Picrust2 - fragment-insertion error


(Ellie) #1

Hello all,

I love that Qiime2 is working in plugins from outside developers. While working on the new plugin to run Picrust2, I came across this error while trying to insert the reference sequences, sequences, and phylogeny into the pipeline.

Command ‘[‘run-sepp.sh’, ‘/tmp/qiime2-archive-pdq9qqez/5d9b382b-c735-4659-a7b7-1ce12127a7cc/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘1’, ‘-A’, ‘1000’, ‘-P’, ‘5000’, ‘-a’, ‘/tmp/qiime2-archive-q5zptwhb/6e317993-c994-454b-becd-4606de3e1caf/data/aligned-dna-sequences.fasta’, ‘-t’, ‘/tmp/qiime2-archive-0wdktzq4/f3bc220d-dae4-4dc0-8c4c-dfc3f03c25b1/data/tree.nwk’]’ returned non-zero exit status 1

If anyone has time to help work through this error message with me, it would be greatly appreciated.


(Nicholas Bokulich) #2

Hi @ereinhar,
Let’s see what @gmdouglas thinks. In the mean time, please post the following:

  1. the full error message (including the contents of any log files that are mentioned in the error report
  2. the QIIME 2 command that you are trying to use

(Gavin Douglas) #3

Hi @ereinhar,

I’m the developer of this plugin - I’m not sure what the problem is currently, but I’ll likely be able to help if you post the details requested above.

Best,

Gavin


(Ellie) #4

Hello @Nicholas_Bokulich and @gmdouglas. Thank you for helping out for the expedience, the help is incredibly appreicated.

The full command and verbose output:

(qiime2-2018.8) [[email protected] scratch]$ qiime fragment-insertion sepp --i-representative-sequences rep-seqs.qza \
>                               --p-threads 1 --i-reference-alignment aligned-rep-seqs.qza \
>                               --i-reference-phylogeny rooted-tree.qza \
>                               --output-dir tutorial_placed_out --verbose
Removing /tmp/tmp.iwpI1rP40p/sepp-tmp-WQiWO
Traceback (most recent call last):
  File "/users/ereinhar/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py", line 274, in __call__
    results = action(**arguments)
  File "<decorator-gen-286>", line 2, in sepp
  File "/users/ereinhar/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
    output_types, provenance)
  File "/users/ereinhar/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 362, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/users/ereinhar/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_fragment_insertion/_insertion.py", line 179, in sepp
    reference_alignment, reference_phylogeny, debug)
  File "/users/ereinhar/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_fragment_insertion/_insertion.py", line 137, in _run
    subprocess.run(cmd, check=True, cwd=cwd)
  File "/users/ereinhar/miniconda3/envs/qiime2-2018.8/lib/python3.5/subprocess.py", line 398, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run-sepp.sh', '/tmp/qiime2-archive-kzwg9l2x/5d9b382b-c735-4659-a7b7-1ce12127a7cc/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-fz990c7i/6e317993-c994-454b-becd-4606de3e1caf/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-47pqihxn/f3bc220d-dae4-4dc0-8c4c-dfc3f03c25b1/data/tree.nwk']' returned non-zero exit status 1

Plugin error from fragment-insertion:

  Command '['run-sepp.sh', '/tmp/qiime2-archive-kzwg9l2x/5d9b382b-c735-4659-a7b7-1ce12127a7cc/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-fz990c7i/6e317993-c994-454b-becd-4606de3e1caf/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-47pqihxn/f3bc220d-dae4-4dc0-8c4c-dfc3f03c25b1/data/tree.nwk']' returned non-zero exit status 1

(Gavin Douglas) #5

Hi @ereinhar,

Thanks for posting these details. What do aligned-rep-seqs.qza and rooted-tree.qza correspond to in your command? If you want to place ASVs for use with PICRUSt2 then you should place them into the PICRUSt2 reference files (reference.fna.qza and reference.tre.qza) in the q2-picrust2 tutorial: https://github.com/picrust/picrust2/wiki/q2-picrust2-Tutorial

Gavin