Generating phylogenic tree for diversity analyses

Hi, I am running the following script but getting an error. Do you have any suggestions to troubleshoot? Thank you.

$ qiime phylogeny align-to-tree-mafft-fasttree \

--i-sequences oral_rep-seqs-DADA2.qza \

--o-alignment aligned-oral_rep-seqs.qza \

--o-masked-alignment masked-aligned-oral_rep-seqs.qza \

--o-tree unrooted-tree_oral.qza \

--o-rooted-tree rooted-tree_oral.qza

Plugin error from phylogeny:

Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2-archive-t3xk8thq/f1f632be-0626-4bae-8641-906e69a835be/data/dna-sequences.fasta']' returned non-zero exit status 1.

Hi @TM3197,
Could you rerun the command with the --verbose flag?

Thanks a lot for the reply. This is what I get.

$ qiime phylogeny align-to-tree-mafft-fasttree \

--i-sequences oral_rep-seqs-DADA2.qza
--o-alignment aligned-oral_rep-seqs.qza
--o-masked-alignment masked-aligned-oral_rep-seqs.qza
--o-tree unrooted-tree_oral.qza
--o-rooted-tree rooted-tree_oral.qza
--verbose
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: mafft --preservecase --inputorder --thread 1 /tmp/qiime2-archive-w3m35grq/f1f632be-0626-4bae-8641-906e69a835be/data/dna-sequences.fasta

inputfile = orig
13007 x 507 - 268 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: -1 kb
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00

Making a distance matrix ..
13001 / 13007 (thread 0)
done.

Constructing a UPGMA tree (efffree=0) ...
13000 / 13007
done.

Progressive alignment 1/2...
STEP 10601 / 13006 (thread 0) f
Reallocating..done. *alloclen = 2021
STEP 12201 / 13006 (thread 0) f
Reallocating..done. *alloclen = 3043
STEP 12301 / 13006 (thread 0) f
Reallocating..done. *alloclen = 4210
STEP 12601 / 13006 (thread 0) f
Reallocating..done. *alloclen = 5502

Reallocating..done. *alloclen = 7249
Allocation error( 4049 int vec )
Traceback (most recent call last):
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in align_to_tree_mafft_fasttree
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 484, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_phylogeny/_align_to_tree_mafft_fasttree.py", line 20, in align_to_tree_mafft_fasttree
parttree=parttree)
File "", line 2, in mafft
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_alignment/_mafft.py", line 127, in mafft
return _mafft(sequences_fp, None, n_threads, parttree)
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_alignment/_mafft.py", line 99, in _mafft
run_command(cmd, result_fp)
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_alignment/_mafft.py", line 26, in run_command
subprocess.run(cmd, stdout=output_f, check=True)
File "/usr/local/anaconda3/2020.07/envs/qiime2-2020.6/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2-archive-w3m35grq/f1f632be-0626-4bae-8641-906e69a835be/data/dna-sequences.fasta']' returned non-zero exit status 1.

Plugin error from phylogeny:

Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2-archive-w3m35grq/f1f632be-0626-4bae-8641-906e69a835be/data/dna-sequences.fasta']' returned non-zero exit status 1.

See above for debug info.

@TM3197

My best bet is this is a memory issue. How are you running this command? How much ram does your set up have?

Thanks a lot for the reply. I am working on Artemis. After requesting more RAM, I could successfully run the script. Thanks again.

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