: 0.080 sec (0h:0m:0s)
---> START RUN NUMBER 4 (seed: 618344)
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 (0.021 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00103116 secs using 194.5% CPU
Computing ML distances took 0.001116 sec (of wall-clock time) 0.002107 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 6.50883e-05 secs using 89.11% CPU
Constructing RapidNJ tree: done in 0.000127792 secs using 101.7% CPU
Computing RapidNJ tree took 0.000240 sec (of wall-clock time) 0.000242 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 0.00922799 secs using 192.5% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.961
Optimizing NNI: done in 0.023401 secs using 190.9% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.961 / CPU time: 0.043
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 (0.012 sec)
BEST SCORE FOUND : -1387.424
Total tree length: 6.743
Total number of iterations: 2
CPU time used for tree search: 0.081 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.043 sec (0h:0m:0s)
Total CPU time used: 0.165 sec (0h:0m:0s)
Total wall-clock time used: 0.088 sec (0h:0m:0s)
---> START RUN NUMBER 5 (seed: 619344)
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: -1495.863
2. Current log-likelihood: -1402.072
3. Current log-likelihood: -1396.809
4. Current log-likelihood: -1395.391
5. Current log-likelihood: -1394.657
Optimal log-likelihood: -1394.080
Rate parameters: A-C: 0.27275 A-G: 2.35291 A-T: 2.09125 C-G: 1.19606 C-T: 3.26638 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: 1.387
Parameters optimization took 5 rounds (0.022 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000870943 secs using 197.5% CPU
Computing ML distances took 0.000921 sec (of wall-clock time) 0.001816 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 8.79765e-05 secs using 93.21% CPU
Constructing RapidNJ tree: done in 6.98566e-05 secs using 118.8% CPU
Computing RapidNJ tree took 0.000220 sec (of wall-clock time) 0.000219 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 0.00927091 secs using 195.6% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.217
Optimizing NNI: done in 0.015862 secs using 188.3% CPU
BETTER TREE FOUND at iteration 2: -1388.189
Finish initializing candidate tree set (4)
Current best tree score: -1388.189 / 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: -1388.189
2. Current log-likelihood: -1387.974
3. Current log-likelihood: -1387.831
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: 0.36986 A-G: 2.31018 A-T: 2.11746 C-G: 1.22267 C-T: 3.27882 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 (0.015 sec)
BEST SCORE FOUND : -1387.534
Total tree length: 7.502
Total number of iterations: 2
CPU time used for tree search: 0.059 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.031 sec (0h:0m:0s)
Total CPU time used: 0.146 sec (0h:0m:0s)
Total wall-clock time used: 0.079 sec (0h:0m:0s)
---> START RUN NUMBER 6 (seed: 620344)
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 (0.023 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00104499 secs using 198.7% CPU
Computing ML distances took 0.001111 sec (of wall-clock time) 0.002182 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 2.69413e-05 secs using 133.6% CPU
Constructing RapidNJ tree: done in 8.4877e-05 secs using 161.4% CPU
Computing RapidNJ tree took 0.000161 sec (of wall-clock time) 0.000208 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 0.00987816 secs using 190.3% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.961
Optimizing NNI: done in 0.0226622 secs using 192.1% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.961 / CPU time: 0.042
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: 0.080 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.042 sec (0h:0m:0s)
Total CPU time used: 0.167 sec (0h:0m:0s)
Total wall-clock time used: 0.089 sec (0h:0m:0s)
---> START RUN NUMBER 7 (seed: 621344)
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 (0.022 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000887871 secs using 195.2% CPU
Computing ML distances took 0.000983 sec (of wall-clock time) 0.001792 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 2.88486e-05 secs using 76.26% CPU
Constructing RapidNJ tree: done in 6.50883e-05 secs using 98.33% CPU
Computing RapidNJ tree took 0.000146 sec (of wall-clock time) 0.000120 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 0.0100591 secs using 180.7% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.214
Optimizing NNI: done in 0.009197 secs using 198% CPU
Finish initializing candidate tree set (3)
Current best tree score: -1388.214 / CPU time: 0.024
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 (0.014 sec)
BEST SCORE FOUND : -1387.519
Total tree length: 6.815
Total number of iterations: 2
CPU time used for tree search: 0.046 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.024 sec (0h:0m:0s)
Total CPU time used: 0.134 sec (0h:0m:0s)
Total wall-clock time used: 0.071 sec (0h:0m:0s)
---> START RUN NUMBER 8 (seed: 622344)
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: -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 0.000859022 secs using 197.8% CPU
Computing ML distances took 0.000906 sec (of wall-clock time) 0.001794 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 2.7895e-05 secs using 93.21% CPU
Constructing RapidNJ tree: done in 5.38826e-05 secs using 152.2% CPU
Computing RapidNJ tree took 0.000119 sec (of wall-clock time) 0.000149 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 0.00978017 secs using 187.6% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.217
Optimizing NNI: done in 0.0150361 secs using 191.2% CPU
BETTER TREE FOUND at iteration 2: -1388.188
Finish initializing candidate tree set (4)
Current best tree score: -1388.188 / 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: -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 (0.015 sec)
BEST SCORE FOUND : -1387.534
Total tree length: 7.502
Total number of iterations: 2
CPU time used for tree search: 0.059 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.032 sec (0h:0m:0s)
Total CPU time used: 0.150 sec (0h:0m:0s)
Total wall-clock time used: 0.081 sec (0h:0m:0s)
---> START RUN NUMBER 9 (seed: 623344)
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: -1492.389
2. Current log-likelihood: -1401.890
3. Current log-likelihood: -1396.534
4. Current log-likelihood: -1395.117
5. Current log-likelihood: -1394.389
Optimal log-likelihood: -1393.814
Rate parameters: A-C: 0.27026 A-G: 2.39526 A-T: 2.16931 C-G: 1.24752 C-T: 3.29290 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.027
Gamma shape alpha: 1.415
Parameters optimization took 5 rounds (0.022 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00085187 secs using 199.3% CPU
Computing ML distances took 0.000899 sec (of wall-clock time) 0.001784 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 7.60555e-05 secs using 30.24% CPU
Constructing RapidNJ tree: done in 7.20024e-05 secs using 129.2% CPU
Computing RapidNJ tree took 0.000186 sec (of wall-clock time) 0.000148 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.793
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Do NNI search on 2 best initial trees
Optimizing NNI: done in 0.00938892 secs using 189.6% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1388.213
Optimizing NNI: done in 0.0095129 secs using 193.7% CPU
Finish initializing candidate tree set (3)
Current best tree score: -1388.213 / CPU time: 0.024
Number of iterations: 2
TREE SEARCH COMPLETED AFTER 2 ITERATIONS / Time: 0h:0m:0s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.050)
1. Initial log-likelihood: -1388.213
2. Current log-likelihood: -1388.014
3. Current log-likelihood: -1387.868
4. Current log-likelihood: -1387.759
5. Current log-likelihood: -1387.676
6. Current log-likelihood: -1387.611
7. Current log-likelihood: -1387.560
Optimal log-likelihood: -1387.519
Rate parameters: A-C: 0.35532 A-G: 2.35213 A-T: 2.13937 C-G: 1.20295 C-T: 3.37020 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.004
Gamma shape alpha: 1.361
Parameters optimization took 7 rounds (0.014 sec)
BEST SCORE FOUND : -1387.519
Total tree length: 6.816
Total number of iterations: 2
CPU time used for tree search: 0.045 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.024 sec (0h:0m:0s)
Total CPU time used: 0.134 sec (0h:0m:0s)
Total wall-clock time used: 0.071 sec (0h:0m:0s)
---> START RUN NUMBER 10 (seed: 624344)
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 (0.025 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00087285 secs using 197.5% CPU
Computing ML distances took 0.000953 sec (of wall-clock time) 0.001824 sec (of CPU time)
WARNING: Some pairwise ML distances are too long (saturated)
Setting up auxiliary I and S matrices: done in 3.69549e-05 secs using 132.6% CPU
Constructing RapidNJ tree: done in 6.19888e-05 secs using 95.18% CPU
Computing RapidNJ tree took 0.000216 sec (of wall-clock time) 0.000154 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 0.00917196 secs using 193.4% CPU
Estimate model parameters (epsilon = 0.500)
BETTER TREE FOUND at iteration 1: -1387.961
Optimizing NNI: done in 0.024919 secs using 182.6% CPU
Finish initializing candidate tree set (4)
Current best tree score: -1387.961 / CPU time: 0.044
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 (0.013 sec)
BEST SCORE FOUND : -1387.424
Total tree length: 6.743
Total number of iterations: 2
CPU time used for tree search: 0.081 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.044 sec (0h:0m:0s)
Total CPU time used: 0.169 sec (0h:0m:0s)
Total wall-clock time used: 0.093 sec (0h:0m:0s)
---> SUMMARIZE RESULTS FROM 10 RUNS
Run 2 gave best log-likelihood: -1387.424
Total CPU time for 10 runs: 1.525 seconds.
