fragment-insertion sepp error

Hi @colinbrislawn,

I encountered a similar error.
qiime version 2019.10

My input file size is 815KB. I also tried another with 794KB but had the same issues. I am using Imac with 32GB memory.
What could be the problem?

coomand:

qiime fragment-insertion sepp --i-representative-sequences “my_rep_seq.qza” --i-reference-database “Silva 128 SEPP reference from qiime2 data resources” --output-dir “my folder”
–p-threads 3 # I used the default as well

My log 1:

Removing /var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/sepp-tmp-XXXXXXXXXX.EJA26q08
Traceback (most recent call last):
File “/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File “</Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-299>”, line 2, in sepp
File “/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py”, line 77, in sepp
debug)
File “/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py”, line 53, in _run
subprocess.run(cmd, check=True, cwd=cwd)
File “/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run-sepp.sh’, ‘/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-lllqk149/641e4de1-9653-4f01-9190-90ae951bcd70/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘1’, ‘-A’, ‘1000’, ‘-P’, ‘5000’, ‘-a’, ‘/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-ewyuo4qr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta’, ‘-t’, ‘/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-ewyuo4qr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk’, ‘-r’, ‘/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-ewyuo4qr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt’]’ returned non-zero exit status 1.

debug log 2:

Removing /var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/sepp-tmp-XXXXXXXXXX.GXBXL5J5
Traceback (most recent call last):
File “/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File “</Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-299>”, line 2, in sepp
File “/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py”, line 77, in sepp
debug)
File “/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py”, line 53, in _run
subprocess.run(cmd, check=True, cwd=cwd)
File “/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run-sepp.sh’, ‘/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-oof6sjxh/31d92a56-ab3c-48df-8177-287b5a800d0d/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘3’, ‘-A’, ‘1000’, ‘-P’, ‘5000’, ‘-a’, ‘/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-ivtnnjdu/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta’, ‘-t’, ‘/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-ivtnnjdu/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk’, ‘-r’, ‘/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-ivtnnjdu/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt’]’ returned non-zero exit status 1.

Hello!

Those files aren’t too big and you have plenty of RAM! I think the issue must be something else…

Can you try rerunning this using the --p-debug and --verbose flags so we can get more detailed log files?

Colin

1 Like

Hi @colinbrislawn,

The detailed log files are below for your reference. Thanks for your assistance.

qiime fragment-insertion sepp --i-representative-sequences rep_seqs.qza --i-reference-database ~/Downloads/sepp-refs-silva-128.qza --output-dir results_sepp --p-threads 3 --p-debug --verbose 
========= Execution of SEPP failed with exit code 1 =================
temporary working directories are NOT deleted for further inspection:
  $tmp = /var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/sepp-tmp-XXXXXXXXXX.1PRrMW48
  $tmpssd = /var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/sepp-tempssd-XXXXXXXXXX.mqIDt7TM
--------- Content of STDOUT -----------------------------------------
--------- Content of STDERR -----------------------------------------
Traceback (most recent call last):
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/bin/run_sepp.py", line 4, in <module>
    __import__('pkg_resources').run_script('sepp==4.3.10', 'run_sepp.py')
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1462, in run_script
    exec(code, namespace, namespace)
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/sepp-4.3.10-py3.6.egg-info/scripts/run_sepp.py", line 3, in <module>
    from sepp.exhaustive import ExhaustiveAlgorithm
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/sepp/exhaustive.py", line 6, in <module>
    from sepp.algorithm import AbstractAlgorithm
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/sepp/algorithm.py", line 11, in <module>
    from sepp.tree import PhylogeneticTree
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/sepp/tree.py", line 23, in <module>
    from dendropy import Tree, Taxon, treecalc
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/dendropy/__init__.py", line 24, in <module>
    from dendropy.dataio.nexusprocessing import get_rooting_argument
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/dendropy/dataio/__init__.py", line 20, in <module>
    from dendropy.dataio import newickreader
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/dendropy/dataio/newickreader.py", line 27, in <module>
    from dendropy.utility.textprocessing import StringIO
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/dendropy/utility/textprocessing.py", line 40, in <module>
    ENCODING = locale.getdefaultlocale()[1]
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/locale.py", line 562, in getdefaultlocale
    return _parse_localename(localename)
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/locale.py", line 490, in _parse_localename
    raise ValueError('unknown locale: %s' % localename)
ValueError: unknown locale: UTF-8
=====================================================================
Traceback (most recent call last):
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 328, in __call__
    results = action(**arguments)
  File "</Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-299>", line 2, in sepp
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
    output_types, provenance)
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 77, in sepp
    debug)
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 53, in _run
    subprocess.run(cmd, check=True, cwd=cwd)
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/subprocess.py", line 418, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run-sepp.sh', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-ifds0mzy/641e4de1-9653-4f01-9190-90ae951bcd70/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '3', '-A', '1000', '-P', '5000', '-a', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-rpcsqqls/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-rpcsqqls/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-rpcsqqls/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt', '-b', '1']' returned non-zero exit status 1.

