Hello and thank you for this great plugin!
I ran into the same error:
(qiime2-2018.11) ➜ q2-picrust2_PSC qiime fragment-insertion sepp --i-representative-sequences rep-seqs-merged.qza
–p-threads 1 --i-reference-alignment reference.fna.qza
–i-reference-phylogeny reference.tre.qza
–output-dir Picrust_Results --verbose
Removing /var/folders/k6/6hcwnkcn099frbhql59cjg900000gn/T/sepp-tmp-XXXXX.v5cuYeYV
Traceback (most recent call last):
File “/Users/lenalapidot/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in sepp
File “/Users/lenalapidot/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/Users/lenalapidot/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 362, in callable_executor
output_views = self._callable(**view_args)
File “/Users/lenalapidot/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_fragment_insertion/_insertion.py”, line 179, in sepp
reference_alignment, reference_phylogeny, debug)
File “/Users/lenalapidot/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_fragment_insertion/_insertion.py”, line 137, in _run
subprocess.run(cmd, check=True, cwd=cwd)
File “/Users/lenalapidot/miniconda2/envs/qiime2-2018.11/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run-sepp.sh’, ‘/var/folders/k6/6hcwnkcn099frbhql59cjg900000gn/T/qiime2-archive-f7x4q8_q/653c2d02-8488-47fa-b74b-85664abdad14/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘1’, ‘-A’, ‘1000’, ‘-P’, ‘5000’, ‘-a’, ‘/var/folders/k6/6hcwnkcn099frbhql59cjg900000gn/T/qiime2-archive-mvzzt5yb/87909524-fa4f-4b28-abd6-c7c89a3c7da7/data/aligned-dna-sequences.fasta’, ‘-t’, ‘/var/folders/k6/6hcwnkcn099frbhql59cjg900000gn/T/qiime2-archive-tfsejey7/f4e69728-a745-4069-b432-3f14951089fd/data/tree.nwk’]’ returned non-zero exit status 1
Plugin error from fragment-insertion:
Command ‘[‘run-sepp.sh’, ‘/var/folders/k6/6hcwnkcn099frbhql59cjg900000gn/T/qiime2-archive-f7x4q8_q/653c2d02-8488-47fa-b74b-85664abdad14/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘1’, ‘-A’, ‘1000’, ‘-P’, ‘5000’, ‘-a’, ‘/var/folders/k6/6hcwnkcn099frbhql59cjg900000gn/T/qiime2-archive-mvzzt5yb/87909524-fa4f-4b28-abd6-c7c89a3c7da7/data/aligned-dna-sequences.fasta’, ‘-t’, ‘/var/folders/k6/6hcwnkcn099frbhql59cjg900000gn/T/qiime2-archive-tfsejey7/f4e69728-a745-4069-b432-3f14951089fd/data/tree.nwk’]’ returned non-zero exit status 1
See above for debug info.
Where is my mistake?
Thank you,
Lena