Total wall-clock time for 10 runs: 0.841 seconds.
Analysis results written to:
IQ-TREE report: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpoxagra72/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpoxagra72/q2iqtree.treefile
Trees from independent runs: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpoxagra72/q2iqtree.runtrees
Likelihood distances: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpoxagra72/q2iqtree.mldist
Screen log file: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpoxagra72/q2iqtree.log
Date and Time: Thu Apr 4 14:00:35 2024
n cores 1
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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpoxagra72/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 2.2.6 COVID-edition for Mac OS X 64-bit built Dec 8 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: eduroam-lfx-dock-1-371.intern.ethz.ch (AVX512, FMA3, 32 GB RAM)
Command: iqtree -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmplf9075a9/q2iqtree -nt 1 -alrt 1000 -abayes -lbp 1000
Seed: 223326 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Apr 4 14:00:44 2024
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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000108957 secs using 82.6% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000247002 secs using 63.56% 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 89.88% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 4.1008e-05 secs using 70.72% 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 0.286 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000874996 secs using 98.51% CPU
Computing ML distances took 0.001016 sec (of wall-clock time) 0.000958 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 3.00407e-05 secs using 76.56% CPU
Constructing RapidNJ tree: done in 5.60284e-05 secs using 142.8% CPU
Computing RapidNJ tree took 0.000131 sec (of wall-clock time) 0.000133 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.727
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.062 second
Computing log-likelihood of 98 initial trees ... 0.067 seconds
Current best score: -1392.727
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.010072 secs using 193.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.357
Optimizing NNI: done in 0.00817204 secs using 191% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1387.266
Optimizing NNI: done in 0.00706506 secs using 197% CPU
Optimizing NNI: done in 0.00655913 secs using 198.2% CPU
Optimizing NNI: done in 0.00710702 secs using 192.9% CPU
Optimizing NNI: done in 0.00661087 secs using 199.4% CPU
Optimizing NNI: done in 0.00751901 secs using 180.6% CPU
Optimizing NNI: done in 0.00751495 secs using 180% CPU
Optimizing NNI: done in 0.00684595 secs using 98.88% CPU
Optimizing NNI: done in 0.0066762 secs using 98.98% CPU
Iteration 10 / LogL: -1387.735 / Time: 0h:0m:0s
Optimizing NNI: done in 0.006567 secs using 99.95% CPU
Optimizing NNI: done in 0.0122631 secs using 99.45% CPU
Optimizing NNI: done in 0.0125289 secs using 99.38% CPU
Optimizing NNI: done in 0.0125449 secs using 99.63% CPU
Optimizing NNI: done in 0.012099 secs using 99.94% CPU
Optimizing NNI: done in 0.0123012 secs using 99.69% CPU
Optimizing NNI: done in 0.0127809 secs using 98.92% CPU
Optimizing NNI: done in 0.012305 secs using 99.88% CPU
Optimizing NNI: done in 0.0120511 secs using 99.69% CPU
Optimizing NNI: done in 0.012121 secs using 99.55% CPU
Iteration 20 / LogL: -1387.280 / Time: 0h:0m:0s
Finish initializing candidate tree set (2)
Current best tree score: -1387.266 / CPU time: 0.335
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0187881 secs using 94.12% CPU
Optimizing NNI: done in 0.0115871 secs using 98.61% CPU
Optimizing NNI: done in 0.0150101 secs using 98.55% CPU
Optimizing NNI: done in 0.013593 secs using 96.67% CPU
Optimizing NNI: done in 0.015075 secs using 95.3% CPU
Optimizing NNI: done in 0.012373 secs using 96.31% CPU
Optimizing NNI: done in 0.01054 secs using 98.58% CPU
Optimizing NNI: done in 0.0131581 secs using 96.87% CPU
Optimizing NNI: done in 0.0280781 secs using 96.97% CPU
Optimizing NNI: done in 0.023005 secs using 96.97% CPU
Iteration 30 / LogL: -1387.350 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.0134962 secs using 96.84% CPU
Optimizing NNI: done in 0.040437 secs using 96.45% CPU
Optimizing NNI: done in 0.00562501 secs using 98.93% CPU
Optimizing NNI: done in 0.0243938 secs using 98.03% CPU
Optimizing NNI: done in 0.0127671 secs using 98.19% CPU
Optimizing NNI: done in 0.0143828 secs using 98.61% CPU
Optimizing NNI: done in 0.0124578 secs using 97.71% CPU
Optimizing NNI: done in 0.0190201 secs using 97.29% CPU
Optimizing NNI: done in 0.0148509 secs using 97.89% CPU
Optimizing NNI: done in 0.0213962 secs using 98.98% CPU
Iteration 40 / LogL: -1387.352 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.0143321 secs using 99.01% CPU
Optimizing NNI: done in 0.0289049 secs using 98.85% CPU
Optimizing NNI: done in 0.00691295 secs using 99.81% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.257
Optimizing NNI: done in 0.022505 secs using 98.16% CPU
Optimizing NNI: done in 0.0130701 secs using 99.88% CPU
Optimizing NNI: done in 0.016973 secs using 98.73% CPU
Optimizing NNI: done in 0.0205379 secs using 99.57% CPU
Optimizing NNI: done in 0.023252 secs using 98.78% CPU
Optimizing NNI: done in 0.00876117 secs using 97.24% CPU
Optimizing NNI: done in 0.017983 secs using 93.65% CPU
Iteration 50 / LogL: -1387.351 / Time: 0h:0m:1s (0h:0m:1s left)
Optimizing NNI: done in 0.0125079 secs using 94.8% CPU
Optimizing NNI: done in 0.0242541 secs using 95.96% CPU
Optimizing NNI: done in 0.013442 secs using 97.72% CPU
Optimizing NNI: done in 0.037149 secs using 95.94% CPU
Optimizing NNI: done in 0.00375295 secs using 96.62% CPU
Optimizing NNI: done in 0.0193419 secs using 99.02% CPU
Optimizing NNI: done in 0.0213001 secs using 98.9% CPU
Optimizing NNI: done in 0.0100949 secs using 99.41% CPU
Optimizing NNI: done in 0.0181811 secs using 98.68% CPU
Optimizing NNI: done in 0.01668 secs using 99.32% CPU
Iteration 60 / LogL: -1396.311 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0155132 secs using 97.13% CPU
Optimizing NNI: done in 0.0164309 secs using 99.35% CPU
Optimizing NNI: done in 0.00835204 secs using 98.43% CPU
Optimizing NNI: done in 0.0172062 secs using 97.05% CPU
Optimizing NNI: done in 0.0166008 secs using 97.71% CPU
Optimizing NNI: done in 0.00936103 secs using 98.89% CPU
Optimizing NNI: done in 0.018189 secs using 96.9% CPU
Optimizing NNI: done in 0.014035 secs using 97.94% CPU
Optimizing NNI: done in 0.019664 secs using 98.46% CPU
Optimizing NNI: done in 0.0144019 secs using 96.83% CPU
Iteration 70 / LogL: -1387.482 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0358522 secs using 98.5% CPU
Optimizing NNI: done in 0.0202849 secs using 97.09% CPU
Optimizing NNI: done in 0.0137391 secs using 99.37% CPU
Optimizing NNI: done in 0.0131271 secs using 99.06% CPU
Optimizing NNI: done in 0.016607 secs using 99.1% CPU
Optimizing NNI: done in 0.0161519 secs using 96.07% CPU
Optimizing NNI: done in 0.020927 secs using 97.09% CPU
Optimizing NNI: done in 0.0179639 secs using 96.4% CPU
Optimizing NNI: done in 0.0106499 secs using 99.77% CPU
Optimizing NNI: done in 0.0102692 secs using 98.12% CPU
Iteration 80 / LogL: -1387.370 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0173471 secs using 98.29% CPU
Optimizing NNI: done in 0.0138941 secs using 99.58% CPU
Optimizing NNI: done in 0.014199 secs using 99.77% CPU
Optimizing NNI: done in 0.0182419 secs using 98.74% CPU
Optimizing NNI: done in 0.015003 secs using 97.83% CPU
Optimizing NNI: done in 0.0158529 secs using 98.92% CPU
Optimizing NNI: done in 0.00884604 secs using 98.9% CPU
Optimizing NNI: done in 0.0243118 secs using 98.45% CPU
Optimizing NNI: done in 0.0171089 secs using 98.06% CPU
Optimizing NNI: done in 0.020107 secs using 97.09% CPU
Iteration 90 / LogL: -1387.351 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.012589 secs using 97.2% CPU
Optimizing NNI: done in 0.01614 secs using 97.22% CPU
Optimizing NNI: done in 0.022135 secs using 95.92% CPU
Optimizing NNI: done in 0.0177131 secs using 98.55% CPU
Optimizing NNI: done in 0.0112281 secs using 99.94% CPU
Optimizing NNI: done in 0.0100639 secs using 99.02% CPU
Optimizing NNI: done in 0.0158851 secs using 97.45% CPU
Optimizing NNI: done in 0.0146201 secs using 94.79% CPU
Optimizing NNI: done in 0.015769 secs using 97.98% CPU
Optimizing NNI: done in 0.0115039 secs using 98.92% CPU
Iteration 100 / LogL: -1387.404 / Time: 0h:0m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.009866 secs using 95.96% CPU
Optimizing NNI: done in 0.0193331 secs using 97.85% CPU
Optimizing NNI: done in 0.00711799 secs using 95.08% CPU
TREE SEARCH COMPLETED AFTER 103 ITERATIONS / Time: 0h:0m:2s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.257
Optimal log-likelihood: -1387.253
Rate parameters: A-C: 0.33719 A-G: 2.28217 A-T: 2.16057 C-G: 1.18413 C-T: 3.30733 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: 1.320
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...
0.046 sec.
