# fragment-insertion sepp debug help

**URL:** https://forum.qiime2.org/t/fragment-insertion-sepp-debug-help/18178
**Category:** Technical Support
**Tags:** fragment-insertion
**Created:** [January 22, 2021, 2:13pm UTC](https://forum.qiime2.org/t/fragment-insertion-sepp-debug-help/18178 "2021-01-22T14:13:00Z")
**Posts on this page:** 9
**Page:** 1

<div class="post-metadata">

### Author: ![dylan](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/d/e95f7d/32.png) [@dylan](https://forum.qiime2.org/u/dylan)
#### Post date: [January 22, 2021, 2:13pm UTC](https://forum.qiime2.org/t/fragment-insertion-sepp-debug-help/18178/1 "2021-01-22T14:13:01Z")

</div>

Running this command

> ```
> qiime fragment-insertion sepp \
> --i-representative-sequences output/representative_sequences.qza \
> --i-reference-database input/sepp-refs-silva-128.qza \
> --o-tree output/rooted_tree \
> --o-placements output/placements \
> --p-threads 12 \
> --verbose \
> --p-debug
> 
> ```

with [the edit to run-sepp.sh mentioned here](https://forum.qiime2.org/t/run-sepp-sh-returned-non-zero-exit-status-1/4071/2) (is this the same as the debug flag?) yields the following message:

> ```
> File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/commands.py", line 329, in __call__
> results = action(**arguments)
> File "<decorator-gen-303>", line 2, in sepp
> File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
> output_types, provenance)
> File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in _callable_executor_
> output_views = self._callable(**view_args)
> File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 77, in sepp
> debug)
> File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 53, in _run
> subprocess.run(cmd, check=True, cwd=cwd)
> File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/subprocess.py", line 438, in run
> output=stdout, stderr=stderr)
> subprocess.CalledProcessError: Command '['run-sepp.sh', '/tmp/qiime2-archive-05j3igqe/19e4fc78-44a3-443b-9ee3-41ae8102598d/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '12', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-jsk6s5yy/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-jsk6s5yy/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2-archive-jsk6s5yy/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt', '-b', '1']' returned non-zero exit status 1.
> 
> Plugin error from fragment-insertion:
> 
> Command '['run-sepp.sh', '/tmp/qiime2-archive-05j3igqe/19e4fc78-44a3-443b-9ee3-41ae8102598d/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '12', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-jsk6s5yy/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-jsk6s5yy/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2-archive-jsk6s5yy/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt', '-b', '1']' returned non-zero exit status 1.
> 
> See above for debug info.
> 
> ```

I'm running WSL with a 12 core processor and 32 gigs of RAM plus 96 gigs of swap.

Any help would be appreciated.

---

<div class="post-metadata">

### Author: ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [January 22, 2021, 2:14pm UTC](https://forum.qiime2.org/t/fragment-insertion-sepp-debug-help/18178/2 "2021-01-22T14:14:54Z")

</div>

Hi @dylan!

> [@dylan](#):
>
> is this the same as the debug flag?

No, I don't think so - I hate to ask this, but we'll need you to rerun the command above, in a fresh QIIME 2 environment that hasn't had the source files edited, in order to help diagnose. Thanks!

---

<div class="post-metadata">

### Author: ![Stefan](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/s/bbce88/32.png) [@Stefan](https://forum.qiime2.org/u/Stefan)
#### Post date: [January 22, 2021, 3:31pm UTC](https://forum.qiime2.org/t/fragment-insertion-sepp-debug-help/18178/3 "2021-01-22T15:31:39Z")

</div>

you could try to operate on a smaller version of `output/representative_sequences.qza`. Just take e.g. the first 10 sequences from this file and check if this runs through.

It might also help to reduce `--p-threads 12` to just 3. Otherwise each core only gets 32/12 = 2.6 GB per task, which might be too low.

