# Error when running insert-fragment sequences using SEPP
**URL:** https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856
**Category:** Technical Support
**Tags:** q2studio, fragment-insertion
**Created:** [May 20, 2019, 4:51pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856 "2019-05-20T16:51:35Z")
**Posts on this page:** 16
**Page:** 1
### Author:  [@TKOneal](https://forum.qiime2.org/u/TKOneal)
#### Post date: [May 20, 2019, 4:51pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/1 "2019-05-20T16:51:35Z")
Hi all,
I've attempted to run fragment-insertion on both the command line and in q2studio to see if I can identify why it keeps failing.
Running it in the q2studio with debug finally gave me this error report:
Traceback (most recent call last):
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/sepp/scheduler.py", line 298, in call\_back
join.\_tick(job)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/sepp/scheduler.py", line 232, in \_tick
self.perform()
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/sepp/exhaustive.py", line 83, in perform
self.figureout\_fragment\_subset()
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/sepp/exhaustive.py", line 49, in figureout\_fragment\_subset
search\_res = fragment\_chunk\_problem.get\_job\_result\_by\_name("hmmsearch")
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/sepp/problem.py", line 99, in get\_job\_result\_by\_name
with open(job.result, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/sepp-tempssd-XXXX.Mnzb9sur/q2-fragment-insertion.2gn3nj0g/root/P\_0/A\_0\_0/FC\_0\_0\_0/hmmsearch.results.y42\_fepn'
Traceback (most recent call last):
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/sepp/jobs.py", line 131, in run
self.read\_stderr() if self.read\_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/.sepp/bundled-v4.3.5/hmmsearch --noali --cpu 1 -o /var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/sepp-tempssd-XXXX.Mnzb9sur/q2-fragment-insertion.2gn3nj0g/root/P\_12/A\_12\_2/FC\_12\_2\_19/hmmsearch.results.5x7xf768 -E 99999999 --max /var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/sepp-tempssd-XXXX.Mnzb9sur/q2-fragment-insertion.2gn3nj0g/root/P\_12/A\_12\_2/hmmbuild.model.iu6u\_gab /var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/sepp-tempssd-XXXX.Mnzb9sur/q2-fragment-insertion.2gn3nj0g/fragment\_chunks/fragment\_chunk\_19uh5rymx3.fasta
Error: File existence/permissions problem in trying to open HMM file /var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/sepp-tempssd-XXXX.Mnzb9sur/q2-fragment-insertion.2gn3nj0g/root/P\_12/A\_12\_2/hmmbuild.model.iu6u\_gab.
HMM file /var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/sepp-tempssd-XXXX.Mnzb9sur/q2-fragment-insertion.2gn3nj0g/root/P\_12/A
Traceback (most recent call last):
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/sepp/jobs.py", line 131, in run
self.read\_stderr() if self.read\_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/.sepp/bundled-v4.3.5/hmmsearch --noali --cpu 1 -o /var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/sepp-tempssd-XXXX.Mnzb9sur/q2-fragment-insertion.2gn3nj0g/root/P\_12/A\_12\_2/FC\_12\_2\_18/hmmsearch.results.w3lt\_z80 -E 99999999 --max /var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/sepp-tempssd-XXXX.Mnzb9sur/q2-fragment-insertion.2gn3nj0g/root/P\_12/A\_12\_2/hmmbuild.model.iu6u\_gab /var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/sepp-tempssd-XXXX.Mnzb9sur/q2-fragment-insertion.2gn3nj0g/fragment\_chunks/fragment\_chunk\_18x8grlaol.fasta
Error: File existence/permissions problem in trying to open HMM file /var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/sepp-tempssd-XXXX.Mnzb9sur/q2-fragment-insertion.2gn3nj0g/root/P\_12/A\_12\_2/hmmbuild.model.iu6u\_gab.