Total tree length: 6.725
Total number of iterations: 103
CPU time used for tree search: 1.888 sec (0h:0m:1s)
Wall-clock time used for tree search: 1.755 sec (0h:0m:1s)
Total CPU time used: 2.229 sec (0h:0m:2s)
Total wall-clock time used: 2.102 sec (0h:0m:2s)
Analysis results written to:
IQ-TREE report: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmplf9075a9/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmplf9075a9/q2iqtree.treefile
Likelihood distances: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmplf9075a9/q2iqtree.mldist
Screen log file: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmplf9075a9/q2iqtree.log
Date and Time: Thu Apr 4 14:00:46 2024
n cores 1
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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmplf9075a9/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 2.2.6 COVID-edition for Mac OS X 64-bit built Dec 8 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: eduroam-lfx-dock-1-371.intern.ethz.ch (AVX512, FMA3, 32 GB RAM)
Command: iqtree -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpnastkljb/q2iqtree -nt 1 -nstop 200 -pers 0.200000
Seed: 692553 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Apr 4 14:00:54 2024
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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000105858 secs using 86.91% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000202894 secs using 70.97% 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 89.88% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 3.38554e-05 secs using 70.89% 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 0.01582 secs using 98.94% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1389.605
Optimal log-likelihood: -1388.793
Rate parameters: A-C: 0.37543 A-G: 2.37167 A-T: 2.15334 C-G: 1.24271 C-T: 3.32366 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.034
Gamma shape alpha: 1.400
Parameters optimization took 1 rounds (0.003 sec)
Time for fast ML tree search: 0.035 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 484 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1402.600 45 2895.200 2919.843 3046.669
2 GTR+F+I 1401.121 46 2894.242 2920.135 3049.077
3 GTR+F+G4 1387.358 46 2866.716 2892.609 3021.551
4 GTR+F+I+G4 1387.726 47 2869.452 2896.633 3027.653
5 GTR+F+R2 1382.364 47 2858.729 2885.910 3016.930
6 GTR+F+R3 1382.420 49 2862.840 2892.718 3027.773
14 GTR+F+I+R2 1382.418 48 2860.837 2889.346 3022.403
15 GTR+F+I+R3 1382.449 50 2864.898 2896.186 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/tmpnastkljb/q2iqtree.model.gz
CPU time for ModelFinder: 0.784 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.797 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 (0.002 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000622988 secs using 97.75% CPU
Computing ML distances took 0.000675 sec (of wall-clock time) 0.000646 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 2.7895e-05 secs using 96.79% CPU
Constructing RapidNJ tree: done in 5.60284e-05 secs using 162.4% CPU
Computing RapidNJ tree took 0.000129 sec (of wall-clock time) 0.000163 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.820
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.062 second
Computing log-likelihood of 96 initial trees ... 0.046 seconds
Current best score: -1385.924
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.0024538 secs using 184.2% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.880
Optimizing NNI: done in 0.00670886 secs using 189.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -1385.311
Optimizing NNI: done in 0.005018 secs using 199.6% CPU
Optimizing NNI: done in 0.007797 secs using 197.8% CPU
Optimizing NNI: done in 0.00672793 secs using 197.4% CPU
Optimizing NNI: done in 0.00636816 secs using 197.5% CPU
Optimizing NNI: done in 0.00650811 secs using 196.3% CPU
Optimizing NNI: done in 0.0068171 secs using 188.7% CPU
Optimizing NNI: done in 0.00666904 secs using 194% CPU
Optimizing NNI: done in 0.00638485 secs using 198.5% CPU
Iteration 10 / LogL: -1385.344 / Time: 0h:0m:0s
Optimizing NNI: done in 0.00571704 secs using 197.1% CPU
Optimizing NNI: done in 0.00680995 secs using 195.9% CPU
Optimizing NNI: done in 0.00659394 secs using 155.3% CPU
Optimizing NNI: done in 0.00708508 secs using 97.81% CPU
Optimizing NNI: done in 0.0066061 secs using 99.82% CPU
Optimizing NNI: done in 0.00615692 secs using 99.84% CPU
Optimizing NNI: done in 0.00631213 secs using 99.22% CPU
Optimizing NNI: done in 0.0063808 secs using 98.61% CPU
Optimizing NNI: done in 0.00648379 secs using 99.85% CPU
Optimizing NNI: done in 0.00630999 secs using 99.94% CPU
Iteration 20 / LogL: -1385.335 / Time: 0h:0m:0s
Finish initializing candidate tree set (2)
Current best tree score: -1385.311 / CPU time: 0.245
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.00490093 secs using 99.9% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.311
Optimizing NNI: done in 0.00297499 secs using 96.61% CPU
Optimizing NNI: done in 0.00544 secs using 99.6% CPU
Optimizing NNI: done in 0.010406 secs using 97.49% CPU
Optimizing NNI: done in 0.00975299 secs using 99.33% CPU
Optimizing NNI: done in 0.00401306 secs using 98.88% CPU
Optimizing NNI: done in 0.00581598 secs using 99.64% CPU
Optimizing NNI: done in 0.00671196 secs using 98.44% CPU
Optimizing NNI: done in 0.00681901 secs using 98.23% CPU
Optimizing NNI: done in 0.0052278 secs using 99.85% CPU
Iteration 30 / LogL: -1385.928 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.00958014 secs using 99.69% CPU
Optimizing NNI: done in 0.00312495 secs using 99.94% CPU
Optimizing NNI: done in 0.00535488 secs using 98.66% CPU
Optimizing NNI: done in 0.00232983 secs using 99.96% CPU
Optimizing NNI: done in 0.00605202 secs using 99.72% CPU
Optimizing NNI: done in 0.00453806 secs using 98.59% CPU
