fragment_insertion

Hello there!
I am facing an issue in running qiime fragment-insertion sepp command. I checked the forum and I already add memory and it did not work. I could not get other suggestions from the forum. I apologize if this is a repetition.

I run the following command

qiime fragment-insertion sepp --i-representative-sequences rep_seq_filtered4m.qza
–i-reference-database sepp-refs-silva-128.qza --o-tree redsea_101020_tree.qza --o-placements tree_placements_redsea_101020.qza --p-threads 1

and I got the following error
Traceback (most recent call last):
File “/galileo/home/userexternal/cconte00/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File “</galileo/home/userexternal/cconte00/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-299>”, line 2, in sepp
File “/galileo/home/userexternal/cconte00/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/galileo/home/userexternal/cconte00/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in _callable_executor
output_views = self._callable(**view_args)
File “/galileo/home/userexternal/cconte00/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py”, line 77, in sepp
debug)
File “/galileo/home/userexternal/cconte00/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py”, line 53, in _run
subprocess.run(cmd, check=True, cwd=cwd)
File “/galileo/home/userexternal/cconte00/miniconda2/envs/qiime2-2019.10/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)

subprocess.CalledProcessError: Command ‘[‘run-sepp.sh’, ‘/scratch_local/slurm_job.5602551/qiime2-archive-c5cxgk0_/185cbed2-a15a-410d-b3a1-6d43c62ff10a/data/raxml-info.txt’, ‘-b’, ‘1’]’ returned non-zero exit status 1.

Plugin error from fragment-insertion:

Command ‘[‘run-sepp.sh’, ‘/scratch_local/slurm_job.5602551/qiime2-archive-c5cxgk0_/185cbed2-a15a-410d-b3a1-6d43c62ff10a/data/dna-sequences.fasta’, ‘q2-fra’]’ returned non-zero exit status 1.

I cannot figure it out.

Any clue?

Thanks in advance!

Hi @chiara,

How many sequences are you trying to insert into the silva tree? How much available memory and storage do you have on your system?

Here are a couple of other related threads:


-Mike

Hello @SoilRotifer,
Thanks for the suggestions, unfortunaltely, none of the shared links worked for me.

I am working with 506 sequences and I have 50GB of memory and 23T of space.
I rerun the command and I received the following error:
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/galileo/home/userexternal/cconte00/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py”, line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/galileo/home/userexternal/cconte00/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py”, line 555, in invoke
return callback(*args, **kwargs)
File “/galileo/home/userexternal/cconte00/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py”, line 351, in call
path = result.save(output)
File “/galileo/home/userexternal/cconte00/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 149, in save
self._archiver.save(filepath)
File “/galileo/home/userexternal/cconte00/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/core/archive/archiver.py”, line 353, in save
self.CURRENT_ARCHIVE.save(self.path, filepath)
File “/galileo/home/userexternal/cconte00/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/core/archive/archiver.py”, line 167, in save
allowZip64=True) as zf:
File “/galileo/home/userexternal/cconte00/miniconda2/envs/qiime2-2019.10/lib/python3.6/zipfile.py”, line 1113, in init
self.fp = io.open(file, filemode)
OSError: [Errno 28] No space left on device: '/gpfs/scratch/userexternal/cconte00/qiime2analyses/filtered_sample/filtered_tab_seqs/frag_insertion/halo_seq.tree.qza

How much memory/space do I need?

Thanks in advance,
Chiara

Quite often tmp directories have a size limit, even though there is ample storage on the system. There are a variety of ways to set your TMPDIR to alleviate this issue. Hopefully, one of those threads will help.

-Mike

2 Likes

Thanks @SoilRotifer!
I upgraded --p-threads at 2 and it worked!
Thanks for your time and your support,
Chiara

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