HMM file /var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/sepp-tempssd-XXXX.Mnzb9sur/q2-fragment-insertion.2gn3nj0g/root/P\_12/A
Traceback (most recent call last):
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/share/fragment-insertion//sepp/run\_sepp.py", line 25, in
ExhaustiveAlgorithm().run()
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/sepp/algorithm.py", line 169, in run
if (not JobPool().wait\_for\_all\_jobs()):
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/share/fragment-insertion/sepp/sepp/scheduler.py", line 342, in wait\_for\_all\_jobs
raise Exception(job.errors[0])
Exception: [Errno 2] No such file or directory: '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/sepp-tempssd-XXXX.Mnzb9sur/q2-fragment-insertion.2gn3nj0g/root/P\_0/A\_0\_0/FC\_0\_0\_0/hmmsearch.results.y42\_fepn'
followed by the STDERR::
concurrent.futures.process.\_RemoteTraceback:
"""
Traceback (most recent call last):
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/concurrent/futures/process.py", line 175, in \_process\_worker
r = call\_item.fn(\*call\_item.args, \*\*call\_item.kwargs)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 34, in \_subprocess\_apply
results = action(\*args, \*\*kwargs)
File "\", line 2, in sepp
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound\_callable
output\_types, provenance)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in _callable\_executor_
output\_views = self.\_callable(\*\*view\_args)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2\_fragment\_insertion/\_insertion.py", line 179, in sepp
reference\_alignment, reference\_phylogeny, debug)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2\_fragment\_insertion/\_insertion.py", line 137, in \_run
subprocess.run(cmd, check=True, cwd=cwd)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run-sepp.sh', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-5zwbdq8o/d9988cbe-1ac2-4959-87a4-578f89207565/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '13', '-A', '1000', '-P', '5000', '-a', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-fa\_lfted/6920b923-8e48-4bbf-9dd3-ea42fbec4e02/data/aligned-dna-sequences.fasta', '-t', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-vhe40z07/51ec41c3-b6de-4f01-a8f7-7547e76aa1fb/data/tree.nwk', '-b', '1']' returned non-zero exit status 1.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/environmentalmicrobiologyteam/Desktop/Qiime2/q2studio-2019.1.0/q2studio/api/jobs.py", line 156, in callback
results = future.result()
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/concurrent/futures/\_base.py", line 425, in result
return self.\_\_get\_result()
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/concurrent/futures/\_base.py", line 384, in \_\_get\_result
raise self.\_exception
subprocess.CalledProcessError: Command '['run-sepp.sh', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-5zwbdq8o/d9988cbe-1ac2-4959-87a4-578f89207565/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '13', '-A', '1000', '-P', '5000', '-a', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-fa\_lfted/6920b923-8e48-4bbf-9dd3-ea42fbec4e02/data/aligned-dna-sequences.fasta', '-t', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-vhe40z07/51ec41c3-b6de-4f01-a8f7-7547e76aa1fb/data/tree.nwk', '-b', '1']' returned non-zero exit status 1.
Thanks for any and all help and opinions!
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [May 21, 2019, 12:46pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/2 "2019-05-21T12:46:30Z")
Hi @TKOneal,
I am cc:ing the fragment-insertion developer @Stefan to look into this. Thanks for your patience!
---
### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [May 21, 2019, 2:03pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/3 "2019-05-21T14:03:45Z")
Hi @TKOneal,
With the caveat that your milage may vary, my experience is that SEPP is one of the few programs in QIIME 2 that assumes you're working in a specific linguistic environment. Which means that I get a similar fragment insertion failure on my Swedish machine, but not my American one.
Could you check your location settings by running
```auto
locale
```
in your terminal?
If you don't have a LC\_ALL listed, I suggest running
```auto
export LANG='en_US.utf8'
```
If that doesn't work, IDK, but its at least something?
---
### Author:  [@Stefan](https://forum.qiime2.org/u/Stefan)
#### Post date: [May 21, 2019, 2:51pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/4 "2019-05-21T14:51:56Z")
Hi @TKOneal,
reading your error report let's me first think about concurrency issues. What kind of computational environment are you using? Is it a single laptop, or are you running SEPP in a grid environment. It could be that one thread is creating a temporary directory in /var/tmp which another thread overwrites / deletes and thus the first cannot find expected files. If that is the case, you should change the default tmp dir to something more stable across nodes in your grid.
@jwdebelius I have not yet encountered issues with different localizations, but I also only tested German and American envs. I'd be eager to see a concrete error message should you once again have this issue. Would be good to fix that in SEPP itself instead of having users to set this environment variable.
Best,
Stefan
---
### Author:  [@TKOneal](https://forum.qiime2.org/u/TKOneal)
#### Post date: [May 21, 2019, 8:09pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/5 "2019-05-21T20:09:24Z")
Hi jwdebelius!