Optimizing NNI: done in 0.00387788 secs using 99.87% CPU
Optimizing NNI: done in 0.00375795 secs using 99.84% CPU
Optimizing NNI: done in 0.00552106 secs using 97.75% CPU
Optimizing NNI: done in 0.00636482 secs using 99.94% CPU
Iteration 40 / LogL: -1385.931 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.00880504 secs using 99.76% CPU
Optimizing NNI: done in 0.0061779 secs using 99.47% CPU
Optimizing NNI: done in 0.00731111 secs using 98.77% CPU
Optimizing NNI: done in 0.009269 secs using 99.34% CPU
Optimizing NNI: done in 0.00541615 secs using 99.72% CPU
Optimizing NNI: done in 0.00647187 secs using 99.82% CPU
Optimizing NNI: done in 0.00710607 secs using 99.83% CPU
Optimizing NNI: done in 0.00957704 secs using 97.93% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.311
Optimizing NNI: done in 0.00788713 secs using 99.2% CPU
Optimizing NNI: done in 0.00248504 secs using 99.92% CPU
Iteration 50 / LogL: -1385.928 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.00515699 secs using 98.91% CPU
Optimizing NNI: done in 0.00452018 secs using 99.95% CPU
Optimizing NNI: done in 0.012109 secs using 98.75% CPU
Optimizing NNI: done in 0.00777316 secs using 99.53% CPU
Optimizing NNI: done in 0.0042119 secs using 99.79% CPU
Optimizing NNI: done in 0.00604796 secs using 99.87% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.311
Optimizing NNI: done in 0.00444508 secs using 96.83% CPU
Optimizing NNI: done in 0.00413322 secs using 99.95% CPU
Optimizing NNI: done in 0.00319791 secs using 97.56% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.310
Optimizing NNI: done in 0.00474 secs using 99.81% CPU
Iteration 60 / LogL: -1385.313 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.00427103 secs using 99.55% CPU
Optimizing NNI: done in 0.010648 secs using 97.96% CPU
Optimizing NNI: done in 0.00331998 secs using 99.4% CPU
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Optimizing NNI: done in 0.004848 secs using 95.3% CPU
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Optimizing NNI: done in 0.00513506 secs using 99.98% CPU
Iteration 70 / LogL: -1385.928 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.00515199 secs using 99.92% CPU
Optimizing NNI: done in 0.00607491 secs using 99.67% CPU
Optimizing NNI: done in 0.00816298 secs using 99.85% CPU
Optimizing NNI: done in 0.00254512 secs using 99.29% CPU
UPDATE BEST LOG-LIKELIHOOD: -1385.310
Optimizing NNI: done in 0.00776601 secs using 99.95% CPU
Optimizing NNI: done in 0.0094521 secs using 98.7% CPU
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Optimizing NNI: done in 0.012228 secs using 99.42% CPU
Optimizing NNI: done in 0.00820398 secs using 99.16% CPU
Iteration 80 / LogL: -1385.931 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.00546288 secs using 99.91% CPU
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Iteration 90 / LogL: -1385.641 / Time: 0h:0m:0s (0h:0m:0s left)
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Iteration 100 / LogL: -1385.940 / Time: 0h:0m:0s (0h:0m:0s left)
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Iteration 110 / LogL: -1385.664 / Time: 0h:0m:0s (0h:0m:0s left)
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Iteration 120 / LogL: -1385.759 / Time: 0h:0m:0s (0h:0m:0s left)
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Iteration 130 / LogL: -1385.313 / Time: 0h:0m:0s (0h:0m:0s left)
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Iteration 140 / LogL: -1385.314 / Time: 0h:0m:1s (0h:0m:0s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.310
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Iteration 150 / LogL: -1385.313 / Time: 0h:0m:1s (0h:0m:0s left)
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Iteration 160 / LogL: -1385.313 / Time: 0h:0m:1s (0h:0m:0s left)
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Iteration 170 / LogL: -1385.311 / Time: 0h:0m:1s (0h:0m:0s left)
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Iteration 180 / LogL: -1385.510 / Time: 0h:0m:1s (0h:0m:0s left)
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Iteration 190 / LogL: -1385.854 / Time: 0h:0m:1s (0h:0m:0s left)
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Iteration 200 / LogL: -1388.648 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00520396 secs using 99.89% CPU
Optimizing NNI: done in 0.00258803 secs using 99.88% CPU
Optimizing NNI: done in 0.00539804 secs using 92.77% 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: -1385.310
Optimal log-likelihood: -1385.306
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 (0.003 sec)
BEST SCORE FOUND : -1385.306
Total tree length: 6.847
Total number of iterations: 203
CPU time used for tree search: 1.507 sec (0h:0m:1s)
Wall-clock time used for tree search: 1.347 sec (0h:0m:1s)
Total CPU time used: 1.524 sec (0h:0m:1s)
Total wall-clock time used: 1.364 sec (0h:0m:1s)
Analysis results written to:
IQ-TREE report: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpnastkljb/q2iqtree.iqtree
Maximum-likelihood tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpnastkljb/q2iqtree.treefile
Likelihood distances: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpnastkljb/q2iqtree.mldist
Screen log file: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpnastkljb/q2iqtree.log
Date and Time: Thu Apr 4 14:00:56 2024
n cores 1
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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpnastkljb/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 2.2.6 COVID-edition for Mac OS X 64-bit built Dec 8 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: eduroam-lfx-dock-1-371.intern.ethz.ch (AVX512, FMA3, 32 GB RAM)
Command: iqtree -bb 1000 -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp70g7y68j/q2iqtreeufboot -nt 1 -nstop 200 -pers 0.200000
Seed: 358301 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Apr 4 14:01:05 2024