Plugin error from fragment-insertion:

  Command '['run-sepp.sh', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-ifds0mzy/641e4de1-9653-4f01-9190-90ae951bcd70/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '3', '-A', '1000', '-P', '5000', '-a', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-rpcsqqls/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-rpcsqqls/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-rpcsqqls/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt', '-b', '1']' returned non-zero exit status 1.

See above for debug info.

  1. I used the default --p-threads
qiime fragment-insertion sepp --i-representative-sequences rep_seqs.qza --i-reference-database ~/Downloads/sepp-refs-silva-128.qza --output-dir results_sepp  --p-debug --verbose 
========= Execution of SEPP failed with exit code 1 =================
temporary working directories are NOT deleted for further inspection:
  $tmp = /var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/sepp-tmp-XXXXXXXXXX.pnS1JMyw
  $tmpssd = /var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/sepp-tempssd-XXXXXXXXXX.GtAJAVdb
--------- Content of STDOUT -----------------------------------------
--------- Content of STDERR -----------------------------------------
Traceback (most recent call last):
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/bin/run_sepp.py", line 4, in <module>
    __import__('pkg_resources').run_script('sepp==4.3.10', 'run_sepp.py')
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1462, in run_script
    exec(code, namespace, namespace)
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/sepp-4.3.10-py3.6.egg-info/scripts/run_sepp.py", line 3, in <module>
    from sepp.exhaustive import ExhaustiveAlgorithm
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/sepp/exhaustive.py", line 6, in <module>
    from sepp.algorithm import AbstractAlgorithm
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/sepp/algorithm.py", line 11, in <module>
    from sepp.tree import PhylogeneticTree
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/sepp/tree.py", line 23, in <module>
    from dendropy import Tree, Taxon, treecalc
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/dendropy/__init__.py", line 24, in <module>
    from dendropy.dataio.nexusprocessing import get_rooting_argument
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/dendropy/dataio/__init__.py", line 20, in <module>
    from dendropy.dataio import newickreader
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/dendropy/dataio/newickreader.py", line 27, in <module>
    from dendropy.utility.textprocessing import StringIO
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/dendropy/utility/textprocessing.py", line 40, in <module>
    ENCODING = locale.getdefaultlocale()[1]
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/locale.py", line 562, in getdefaultlocale
    return _parse_localename(localename)
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/locale.py", line 490, in _parse_localename
    raise ValueError('unknown locale: %s' % localename)
ValueError: unknown locale: UTF-8
=====================================================================
Traceback (most recent call last):
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 328, in __call__
    results = action(**arguments)
  File "</Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-299>", line 2, in sepp
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
    output_types, provenance)
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 77, in sepp
    debug)
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 53, in _run
    subprocess.run(cmd, check=True, cwd=cwd)
  File "/Users/arc/miniconda2/envs/qiime2-2019.10/lib/python3.6/subprocess.py", line 418, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run-sepp.sh', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-lka1ue2q/641e4de1-9653-4f01-9190-90ae951bcd70/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000', '-a', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-329wi6p8/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-329wi6p8/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-329wi6p8/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt', '-b', '1']' returned non-zero exit status 1.

Plugin error from fragment-insertion:

  Command '['run-sepp.sh', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-lka1ue2q/641e4de1-9653-4f01-9190-90ae951bcd70/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000', '-a', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-329wi6p8/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-329wi6p8/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/var/folders/rz/v666w_cn74n5790222zycgfr0000gn/T/qiime2-archive-329wi6p8/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt', '-b', '1']' returned non-zero exit status 1.

See above for debug info.

For both commands, it looks like the same error:

I searched for that command online, and found this page:

Do any of those suggestions work for you?

Colin

Hello @colinbrislawn,

Thanks for the suggestion. It worked after following the recommendation.
It took about 17 hours to complete though.

Best regards

1 Like

Yep, sepp is slow. :evergreen_tree: :hourglass:

Out of all the suggestions on that page, which one worked for you? That could be very helpful for other users who have that issue!

1 Like

By adding this to my ~/.bash_profile

export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8

then

source ~/.bash_profile

Work in a new terminal window after source ~/.bash_profile

1 Like