Thanks for responding. Running locale shows the following:;
LANG="en\_US.UTF-8"
LC\_COLLATE="en\_US.UTF-8"
LC\_CTYPE="en\_US.UTF-8"
LC\_MESSAGES="en\_US.UTF-8"
LC\_MONETARY="en\_US.UTF-8"
LC\_NUMERIC="en\_US.UTF-8"
LC\_TIME="en\_US.UTF-8"
LC\_ALL=
---
### Author:  [@TKOneal](https://forum.qiime2.org/u/TKOneal)
#### Post date: [May 21, 2019, 8:24pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/6 "2019-05-21T20:24:36Z")
Hi Stefan,
I am running Qiime2 locally. Here are some basic system details::
MacOS Mojave v10.14.4
MacPro (late 2013)
processors 2.7GHz 12-core intel xeon E5
memory 64GB 1866 MHz DDR3
I ran the fragment-insertion plugin with 20 threads of the machines 24.
The following is directly from my run records:
qiime fragment-insertion sepp
--i-representative-sequences non-aligned-rep-seqs.qza
--p-threads 20
--p-alignment-subset-size 1000
--p-placement-subset-size 5000
--o-tree tree\_frag-insertion\_SEPP.qza
--o-placements insertion-placements\_SEPP.qza
--verbose
I use default settings. I am concerned this may be some sort of memory issues. On another thread here on the forum I've been speaking with Nicholas\_Bokulich about the size of my data set. Which is comprised of 32 samples with 389,340 features and a total frequency of 2,877,374.
---
### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [May 22, 2019, 3:24pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/7 "2019-05-22T15:24:20Z")
Hi @TKOneal,
Okay, so probably not the same problem Im getting! That's at least one thing
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [May 24, 2019, 12:44pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/8 "2019-05-24T12:44:06Z")
An off-topic reply has been split into a new topic: [fragment-insertion ValueError: unknown locale: UTF-8](https://forum.qiime2.org/t/fragment-insertion-valueerror-unknown-locale-utf-8/9939)
Please keep replies on-topic in the future.
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [May 24, 2019, 12:45pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/9 "2019-05-24T12:45:00Z")
pinging @Stefan
:qiime2:
---
### Author:  [@TKOneal](https://forum.qiime2.org/u/TKOneal)
#### Post date: [May 31, 2019, 8:13pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/10 "2019-05-31T20:13:23Z")
Hi Stefan,
Just an update, I updated my qiime 2 version to qiime2-2019.4 and now I can't seem to get the fragment-insertion SEPP to run at all. I'm not sure if what sort of error it is but I wanted to post the report encase anyone else has the same issue.
input:
```
qiime fragment-insertion sepp \
--i-representative-sequences rep-seqs.qza \
--i-reference-alignment gg_99_otus_aligned.qza \
--i-reference-phylogeny gg_99_otus_annotated_tre.qza \
--p-threads 0 \
--o-tree insertion-tree.qza \
--o-placements insertion-placements.qza \
--output-dir fragment-insertion_SEPP \
--verbose
```
Removing /var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/sepp-tmp-XXXXX.t2128idL
Traceback (most recent call last):
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py", line 311, in **call**
results = action(\*\*arguments)
File "\", line 2, in sepp
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound\_callable
output\_types, provenance)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in _callable\_executor_
output\_views = self.\_callable(\*\*view\_args)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2\_fragment\_insertion/\_insertion.py", line 179, in sepp
reference\_alignment, reference\_phylogeny, debug)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2\_fragment\_insertion/\_insertion.py", line 137, in \_run
subprocess.run(cmd, check=True, cwd=cwd)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.4/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run-sepp.sh', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-wvx96o9l/4d78965a-a2ca-47c4-9589-4b5d9bce4c9b/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '0', '-A', '1000', '-P', '5000', '-a', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-jgb225ve/5d1ee9a7-2723-4502-bc3f-41fac3177d4f/data/aligned-dna-sequences.fasta', '-t', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-huvom3i5/c99314bc-a852-49be-9663-308d299bfe60/data/tree.nwk']' returned non-zero exit status 1.
Plugin error from fragment-insertion:
Command '['run-sepp.sh', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-wvx96o9l/4d78965a-a2ca-47c4-9589-4b5d9bce4c9b/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '0', '-A', '1000', '-P', '5000', '-a', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-jgb225ve/5d1ee9a7-2723-4502-bc3f-41fac3177d4f/data/aligned-dna-sequences.fasta', '-t', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-huvom3i5/c99314bc-a852-49be-9663-308d299bfe60/data/tree.nwk']' returned non-zero exit status 1.
and the same error report comes up if I remove both reference files, changed threads or changed output names, locations.