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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000111818 secs using 85.85% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000310898 secs using 69.48% 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 89.88% CPU
1 e84fcf85a6a4065231dcf343bb862f1cb32abae6 40.65% passed 90.91%
2 5525fb6dab7b6577960147574465990c6df070ad 42.99% passed 99.80%
3 eb3564a35320b53cef22a77288838c7446357327 42.99% passed 25.49%
4 418f1d469f08c99976b313028cf6d3f18f61dd55 43.93% passed 71.86%
5 2e3b2c075901640c4de739473f9246385430b1ed 31.31% passed 90.76%
6 0469f8d819bd45c7638d1c8b0895270a05f34267 38.79% passed 92.82%
7 d162ed685007f5adede58f14aece31dfa1b60c18 40.65% passed 97.17%
8 1d45b2bce36cd995c5dcb755babf512e612ce8b9 41.59% passed 39.04%
9 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 31.31% passed 87.21%
10 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae 42.99% passed 85.00%
11 606c23e79bb730ad74e3c6efd72004c36674c17a 47.20% passed 87.78%
12 682e91d7e510ab134d0625234ad224f647c14eb0 41.59% passed 31.01%
13 6a36152105590b1eb095b9503e8f1f226fc73e43 39.25% passed 86.29%
14 6ca685c39a33bfbcb3123129e7af88d573df7d6f 42.06% failed 0.02%
15 8a1c44eb462ed58b21f3fdd72dd22bb657db2980 31.78% passed 54.40%
16 9b220cae8d375ea38b8b481cb95949cda8722fcb 36.92% passed 88.78%
17 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 37.85% passed 90.52%
18 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 31.78% passed 72.69%
19 d44b129a6181f052198bda3813f0802a91612441 41.59% passed 41.69%
20 ed1acad8a98e8579a44370733533ad7d3fed8006 48.13% passed 58.15%
**** TOTAL 39.77% 1 sequences failed composition chi2 test (p-value<5%; df=3)
Checking for duplicate sequences: done in 3.50475e-05 secs using 71.33% 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 0.013824 secs using 97.37% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1391.281
2. Current log-likelihood: -1389.723
Optimal log-likelihood: -1388.882
Rate parameters: A-C: 0.33813 A-G: 2.30739 A-T: 2.15806 C-G: 1.19220 C-T: 3.30147 G-T: 1.00000
Base frequencies: A: 0.243 C: 0.182 G: 0.319 T: 0.256
Proportion of invariable sites: 0.033
Gamma shape alpha: 1.423
Parameters optimization took 2 rounds (0.008 sec)
Time for fast ML tree search: 0.036 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 484 DNA models (sample size: 214) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 1402.497 45 2894.994 2919.637 3046.463
2 GTR+F+I 1401.403 46 2894.806 2920.698 3049.641
3 GTR+F+G4 1387.278 46 2866.557 2892.449 3021.392
4 GTR+F+I+G4 1387.559 47 2869.117 2896.298 3027.318
5 GTR+F+R2 1380.611 47 2855.222 2882.402 3013.422
6 GTR+F+R3 1380.659 49 2859.317 2889.195 3024.250
14 GTR+F+I+R2 1380.757 48 2857.513 2886.023 3019.080
15 GTR+F+I+R3 1380.696 50 2861.392 2892.681 3029.691
25 SYM+G4 1387.155 43 2860.310 2882.568 3005.047
27 SYM+R2 1382.244 44 2852.489 2875.921 3000.592
36 SYM+I+R2 1382.405 45 2854.809 2879.452 3006.278
47 TVM+F+G4 1388.425 45 2866.850 2891.493 3018.319
49 TVM+F+R2 1382.482 46 2856.965 2882.857 3011.799
58 TVM+F+I+R2 1382.560 47 2859.119 2886.300 3017.320
69 TVMe+G4 1387.122 42 2858.244 2879.367 2999.615
71 TVMe+R2 1382.298 43 2850.596 2872.855 2995.333
80 TVMe+I+R2 1382.453 44 2852.907 2876.339 3001.010
91 TIM3+F+G4 1391.457 44 2870.914 2894.346 3019.017
93 TIM3+F+R2 1384.431 45 2858.861 2883.504 3010.330
102 TIM3+F+I+R2 1384.573 46 2861.146 2887.039 3015.981
113 TIM3e+G4 1390.540 41 2863.080 2883.103 3001.085
115 TIM3e+R2 1385.228 42 2854.456 2875.578 2995.827
124 TIM3e+I+R2 1385.391 43 2856.782 2879.040 3001.519
135 TIM2+F+G4 1394.180 44 2876.360 2899.792 3024.463
137 TIM2+F+R2 1386.234 45 2862.469 2887.112 3013.938
146 TIM2+F+I+R2 1386.377 46 2864.755 2890.647 3019.590
157 TIM2e+G4 1397.742 41 2877.483 2897.507 3015.488
159 TIM2e+R2 1391.117 42 2866.235 2887.357 3007.606
168 TIM2e+I+R2 1391.272 43 2868.544 2890.802 3013.281
179 TIM+F+G4 1390.802 44 2869.603 2893.035 3017.706
181 TIM+F+R2 1383.206 45 2856.411 2881.054 3007.880
190 TIM+F+I+R2 1383.340 46 2858.680 2884.572 3013.515
201 TIMe+G4 1394.796 41 2871.592 2891.616 3009.597
203 TIMe+R2 1388.300 42 2860.600 2881.723 3001.971
212 TIMe+I+R2 1388.456 43 2862.912 2885.171 3007.649
223 TPM3u+F+G4 1392.567 43 2871.134 2893.393 3015.871
225 TPM3u+F+R2 1386.368 44 2860.736 2884.168 3008.839
234 TPM3u+F+I+R2 1386.501 45 2863.002 2887.645 3014.471
245 TPM3+G4 1390.540 40 2861.080 2880.039 2995.719
247 TPM3+R2 1385.307 41 2852.614 2872.637 2990.619
256 TPM3+I+R2 1385.459 42 2854.917 2876.040 2996.288
267 TPM2u+F+G4 1395.283 43 2876.566 2898.825 3021.303
269 TPM2u+F+R2 1388.114 44 2864.229 2887.661 3012.332
278 TPM2u+F+I+R2 1388.249 45 2866.497 2891.140 3017.966
289 TPM2+G4 1397.749 40 2875.499 2894.458 3010.138
291 TPM2+R2 1391.198 41 2864.396 2884.419 3002.401
300 TPM2+I+R2 1391.346 42 2866.692 2887.815 3008.063
311 K3Pu+F+G4 1392.050 43 2870.100 2892.359 3014.837
313 K3Pu+F+R2 1385.122 44 2858.245 2881.677 3006.348
322 K3Pu+F+I+R2 1385.245 45 2860.491 2885.134 3011.960
333 K3P+G4 1394.786 40 2869.573 2888.532 3004.212
335 K3P+R2 1388.359 41 2858.717 2878.740 2996.722
344 K3P+I+R2 1388.531 42 2861.061 2882.184 3002.432
355 TN+F+G4 1394.628 43 2875.256 2897.515 3019.993
357 TN+F+R2 1386.824 44 2861.647 2885.079 3009.750
366 TN+F+I+R2 1386.967 45 2863.933 2888.576 3015.402
377 TNe+G4 1397.748 40 2875.497 2894.456 3010.136
379 TNe+R2 1391.134 41 2864.269 2884.292 3002.274
388 TNe+I+R2 1391.289 42 2866.578 2887.701 3007.949
399 HKY+F+G4 1395.752 42 2875.504 2896.627 3016.875
401 HKY+F+R2 1388.691 43 2863.382 2885.640 3008.119
410 HKY+F+I+R2 1388.820 44 2865.639 2889.071 3013.742
421 K2P+G4 1397.753 39 2873.507 2891.438 3004.780
423 K2P+R2 1391.216 40 2862.433 2881.392 2997.072
432 K2P+I+R2 1391.363 41 2864.726 2884.750 3002.731
443 F81+F+G4 1406.478 41 2894.955 2914.979 3032.960
