Hi Stefan,
Just an update, I updated my qiime 2 version to qiime2-2019.4 and now I can't seem to get the fragment-insertion SEPP to run at all. I'm not sure if what sort of error it is but I wanted to post the report encase anyone else has the same issue.
input:
qiime fragment-insertion sepp \
--i-representative-sequences rep-seqs.qza \
--i-reference-alignment gg_99_otus_aligned.qza \
--i-reference-phylogeny gg_99_otus_annotated_tre.qza \
--p-threads 0 \
--o-tree insertion-tree.qza \
--o-placements insertion-placements.qza \
--output-dir fragment-insertion_SEPP \
--verbose
Removing /var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/sepp-tmp-XXXXX.t2128idL
Traceback (most recent call last):
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py", line 311, in call
results = action(**arguments)
File "</Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-299>", line 2, in sepp
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in callable_executor
output_views = self._callable(**view_args)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 179, in sepp
reference_alignment, reference_phylogeny, debug)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 137, in _run
subprocess.run(cmd, check=True, cwd=cwd)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.4/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run-sepp.sh', '/var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-wvx96o9l/4d78965a-a2ca-47c4-9589-4b5d9bce4c9b/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '0', '-A', '1000', '-P', '5000', '-a', '/var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-jgb225ve/5d1ee9a7-2723-4502-bc3f-41fac3177d4f/data/aligned-dna-sequences.fasta', '-t', '/var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-huvom3i5/c99314bc-a852-49be-9663-308d299bfe60/data/tree.nwk']' returned non-zero exit status 1.
Plugin error from fragment-insertion:
Command '['run-sepp.sh', '/var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-wvx96o9l/4d78965a-a2ca-47c4-9589-4b5d9bce4c9b/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '0', '-A', '1000', '-P', '5000', '-a', '/var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-jgb225ve/5d1ee9a7-2723-4502-bc3f-41fac3177d4f/data/aligned-dna-sequences.fasta', '-t', '/var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-huvom3i5/c99314bc-a852-49be-9663-308d299bfe60/data/tree.nwk']' returned non-zero exit status 1.
and the same error report comes up if I remove both reference files, changed threads or changed output names, locations.
I also ran the same input using qiime2-2019.1
Removing /var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/sepp-tmp-XXXXX.aoKUCkEN
Traceback (most recent call last):
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "</Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-290>", line 2, in sepp
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in callable_executor
output_views = self._callable(**view_args)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 179, in sepp
reference_alignment, reference_phylogeny, debug)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 137, in _run
subprocess.run(cmd, check=True, cwd=cwd)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run-sepp.sh', '/var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-borz_lb2/4d78965a-a2ca-47c4-9589-4b5d9bce4c9b/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '0', '-A', '1000', '-P', '5000', '-a', '/var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-6cnfpdp6/5d1ee9a7-2723-4502-bc3f-41fac3177d4f/data/aligned-dna-sequences.fasta', '-t', '/var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-m0kt6fuh/c99314bc-a852-49be-9663-308d299bfe60/data/tree.nwk']' returned non-zero exit status 1.
Plugin error from fragment-insertion:
Command '['run-sepp.sh', '/var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-borz_lb2/4d78965a-a2ca-47c4-9589-4b5d9bce4c9b/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '0', '-A', '1000', '-P', '5000', '-a', '/var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-6cnfpdp6/5d1ee9a7-2723-4502-bc3f-41fac3177d4f/data/aligned-dna-sequences.fasta', '-t', '/var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-m0kt6fuh/c99314bc-a852-49be-9663-308d299bfe60/data/tree.nwk']' returned non-zero exit status 1.
Hope this helps!