Plugin error from phylogeny:

hi I was running the following command when I got the resulting error:
time qiime phylogeny align-to-tree-mafft-fasttree \

--i-sequences rep-seqs.qza
--o-alignment aligned-rep-seqs.qza
--o-masked-alignment masked-aligned-rep-seqs5.qza
--o-tree unrooted-tree.qza
--o-rooted-tree rooted-tree.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 /var/tmp/qiime2-archive-2e4oc_1p/7bf840df-bdc6-4e02-b1af-fc70cb5b3640/data/dna-sequences.fasta

mktemp: failed to create directory via template '/tmp/mafft.XXXXXXXXXX': No such file or directory
mktemp seems to be obsolete. Re-trying without -t
mkdir: cannot create directory '/tmp': Permission denied
mktemp: failed to create directory via template '/tmp/mafft.XXXXXXXXXX': No such file or directory
/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 1070: /infile: Permission denied
/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 1071: /infile: Permission denied
/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 1072: /_addfile: Permission denied
/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 1080: /infile: Permission denied
/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 1082: /_aamtx: Permission denied
/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 1083: /_subalignmentstable: Permission denied
/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 1084: /_guidetree: Permission denied
/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 1085: /_seedtablefile: Permission denied
/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 1086: /_lara.params: Permission denied
/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 1087: /pdblist: Permission denied
/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 1088: /ownlist: Permission denied
/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 1089: /_externalanchors: Permission denied
grep: /infile: No such file or directory
/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 1761: [: -gt: unary operator expected
grep: /infile: No such file or directory
/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 1770: [: -eq: unary operator expected
/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 1777: [: too many arguments
inputfile = orig
0 x 0 - 99999999 p
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
Warning: Only 0 sequence found.

Strategy:
FFT-NS-2 (Fast but rough)
Progressive method (guide trees were built 2 times.)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

/home/wangderder/miniconda3/envs/qiime2-2021.4/bin/mafft: line 2716: /pre: No such file or directory
Traceback (most recent call last):
File "/home/wangderder/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in align_to_tree_mafft_fasttree
File "/home/wangderder/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 244, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/wangderder/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 484, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/home/wangderder/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_phylogeny/_align_to_tree_mafft_fasttree.py", line 19, in align_to_tree_mafft_fasttree
aligned_seq, = mafft(sequences=sequences, n_threads=n_threads,
File "", line 2, in mafft
File "/home/wangderder/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 244, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/wangderder/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home/wangderder/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 128, in mafft
return _mafft(sequences_fp, None, n_threads, parttree, False)
File "/home/wangderder/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 100, in _mafft run_command(cmd, result_fp)
File "/home/wangderder/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 26, in run_command
subprocess.run(cmd, stdout=output_f, check=True)
File "/home/wangderder/miniconda3/envs/qiime2-2021.4/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/var/tmp/qiime2-archive-2e4oc_1p/7bf840df-bdc6-4e02-b1af-fc70cb5b3640/data/dna-sequences.fasta']' returned non-zero exit status 1.

Plugin error from phylogeny:

Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/var/tmp/qiime2-archive-2e4oc_1p/7bf840df-bdc6-4e02-b1af-fc70cb5b3640/data/dna-sequences.fasta']' returned non-zero exit status 1.

See above for debug info.

Any suggestions?

Hi @wangder0, welcome to :qiime2:!

It looks a permissions issue writing to the $TMPDIR:

You can confirm the default TMPDIR path by typing:

echo $TMPDIR

Are you running this on a server? Your own computer? You can change the $TMPDIR path as outlined here, and see if that fixes the issue:

-Mike

thanks,This issue has been resolved

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