445 F81+F+R2 1400.602 42 2885.203 2906.326 3026.574
454 F81+F+I+R2 1400.799 43 2887.598 2909.857 3032.335
465 JC+G4 1408.432 38 2892.865 2909.802 3020.772
467 JC+R2 1403.021 39 2884.041 2901.972 3015.314
476 JC+I+R2 1403.194 40 2886.388 2905.348 3021.028
Akaike Information Criterion: TVMe+R2
Corrected Akaike Information Criterion: TPM3+R2
Bayesian Information Criterion: TPM3+R2
Best-fit model: TPM3+R2 chosen according to BIC
All model information printed to /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp70g7y68j/q2iqtreeufboot.model.gz
CPU time for ModelFinder: 0.875 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.902 seconds (0h:0m:0s)
Generating 1000 samples for ultrafast bootstrap (seed: 358301)...
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1385.307
Optimal log-likelihood: -1385.304
Rate parameters: A-C: 0.39693 A-G: 1.57495 A-T: 1.00000 C-G: 0.39693 C-T: 1.57495 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.723,0.403) (0.277,2.560)
Parameters optimization took 1 rounds (0.002 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000589132 secs using 97.6% CPU
Computing ML distances took 0.000668 sec (of wall-clock time) 0.000612 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 2.7895e-05 secs using 114.7% CPU
Constructing RapidNJ tree: done in 7.9155e-05 secs using 188.2% CPU
Computing RapidNJ tree took 0.000216 sec (of wall-clock time) 0.000261 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1393.836
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| INITIALIZING CANDIDATE TREE SET |
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Generating 98 parsimony trees... 0.059 second
Computing log-likelihood of 98 initial trees ... 0.051 seconds
Current best score: -1385.304
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.00288391 secs using 194.9% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1385.303
Optimizing NNI: done in 0.0120609 secs using 193% CPU
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Iteration 10 / LogL: -1385.338 / Time: 0h:0m:0s
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Iteration 20 / LogL: -1385.338 / Time: 0h:0m:0s
Finish initializing candidate tree set (2)
Current best tree score: -1385.303 / CPU time: 0.346
Number of iterations: 20
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| OPTIMIZING CANDIDATE TREE SET |
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UPDATE BEST LOG-LIKELIHOOD: -1385.303
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Iteration 30 / LogL: -1385.303 / Time: 0h:0m:0s (0h:0m:2s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.303
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Iteration 40 / LogL: -1385.694 / Time: 0h:0m:0s (0h:0m:2s left)
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Iteration 50 / LogL: -1385.748 / Time: 0h:0m:0s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -1416.951
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Iteration 60 / LogL: -1385.696 / Time: 0h:0m:0s (0h:0m:2s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.303
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Iteration 70 / LogL: -1385.694 / Time: 0h:0m:1s (0h:0m:1s left)
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Iteration 80 / LogL: -1385.697 / Time: 0h:0m:1s (0h:0m:1s left)
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Iteration 90 / LogL: -1385.694 / Time: 0h:0m:1s (0h:0m:1s left)
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Iteration 100 / LogL: -1385.311 / Time: 0h:0m:1s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -1416.951
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.992
Optimizing NNI: done in 0.00879598 secs using 99.18% CPU
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Iteration 110 / LogL: -1385.699 / Time: 0h:0m:1s (0h:0m:1s left)
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Iteration 120 / LogL: -1385.310 / Time: 0h:0m:1s (0h:0m:1s left)
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Iteration 130 / LogL: -1385.304 / Time: 0h:0m:1s (0h:0m:0s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.303
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Iteration 140 / LogL: -1385.695 / Time: 0h:0m:1s (0h:0m:0s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.303
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Iteration 150 / LogL: -1385.306 / Time: 0h:0m:2s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -1416.951
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Iteration 160 / LogL: -1385.303 / Time: 0h:0m:2s (0h:0m:0s left)
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Iteration 170 / LogL: -1385.694 / Time: 0h:0m:2s (0h:0m:0s left)
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Iteration 180 / LogL: -1385.694 / Time: 0h:0m:2s (0h:0m:0s left)
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UPDATE BEST LOG-LIKELIHOOD: -1385.303
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Iteration 190 / LogL: -1385.317 / Time: 0h:0m:2s (0h:0m:0s left)
Optimizing NNI: done in 0.010782 secs using 99.85% CPU
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Iteration 200 / LogL: -1385.696 / Time: 0h:0m:2s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -1417.859
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.998
Optimizing NNI: done in 0.00994515 secs using 99.44% CPU
Optimizing NNI: done in 0.00924802 secs using 99.36% CPU
TREE SEARCH COMPLETED AFTER 202 ITERATIONS / Time: 0h:0m:2s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1385.303
Optimal log-likelihood: -1385.303
Rate parameters: A-C: 0.39653 A-G: 1.57282 A-T: 1.00000 C-G: 0.39653 C-T: 1.57282 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Site proportion and rates: (0.723,0.402) (0.277,2.564)
Parameters optimization took 1 rounds (0.002 sec)
BEST SCORE FOUND : -1385.303
Creating bootstrap support values...
