========= Execution of SEPP failed with exit code 1 =================
temporary working directories are NOT deleted for further inspection:
  $tmp = /var/folders/1m/v2hn0_5s66nf5z894vbq8hq40000gq/T/sepp-tmp-XXXXXXXXXX.fPDpEfLy
  $tmpssd = /var/folders/1m/v2hn0_5s66nf5z894vbq8hq40000gq/T/sepp-tempssd-XXXXXXXXXX.7z021rJi
--------- Content of STDOUT -----------------------------------------
--------- Content of STDERR -----------------------------------------
[21:19:12] config.py (line 315):    DEBUG: Main configuration file at /Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/share/sepp/sepp/main.config
[21:19:12] config.py (line 349):     INFO: Seed number: 297834
[21:19:12] algorithm.py (line 258):     INFO: Reading input alignment: <_io.TextIOWrapper name='/var/folders/1m/v2hn0_5s66nf5z894vbq8hq40000gq/T/qiime2/alison.ravenscraft/data/b376f2a2-d9a4-4f3d-b392-7a4229f3bcf8/data/aligned-dna-sequences.fasta' mode='r' encoding='UTF-8'>
[21:19:12] algorithm.py (line 265):     INFO: Reading input tree: <_io.TextIOWrapper name='/var/folders/1m/v2hn0_5s66nf5z894vbq8hq40000gq/T/qiime2/alison.ravenscraft/data/b376f2a2-d9a4-4f3d-b392-7a4229f3bcf8/data/tree.nwk' mode='r' encoding='UTF-8'>
[21:19:12] algorithm.py (line 229):  WARNING: Input placement size larger than total number of sequences!  Setting placement size to 122
[21:19:12] algorithm.py (line 234):  WARNING: Input alignment size larger than total number of sequences!  Setting alignment size to 122
[21:19:12] algorithm.py (line 238):     INFO: Decomposition Sizes are set to alignment: 122 placement: 122
[21:19:12] exhaustive.py (line 350):     INFO: Breaking into 1 placement subsets.
[21:19:12] exhaustive.py (line 361):    DEBUG: Placement subset P_0 has 122 nodes
[21:19:12] exhaustive.py (line 382):    DEBUG: Placement subset P_0 has 1 alignment subsets: [0]
[21:19:12] exhaustive.py (line 385):    DEBUG: Placement subset P_0 has 122 taxa:
[21:19:12] exhaustive.py (line 397):     INFO: Breaking into 1 alignment subsets.
[21:19:12] algorithm.py (line 275):    DEBUG: start reading fragment files and breaking to at least 1 chunks but at most 20000 sequences 
[21:19:12] filemgr.py (line 129):     INFO: Root temp directory built: /var/folders/1m/v2hn0_5s66nf5z894vbq8hq40000gq/T/sepp-tempssd-XXXXXXXXXX.7z021rJi/q2-fragment-insertion.0etyk85c
[21:19:12] alignment.py (line 203):    DEBUG: Writing alignment of type <class 'sepp.alignment.ReadonlySubalignment'> with length 5 to file /var/folders/1m/v2hn0_5s66nf5z894vbq8hq40000gq/T/sepp-tempssd-XXXXXXXXXX.7z021rJi/q2-fragment-insertion.0etyk85c/fragment_chunks/fragment_chunk_09in888gg.fasta
[21:19:12] algorithm.py (line 323):    DEBUG: fragment files read and divided.
[21:19:12] exhaustive.py (line 412):     INFO: Breaking each alignment subset into 1 fragment chunks.
[21:19:12] exhaustive.py (line 414):    DEBUG: Subproblem structure: (((FC_0_0_0)A_0_0)P_0)root
Traceback (most recent call last):
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/bin/run_sepp.py", line 26, in <module>
    ExhaustiveAlgorithm().run()
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/sepp/algorithm.py", line 159, in run
    self.build_jobs()
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/sepp/exhaustive.py", line 441, in build_jobs
    bj.setup_for_subproblem(
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/sepp/jobs.py", line 257, in setup_for_subproblem
    subproblem.write_subalignment_without_allgap_columns(self.infile)
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/sepp/problem.py", line 221, in write_subalignment_without_allgap_columns
    mut_subalg = self.subalignment.get_mutable_alignment()
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/sepp/alignment.py", line 398, in get_mutable_alignment
    ret.set_alignment(self)
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/sepp/alignment.py", line 285, in set_alignment
    for name, seq in alignment.items():
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/_collections_abc.py", line 744, in __iter__
    yield (key, self._mapping[key])
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/sepp/alignment.py", line 385, in __getitem__
    return self.parent_alignment[key]
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/sepp/alignment.py", line 385, in __getitem__
    return self.parent_alignment[key]
KeyError: 'Burkholderia.pseudomultivorans.SUB.INT23.BP2'
=====================================================================
Traceback (most recent call last):
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 520, in __call__
    results = self._execute_action(
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 581, in _execute_action
    results = action(**arguments)
  File "<decorator-gen-434>", line 2, in sepp
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
    outputs = self._callable_executor_(
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 75, in sepp
    _run(str(representative_sequences.file.view(DNAFASTAFormat)),
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 54, in _run
    subprocess.run(cmd, check=True, cwd=cwd)
  File "/Users/alison.ravenscraft/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run-sepp.sh', '/var/folders/1m/v2hn0_5s66nf5z894vbq8hq40000gq/T/qiime2/alison.ravenscraft/data/5f7b4326-9c05-40ba-9d8e-b2fa7dd0adc5/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000', '-a', '/var/folders/1m/v2hn0_5s66nf5z894vbq8hq40000gq/T/qiime2/alison.ravenscraft/data/b376f2a2-d9a4-4f3d-b392-7a4229f3bcf8/data/aligned-dna-sequences.fasta', '-t', '/var/folders/1m/v2hn0_5s66nf5z894vbq8hq40000gq/T/qiime2/alison.ravenscraft/data/b376f2a2-d9a4-4f3d-b392-7a4229f3bcf8/data/tree.nwk', '-r', '/var/folders/1m/v2hn0_5s66nf5z894vbq8hq40000gq/T/qiime2/alison.ravenscraft/data/b376f2a2-d9a4-4f3d-b392-7a4229f3bcf8/data/raxml-info.txt', '-b', '1']' returned non-zero exit status 1.

Plugin error from fragment-insertion:

  Command '['run-sepp.sh', '/var/folders/1m/v2hn0_5s66nf5z894vbq8hq40000gq/T/qiime2/alison.ravenscraft/data/5f7b4326-9c05-40ba-9d8e-b2fa7dd0adc5/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000', '-a', '/var/folders/1m/v2hn0_5s66nf5z894vbq8hq40000gq/T/qiime2/alison.ravenscraft/data/b376f2a2-d9a4-4f3d-b392-7a4229f3bcf8/data/aligned-dna-sequences.fasta', '-t', '/var/folders/1m/v2hn0_5s66nf5z894vbq8hq40000gq/T/qiime2/alison.ravenscraft/data/b376f2a2-d9a4-4f3d-b392-7a4229f3bcf8/data/tree.nwk', '-r', '/var/folders/1m/v2hn0_5s66nf5z894vbq8hq40000gq/T/qiime2/alison.ravenscraft/data/b376f2a2-d9a4-4f3d-b392-7a4229f3bcf8/data/raxml-info.txt', '-b', '1']' returned non-zero exit status 1.

See above for debug info.