---

<div class="post-metadata">

### Author: ![dylan](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/d/e95f7d/32.png) [@dylan](https://forum.qiime2.org/u/dylan)
#### Post date: [January 22, 2021, 3:33pm UTC](https://forum.qiime2.org/t/fragment-insertion-sepp-debug-help/18178/4 "2021-01-22T15:33:05Z")

</div>

Ah, I see why now. Here's the last few lines of debug info from the base version:

```
[07:23:03] alignment.py (line 205): DEBUG: Writing alignment of type <class 'sepp.alignment.ReadonlySubalignment'> with length 3616 to file /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_113/pplacer.backbone.tivih9mx.fasta
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
    if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_12 -j 1 -r /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_12/pplacer.backbone.e98bn9jr.fasta -s /tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_12/pplacer.tree.cru8sdu3.tre --groups 10 /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_12/pplacer.extended.0.ha_v8cyc.fasta
No error messages available
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
    if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_12 -j 1 -r /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_12/pplacer.backbone.2cyxu6c9.fasta -s /tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_12/pplacer.tree.ythm3oai.tre --groups 10 /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_12/pplacer.extended.1.ka5e67hk.fasta
No error messages available
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
    if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_11 -j 1 -r /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_11/pplacer.backbone.r72tz0hg.fasta -s /tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_11/pplacer.tree.u87t_ymn.tre --groups 10 /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_11/pplacer.extended.2.06vearn4.fasta
No error messages available
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
    if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_14 -j 1 -r /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_14/pplacer.backbone.hi_337mh.fasta -s /tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_14/pplacer.tree.5yli2nhx.tre --groups 10 /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_14/pplacer.extended.1.402kay9h.fasta
No error messages available
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
    if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_14 -j 1 -r /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_14/pplacer.backbone.3yirsjh3.fasta -s /tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_14/pplacer.tree.ivfr5iul.tre --groups 10 /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_14/pplacer.extended.2.bo5jnz3t.fasta
No error messages available
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
    if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_14 -j 1 -r /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_14/pplacer.backbone.fzbnpg10.fasta -s /tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_14/pplacer.tree.zn1yjivk.tre --groups 10 /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_14/pplacer.extended.0.oh3gbkt2.fasta
No error messages available
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
    if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_8 -j 1 -r /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_8/pplacer.backbone.cf_f4bef.fasta -s /tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_8/pplacer.tree.k1dkt6sw.tre --groups 10 /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_8/pplacer.extended.0.vrofjcb2.fasta
No error messages available
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
    if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_8 -j 1 -r /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_8/pplacer.backbone.bz1bs0gl.fasta -s /tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_8/pplacer.tree.nyz7yrtt.tre --groups 10 /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_8/pplacer.extended.1.67g9xcb6.fasta
No error messages available
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
    if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_6 -j 1 -r /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_6/pplacer.backbone.lpn28ui4.fasta -s /tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_6/pplacer.tree.r3ype17n.tre --groups 10 /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_6/pplacer.extended.2.gszmxfd_.fasta
No error messages available
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/scheduler.py", line 74, in __call__
    return self.run()
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
    if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_1 -j 1 -r /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_1/pplacer.backbone.fp5d6hyw.fasta -s /tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_1/pplacer.tree.8v7w1eoy.tre --groups 10 /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_1/pplacer.extended.0.z5n04x_e.fasta
No error messages available
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/bin/run_sepp.py", line 26, in <module>
    ExhaustiveAlgorithm().run()
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/algorithm.py", line 174, in run
    if (not JobPool().wait_for_all_jobs()):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/scheduler.py", line 365, in wait_for_all_jobs
    result.get()
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/multiprocessing/pool.py", line 644, in get
    raise self._value
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_1 -j 1 -r /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_1/pplacer.backbone.fp5d6hyw.fasta -s /tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_1/pplacer.tree.8v7w1eoy.tre --groups 10 /tmp/tmp.wHblljACq8/sepp-tempssd-xImh1cyro4/q2-fragment-insertion.5ortsuh_/root/P_1/pplacer.extended.0.z5n04x_e.fasta
No error messages available
=====================================================================
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/commands.py", line 329, in __call__
    results = action(**arguments)
  File "<decorator-gen-303>", line 2, in sepp
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
    output_types, provenance)
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 77, in sepp
    debug)
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 53, in _run
    subprocess.run(cmd, check=True, cwd=cwd)
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/subprocess.py", line 438, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run-sepp.sh', '/tmp/qiime2-archive-xwjdyq_0/19e4fc78-44a3-443b-9ee3-41ae8102598d/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '24', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt', '-b', '1']' returned non-zero exit status 1.

Plugin error from fragment-insertion:

  Command '['run-sepp.sh', '/tmp/qiime2-archive-xwjdyq_0/19e4fc78-44a3-443b-9ee3-41ae8102598d/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '24', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2-archive-u6vrpdmr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt', '-b', '1']' returned non-zero exit status 1.

See above for debug info.