Split supports printed to NEXUS file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp70g7y68j/q2iqtreeufboot.splits.nex
Total tree length: 6.855
Total number of iterations: 202
CPU time used for tree search: 2.807 sec (0h:0m:2s)
Wall-clock time used for tree search: 2.683 sec (0h:0m:2s)
Total CPU time used: 2.864 sec (0h:0m:2s)
Total wall-clock time used: 2.741 sec (0h:0m:2s)
Computing bootstrap consensus tree...
Reading input file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp70g7y68j/q2iqtreeufboot.splits.nex...
20 taxa and 172 splits.
Consensus tree written to /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp70g7y68j/q2iqtreeufboot.contree
Reading input trees file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp70g7y68j/q2iqtreeufboot.contree
Log-likelihood of consensus tree: -1386.236
Analysis results written to:
IQ-TREE report: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp70g7y68j/q2iqtreeufboot.iqtree
Maximum-likelihood tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp70g7y68j/q2iqtreeufboot.treefile
Likelihood distances: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp70g7y68j/q2iqtreeufboot.mldist
Ultrafast bootstrap approximation results written to:
Split support values: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp70g7y68j/q2iqtreeufboot.splits.nex
Consensus tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp70g7y68j/q2iqtreeufboot.contree
Screen log file: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp70g7y68j/q2iqtreeufboot.log
Date and Time: Thu Apr 4 14:01:09 2024
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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -m MFP -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmp70g7y68j/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 2.2.6 COVID-edition for Mac OS X 64-bit built Dec 8 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: eduroam-lfx-dock-1-371.intern.ethz.ch (AVX512, FMA3, 32 GB RAM)
Command: iqtree -bb 1000 -st DNA --runs 1 -s /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/qiime2/elizabethgehret/data/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpui9gqlit/q2iqtreeufboot -nt 1 -alrt 1000 -abayes -lbp 1000 -nstop 200 -pers 0.200000
Seed: 268619 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Apr 4 14:01:17 2024
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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 0.000104904 secs using 85.79% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.000209093 secs using 70.3% 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 1.12057e-05 secs using 71.39% 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 3.60012e-05 secs using 69.44% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
Generating 1000 samples for ultrafast bootstrap (seed: 268619)...
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, 1.239 / LogL: -1394.544
Init pinv, alpha: 0.040, 1.000 / Estimate: 0.010, 1.340 / LogL: -1394.887
Init pinv, alpha: 0.080, 1.000 / Estimate: 0.010, 1.353 / LogL: -1394.887
Init pinv, alpha: 0.120, 1.000 / Estimate: 0.009, 1.352 / LogL: -1394.871
Init pinv, alpha: 0.160, 1.000 / Estimate: 0.009, 1.348 / LogL: -1394.836
Init pinv, alpha: 0.200, 1.000 / Estimate: 0.009, 1.351 / LogL: -1394.862
Init pinv, alpha: 0.240, 1.000 / Estimate: 0.010, 1.352 / LogL: -1394.884
Init pinv, alpha: 0.280, 1.000 / Estimate: 0.008, 1.346 / LogL: -1394.826
Init pinv, alpha: 0.320, 1.000 / Estimate: 0.009, 1.347 / LogL: -1394.838
Init pinv, alpha: 0.360, 1.000 / Estimate: 0.009, 1.348 / LogL: -1394.841
Optimal pinv,alpha: 0.000, 1.239 / LogL: -1394.544
Parameters optimization took 0.274 sec
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000876904 secs using 98.19% CPU
Computing ML distances took 0.000931 sec (of wall-clock time) 0.000901 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 3.40939e-05 secs using 176% CPU
Constructing RapidNJ tree: done in 5.50747e-05 secs using 163.4% CPU
Computing RapidNJ tree took 0.000210 sec (of wall-clock time) 0.000250 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1392.870
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.066 second
Computing log-likelihood of 98 initial trees ... 0.064 seconds
Current best score: -1392.870
Do NNI search on 20 best initial trees
Optimizing NNI: done in 0.015275 secs using 190.7% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -1387.265
Optimizing NNI: done in 0.0159919 secs using 194.7% CPU
Optimizing NNI: done in 0.00998092 secs using 198.4% CPU
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Iteration 10 / LogL: -1387.282 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0183709 secs using 99.35% CPU
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Optimizing NNI: done in 0.0183241 secs using 99.88% CPU
Iteration 20 / LogL: -1387.282 / Time: 0h:0m:0s
Finish initializing candidate tree set (1)
Current best tree score: -1387.265 / CPU time: 0.459
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.00551581 secs using 98.66% CPU
Optimizing NNI: done in 0.0193579 secs using 98.87% CPU
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Optimizing NNI: done in 0.00570297 secs using 99.95% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.259
Optimizing NNI: done in 0.0233591 secs using 98.5% CPU
Optimizing NNI: done in 0.00520682 secs using 99.91% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.258
Iteration 30 / LogL: -1387.258 / Time: 0h:0m:0s (0h:0m:5s left)
Optimizing NNI: done in 0.00588608 secs using 99.81% CPU
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Iteration 40 / LogL: -1387.304 / Time: 0h:0m:1s (0h:0m:4s left)
Optimizing NNI: done in 0.00476313 secs using 99.89% CPU
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Optimizing NNI: done in 0.00689697 secs using 99.17% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.257
Iteration 50 / LogL: -1387.257 / Time: 0h:0m:1s (0h:0m:3s left)
Log-likelihood cutoff on original alignment: -1408.596
Optimizing NNI: done in 0.00582004 secs using 99.76% CPU
Optimizing NNI: done in 0.01508 secs using 97.49% CPU
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Optimizing NNI: done in 0.0170221 secs using 96.08% CPU
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 58: -1387.168
Optimizing NNI: done in 0.018405 secs using 95.11% CPU
Optimizing NNI: done in 0.00716496 secs using 99.4% CPU
Iteration 60 / LogL: -1387.392 / Time: 0h:0m:1s (0h:0m:4s left)
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
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Optimizing NNI: done in 0.015461 secs using 99.58% CPU
BETTER TREE FOUND at iteration 68: -1387.168
Optimizing NNI: done in 0.00992894 secs using 98.45% CPU
Optimizing NNI: done in 0.0243931 secs using 98.66% CPU
Iteration 70 / LogL: -1387.192 / Time: 0h:0m:1s (0h:0m:4s left)
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Iteration 80 / LogL: -1387.476 / Time: 0h:0m:1s (0h:0m:4s left)