I also ran the same input using qiime2-2019.1
Removing /var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/sepp-tmp-XXXXX.aoKUCkEN
Traceback (most recent call last):
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py", line 274, in **call**
results = action(\*\*arguments)
File "\", line 2, in sepp
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound\_callable
output\_types, provenance)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in _callable\_executor_
output\_views = self.\_callable(\*\*view\_args)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2\_fragment\_insertion/\_insertion.py", line 179, in sepp
reference\_alignment, reference\_phylogeny, debug)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2\_fragment\_insertion/\_insertion.py", line 137, in \_run
subprocess.run(cmd, check=True, cwd=cwd)
File "/Users/environmentalmicrobiologyteam/miniconda3/envs/qiime2-2019.1/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run-sepp.sh', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-borz\_lb2/4d78965a-a2ca-47c4-9589-4b5d9bce4c9b/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '0', '-A', '1000', '-P', '5000', '-a', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-6cnfpdp6/5d1ee9a7-2723-4502-bc3f-41fac3177d4f/data/aligned-dna-sequences.fasta', '-t', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-m0kt6fuh/c99314bc-a852-49be-9663-308d299bfe60/data/tree.nwk']' returned non-zero exit status 1.
Plugin error from fragment-insertion:
Command '['run-sepp.sh', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-borz\_lb2/4d78965a-a2ca-47c4-9589-4b5d9bce4c9b/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '0', '-A', '1000', '-P', '5000', '-a', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-6cnfpdp6/5d1ee9a7-2723-4502-bc3f-41fac3177d4f/data/aligned-dna-sequences.fasta', '-t', '/var/folders/8h/80xg\_29d0lb0pdtsmt406gr80000gn/T/qiime2-archive-m0kt6fuh/c99314bc-a852-49be-9663-308d299bfe60/data/tree.nwk']' returned non-zero exit status 1.
Hope this helps!
---
### Author:  [@Stefan](https://forum.qiime2.org/u/Stefan)
#### Post date: [June 1, 2019, 7:36am UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/11 "2019-06-01T07:36:07Z")
Hi @TKOneal,
I think you should at least give SEPP one thread, thus please use `--p-threads 1`. Inserting ~400k fragments into the 200k tips big reference tree is a heavy job. I doubt your 64 GB RAM will suffice for that.
Could you please also add `--p-debug` to your command to get more speaking error information.
---
### Author:  [@TKOneal](https://forum.qiime2.org/u/TKOneal)
#### Post date: [June 3, 2019, 7:33pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/12 "2019-06-03T19:33:30Z")
Hi Stefan,
Thanks for your help. I think I may have fixed part of the issue. I have been filtering my rep-seqs.qza incorrectly. It is currently running with the debug flag. I will let you know if it throws any errors. I'm also running it with 10 threads currently.
---
### Author:  [@TKOneal](https://forum.qiime2.org/u/TKOneal)
#### Post date: [June 7, 2019, 2:52pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/13 "2019-06-07T14:52:03Z")
Hi Stefan,
I've attached the debug report from my most recent run.
[sepp\_error\_STERR.txt.zip (385.4 KB)](https://forum.qiime2.org/uploads/short-url/mGpcZcTJNTyZsmjhJp4nlsDz6L6.zip)
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### Author:  [@Stefan](https://forum.qiime2.org/u/Stefan)
#### Post date: [June 7, 2019, 3:48pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/14 "2019-06-07T15:48:24Z")
to me, it still reads like the same error:
`Error: File existence/permissions problem in trying to open HMM file /var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/sepp-tempssd-XXXX.IEzkn47F/q2-fragment-insertion.bbxsw1we/root/P_11/A_11_5/hmmbuild.model.juw7elj0. HMM file /var/folders/8h/80xg_29d0lb0pdtsmt406gr80000gn/T/sepp-tempssd-XXXX.IEzkn47F/q2-fragment-insertion.bbxsw1we/root/P_11/A`
You might want to take a look into the sepp bash script at `$CONDA_PREFIX/bin/run-sepp.sh`
`
In lines 11, 20, 25 or 29, you can tweak the directory used for temporary files.
I would also play with the number of cores used simultaneously and maybe start with a file containing only the first say 100 sequences for quicker debugging.
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### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [November 6, 2023, 2:58pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/15 "2023-11-06T14:58:34Z")
An off-topic reply has been split into a new topic: [Plugin error from fragment-insertion: 'tree.nwk returned non-zero exit status.'](https://forum.qiime2.org/t/plugin-error-from-fragment-insertion-tree-nwk-returned-non-zero-exit-status/28187)
Please keep replies on-topic in the future.
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### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [November 6, 2023, 2:58pm UTC](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856/16 "2023-11-06T14:58:19Z")