Here's an update:
I thought perhaps the qza file was just too large (17345 ASVs, 1.6 mb) so I filtered it down to only the ASVs we were interested in using this:
qiime feature-table filter-seqs \
--i-data reads_qza/rep-seqs-joined.qza \
--m-metadata-file filt_seqs.csv \
--o-filtered-data rep-seqs-joined_for_tree.qza
The file was now down to 823 kb (7561 ASVs), but I'm still getting the same error:
Plugin error from fragment-insertion:
Command '['run-sepp.sh', '/u1/sdm231/canola/qiime2-tmp/qiime2-archive-jj101gil/14aae9b3-4c59-43b1-aab2-9800e1986ae9/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000']' returned non-zero exit status 1.
Debug info has been saved to /u1/sdm231/canola/qiime2-tmp/qiime2-q2cli-err-yjif63be.log
Here's the log file:
Removing /u1/sdm231/canola/qiime2-tmp/tmp.qQPH2SqCec/sepp-tmp-OLEy3
Traceback (most recent call last):
File "/home/sdm231/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py", line 327, in __call__
results = action(**arguments)
File "</home/sdm231/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-299>", line 2, in sepp
File "/home/sdm231/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/home/sdm231/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/sdm231/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 179, in sepp
reference_alignment, reference_phylogeny, debug)
File "/home/sdm231/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 137, in _run
subprocess.run(cmd, check=True, cwd=cwd)
File "/home/sdm231/miniconda3/envs/qiime2-2019.7/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run-sepp.sh', '/u1/sdm231/canola/qiime2-tmp/qiime2-archive-mrlgbde3/88ef22e1-906f-4338-b8fe-acd59ef74bd9/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000']' returned non-zero exit status 1.
I'm not sure why this is failing—I don't think it's a space issue, but can't seem to figure out the real problem. It's something to do with the run-sepp.sh, but what?
I've attached the file here in case someone can run it on their system using:
qiime fragment-insertion sepp \
--i-representative-sequences rep-seqs-joined_for_tree.qza \
--o-tree insertion-tree.qza \
--o-placements insertion-placements.qza
Help?
rep-seqs-joined_for_tree.qza (822.4 KB)