Q2 fragment-insertion sepp error


(Alexa Johnson) #1

Hi,

I’m trying to run the fragment-insertion sepp and keep getting the following errors. I am using the feature table from a closed reference abundance table so that I can run it through the picrust2 custom tree pipeline next. Thank you. AJ

(qiime2-2018.11) Alexas-Air-5:CR-cluster-output alexajohnson$ qiime fragment-insertion sepp --i-representative-sequences rep-seqs-cr-97.qza --p-threads 20 --i-reference-alignment aligned-CR-rep-seqs.qza --i-reference-phylogeny rooted-CR-tree.qza --output-dir Crout --verbose

Removing /var/folders/5p/57lysxk55pj2d4bv2nh6cgvc0000gn/T/sepp-tmp-XXXXX.jSNwlJm0
Traceback (most recent call last):
File “/miniconda3/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 “/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/miniconda3/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 “/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_fragment_insertion/_insertion.py”, line 179, in sepp
reference_alignment, reference_phylogeny, debug)
File “/miniconda3/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 “/miniconda3/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/5p/57lysxk55pj2d4bv2nh6cgvc0000gn/T/qiime2-archive-li2j_vip/62344488-ce56-4ec9-9ab0-e1bb3e3d9b3c/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘20’, ‘-A’, ‘1000’, ‘-P’, ‘5000’, ‘-a’, ‘/var/folders/5p/57lysxk55pj2d4bv2nh6cgvc0000gn/T/qiime2-archive-tcqx093y/9d28b74f-7758-440d-ab5f-d5d1b3ec57d5/data/aligned-dna-sequences.fasta’, ‘-t’, ‘/var/folders/5p/57lysxk55pj2d4bv2nh6cgvc0000gn/T/qiime2-archive-b_m2_8ir/e9ce8ed8-12cd-4b12-bae7-2e138865a07a/data/tree.nwk’]’ returned non-zero exit status 1

Plugin error from fragment-insertion:

Command ‘[‘run-sepp.sh’, ‘/var/folders/5p/57lysxk55pj2d4bv2nh6cgvc0000gn/T/qiime2-archive-li2j_vip/62344488-ce56-4ec9-9ab0-e1bb3e3d9b3c/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘20’, ‘-A’, ‘1000’, ‘-P’, ‘5000’, ‘-a’, ‘/var/folders/5p/57lysxk55pj2d4bv2nh6cgvc0000gn/T/qiime2-archive-tcqx093y/9d28b74f-7758-440d-ab5f-d5d1b3ec57d5/data/aligned-dna-sequences.fasta’, ‘-t’, ‘/var/folders/5p/57lysxk55pj2d4bv2nh6cgvc0000gn/T/qiime2-archive-b_m2_8ir/e9ce8ed8-12cd-4b12-bae7-2e138865a07a/data/tree.nwk’]’ returned non-zero exit status 1

See above for debug info.


(Matthew Ryan Dillon) #2

Ack, sorry about that @ajohnson — that error message is terrible. My guess is that you are running out of resources (but, this is just a guess) — try dropping --p-n-threads to 10 or so and let us know how it goes. Thanks! :qiime2: