iqtree error for unrooted tree in phylogeny

Technical Support
1

Hello,
I am using Nanopore 16s rRNA data for metagenomics analyses. Since i cant go on from the DADA2 i use the mothur untill the taxonomic classifications. However, i want to use the qiime2 for beta diversity analyses so i transform my aligned sequence fasta file from mothur into the qiime2 FeatureData[AlignedSequence] qza artifact with the qiime tools import method. In order to do diversity analysis, since i have aligned data, instead of align-to-tree-mafft-fasttree tool first i try to construct phylogenetic tree with fasttree it does not end for over 48 hours so i tried with the iqtree but it gives an error as i mentioned below.
İ have 12 samples with 400k reads per sample, 1500 bp length.
I can have meaningfull results from mothur but how can i move forward with qiime2?
thank you in advance

Traceback (most recent call last):
File “/home/sahin/miniconda3/envs/qiime2/lib/python3.6/site-packages/q2cli/commands.py”, line 327, in call
results = action(**arguments)
File “</home/sahin/miniconda3/envs/qiime2/lib/python3.6/site-packages/decorator.py:decorator-gen-221>”, line 2, in iqtree_ultrafast_bootstrap
File “/home/sahin/miniconda3/envs/qiime2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/home/sahin/miniconda3/envs/qiime2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/home/sahin/miniconda3/envs/qiime2/lib/python3.6/site-packages/q2_phylogeny/_iqtree.py”, line 325, in iqtree_ultrafast_bootstrap
run_command(cmd)
File “/home/sahin/miniconda3/envs/qiime2/lib/python3.6/site-packages/q2_phylogeny/_raxml.py”, line 34, in run_command
subprocess.run(cmd, check=True)
File “/home/sahin/miniconda3/envs/qiime2/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘iqtree’, ‘-bb’, ‘1000’, ‘-st’, ‘DNA’, ‘–runs’, ‘1’, ‘-s’, ‘/tmp/qiime2-archive-t5aa9fnz/80a289cb-187f-41d6-830f-e68cd62a08b1/data/aligned-dna-sequences.fasta’, ‘-m’, ‘MFP’, ‘-pre’, ‘/tmp/tmp1puyyang/q2iqtreeufboot’, ‘-nt’, ‘8’]’ died with <Signals.SIGSEGV: 11>.

2

Hello @sahin_srhn,

Welcome to the Qiime 2 forums! :qiime2: As you have discovered, qiime 2 works great for short-read technology, but hopefully we can help you out with longer reads too.

Awesome! Have you clustered, dereplicated, or denoised your reads to make a feature abundance table? How many features or representative reads do you have?

I ask because building a tree is computationally intensive, especially when you have many features as branch tips. Building a tree using every read in your full dataset is probably impossible, but building a tree of representative reads of features in your table should be possible in under 48 hours. :deciduous_tree:

The SIGSEGV error you received is an internal error with iqtree. Hopefully when running a smaller number of features this error will not be an issue.

While the Qiime 2 tutorials use mostly Illumina data, people have used Qiime with Nanopore data! Perhaps instead of processing with Mothur then importing into Qiime, you could process all your data with Qiime as shown in this pipeline:

Let me know what you think.

Colin

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