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Optimizing NNI: done in 0.00701189 secs using 99.57% CPU
Optimizing NNI: done in 0.00355506 secs using 94.51% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.168
Optimizing NNI: done in 0.0172911 secs using 98.1% CPU
Optimizing NNI: done in 0.00373507 secs using 99.94% CPU
UPDATE BEST LOG-LIKELIHOOD: -1387.168
Optimizing NNI: done in 0.0154068 secs using 99.57% CPU
Optimizing NNI: done in 0.00431204 secs using 99.91% CPU
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Optimizing NNI: done in 0.0156169 secs using 99.35% CPU
Iteration 90 / LogL: -1387.168 / Time: 0h:0m:2s (0h:0m:3s left)
Optimizing NNI: done in 0.00470495 secs using 99.92% CPU
Optimizing NNI: done in 0.00310397 secs using 99.9% CPU
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Optimizing NNI: done in 0.026391 secs using 97.29% CPU
Iteration 100 / LogL: -1387.178 / Time: 0h:0m:2s (0h:0m:3s left)
Log-likelihood cutoff on original alignment: -1408.596
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.944
NOTE: UFBoot does not converge, continue at least 100 more iterations
Optimizing NNI: done in 0.00495505 secs using 99.03% CPU
Optimizing NNI: done in 0.00564909 secs using 99.87% CPU
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
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Optimizing NNI: done in 0.00663304 secs using 91.87% CPU
Iteration 110 / LogL: -1387.168 / Time: 0h:0m:2s (0h:0m:3s left)
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
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Iteration 120 / LogL: -1387.168 / Time: 0h:0m:2s (0h:0m:3s left)
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
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Iteration 130 / LogL: -1387.197 / Time: 0h:0m:2s (0h:0m:2s left)
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
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Iteration 140 / LogL: -1387.378 / Time: 0h:0m:2s (0h:0m:2s left)
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Iteration 150 / LogL: -1387.188 / Time: 0h:0m:2s (0h:0m:2s left)
Log-likelihood cutoff on original alignment: -1408.596
Optimizing NNI: done in 0.013195 secs using 99.86% CPU
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Iteration 160 / LogL: -1387.168 / Time: 0h:0m:3s (0h:0m:2s left)
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
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Iteration 170 / LogL: -1387.168 / Time: 0h:0m:3s (0h:0m:1s left)
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Iteration 180 / LogL: -1387.168 / Time: 0h:0m:3s (0h:0m:1s left)
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
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Iteration 190 / LogL: -1387.168 / Time: 0h:0m:3s (0h:0m:1s left)
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Iteration 200 / LogL: -1387.182 / Time: 0h:0m:3s (0h:0m:1s left)
Log-likelihood cutoff on original alignment: -1408.596
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.989
NOTE: UFBoot does not converge, continue at least 100 more iterations
Optimizing NNI: done in 0.010571 secs using 99.37% CPU
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
Iteration 210 / LogL: -1387.168 / Time: 0h:0m:3s (0h:0m:1s left)
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Iteration 220 / LogL: -1387.168 / Time: 0h:0m:4s (0h:0m:1s left)
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Iteration 230 / LogL: -1387.177 / Time: 0h:0m:4s (0h:0m:1s left)
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
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Iteration 240 / LogL: -1387.172 / Time: 0h:0m:4s (0h:0m:1s left)
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
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Iteration 250 / LogL: -1387.168 / Time: 0h:0m:4s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -1408.596
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Iteration 260 / LogL: -1387.176 / Time: 0h:0m:4s (0h:0m:0s left)
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Iteration 270 / LogL: -1387.168 / Time: 0h:0m:4s (0h:0m:0s left)
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Iteration 280 / LogL: -1387.168 / Time: 0h:0m:5s (0h:0m:0s left)
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UPDATE BEST LOG-LIKELIHOOD: -1387.168
Iteration 290 / LogL: -1387.168 / Time: 0h:0m:5s (0h:0m:0s left)
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Iteration 300 / LogL: -1387.168 / Time: 0h:0m:5s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -1408.596
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.997
TREE SEARCH COMPLETED AFTER 300 ITERATIONS / Time: 0h:0m:5s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1387.168
Optimal log-likelihood: -1387.167
Rate parameters: A-C: 0.34636 A-G: 2.32102 A-T: 2.14181 C-G: 1.23360 C-T: 3.21641 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 (0.002 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...
0.045 sec.
Creating bootstrap support values...
Split supports printed to NEXUS file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpui9gqlit/q2iqtreeufboot.splits.nex
Total tree length: 7.606
Total number of iterations: 300
CPU time used for tree search: 5.177 sec (0h:0m:5s)
Wall-clock time used for tree search: 5.158 sec (0h:0m:5s)
Total CPU time used: 5.547 sec (0h:0m:5s)
Total wall-clock time used: 5.535 sec (0h:0m:5s)
Computing bootstrap consensus tree...
Reading input file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpui9gqlit/q2iqtreeufboot.splits.nex...
20 taxa and 156 splits.
Consensus tree written to /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpui9gqlit/q2iqtreeufboot.contree
Reading input trees file /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpui9gqlit/q2iqtreeufboot.contree
Log-likelihood of consensus tree: -1387.392
Analysis results written to:
IQ-TREE report: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpui9gqlit/q2iqtreeufboot.iqtree
Maximum-likelihood tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpui9gqlit/q2iqtreeufboot.treefile
Likelihood distances: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpui9gqlit/q2iqtreeufboot.mldist
Ultrafast bootstrap approximation results written to:
Split support values: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpui9gqlit/q2iqtreeufboot.splits.nex
Consensus tree: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpui9gqlit/q2iqtreeufboot.contree
Screen log file: /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpui9gqlit/q2iqtreeufboot.log
Date and Time: Thu Apr 4 14:01:22 2024
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/97c3aa04-d788-498f-ad21-76965194daed/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/gt/s61zzgwx7gz_npzjm4gxfp3w0000gn/T/tmpui9gqlit/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!