qiime2-picrust plugin - use with SILVA data

[a.w...@uni-bayreuth.de]

Hello,

I have installed the picrust2 plugin in qiime 2018.11 and the provided example data (stool microbiome of wolves, coyotes, etc) could be analyzed without error messages.

I then tried to exchange the following data with my won data:

qiime fragment-insertion sepp \
--i-representative-sequences mammal_seqs.qza \ <<< I used my own representative sequences 
--p-threads 1 --i-reference-alignment reference.fna.qza \ <<< I used the SILVA-132 alignment '97_alignment.fna' (as artifact file 97_alignment.fna.qza)
--i-reference-phylogeny reference.tre.qza \ <<< I used the SILVA-132 reference tree 97_otus.tre.qza (as artifact file 97_otus.tre.qza)
--output-dir output-directory

However, I received the following error message: 

Traceback (most recent call last):
  File "/home/qiime2/miniconda/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py", line 274, in __c
all__
    results = action(**arguments)
  File "<decorator-gen-290>", line 2, in sepp
  File "/home/qiime2/miniconda/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in
bound_callable
    output_types, provenance)
  File "/home/qiime2/miniconda/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 362, in
_callable_executor_
    output_views = self._callable(**view_args)
  File "/home/qiime2/miniconda/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_fragment_insertion/_insertion.py"
, line 179, in sepp
    reference_alignment, reference_phylogeny, debug)
  File "/home/qiime2/miniconda/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_fragment_insertion/_insertion.py"
, line 137, in _run
    subprocess.run(cmd, check=True, cwd=cwd)
  File "/home/qiime2/miniconda/envs/qiime2-2018.11/lib/python3.5/subprocess.py", line 398, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run-sepp.sh', '/tmp/qiime2-archive-afdn5p48/a70f0ff8-3b8e-434a-9188-b35c0
585ae37/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '12', '-A', '1000', '-P', '5000', '-a', '/tmp/qii
me2-archive-wdppvwsb/12e78377-4190-49a0-acd2-e645bdc878bd/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-arc
hive-oe180oyp/337706a5-9ef3-4967-b528-a86ba899b3d8/data/tree.nwk']' returned non-zero exit status 1

Does anybody have a suggestion how to overcome that problem?
Best regards

[Gavin Douglas]

Hi there,

You need to use the same reference tree and alignment as specified in the PICRUSt2 tutorial here: https://github.com/picrust/picrust2/wiki/q2-picrust2-Tutorial. These files need to be used since they contain genome ids within the PICRUSt2 database.

I think the issue is likely that the SILVA tree and alignment you used aren’t formatted correctly for q2-fragment-insertion.

Best,

Gavin

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