```

---

<div class="post-metadata">

### Author: ![dylan](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/d/e95f7d/32.png) [@dylan](https://forum.qiime2.org/u/dylan)
#### Post date: [January 22, 2021, 4:00pm UTC](https://forum.qiime2.org/t/fragment-insertion-sepp-debug-help/18178/5 "2021-01-22T16:00:36Z")

</div>

Thanks @stefan, I incorporated both suggestions and still got the 'non-zero exit status 1' error.

```
[07:51:07] alignment.py (line 205): DEBUG: Writing alignment of type <class 'sepp.alignment.ReadonlySubalignment'> with length 2801 to file /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_108/pplacer.backbone.hrd32des.fasta
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
    if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_64 -j 1 -r /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_64/pplacer.backbone.wei12gfw.fasta -s /tmp/qiime2-archive-n4nno1to/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_64/pplacer.tree.dcpmxhdz.tre --groups 10 /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_64/pplacer.extended.0.uv0iinur.fasta
No error messages available
[07:51:07] jobs.py (line 81): DEBUG: Starting pplacer Job with input: backbone_alignment_file:/tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_108/pplacer.backbone.hrd32des.fasta, tree_file:/tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_108/pplacer.tree.01lt6ohu.tre, info_file:/tmp/qiime2-archive-n4nno1to/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt, extended alignment:/tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_108/pplacer.extended.0.7k4lpgf1.fasta, output:/tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_108/pplacer.extended.0.7k4lpgf1.jplace
[07:51:07] jobs.py (line 108): DEBUG: Invocation of /home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_108 -j 1 -r /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_108/pplacer.backbone.hrd32des.fasta -s /tmp/qiime2-archive-n4nno1to/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_108/pplacer.tree.01lt6ohu.tre --groups 10 /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_108/pplacer.extended.0.7k4lpgf1.fasta
[07:51:07] jobs.py (line 149): DEBUG: Finished pplacer Job with input: backbone_alignment_file:/tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_108/pplacer.backbone.hrd32des.fasta, tree_file:/tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_108/pplacer.tree.01lt6ohu.tre, info_file:/tmp/qiime2-archive-n4nno1to/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt, extended alignment:/tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_108/pplacer.extended.0.7k4lpgf1.fasta, output:/tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_108/pplacer.extended.0.7k4lpgf1.jplace with:
 return code: -11
 output:
 error:
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
    if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_82 -j 1 -r /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_82/pplacer.backbone.00galm9o.fasta -s /tmp/qiime2-archive-n4nno1to/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_82/pplacer.tree.s6bqnws0.tre --groups 10 /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_82/pplacer.extended.0.ga3djgo5.fasta
No error messages available
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
    if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_87 -j 1 -r /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_87/pplacer.backbone.uzfxh8wo.fasta -s /tmp/qiime2-archive-n4nno1to/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_87/pplacer.tree.wmpiz_4f.tre --groups 10 /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_87/pplacer.extended.0.vlh105yz.fasta
No error messages available
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/scheduler.py", line 74, in __call__
    return self.run()
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
    if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_15 -j 1 -r /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_15/pplacer.backbone.wqff6xyc.fasta -s /tmp/qiime2-archive-n4nno1to/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_15/pplacer.tree.plwylyww.tre --groups 10 /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_15/pplacer.extended.0.plzerdgy.fasta
No error messages available
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/bin/run_sepp.py", line 26, in <module>
    ExhaustiveAlgorithm().run()
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/algorithm.py", line 174, in run
    if (not JobPool().wait_for_all_jobs()):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/sepp/scheduler.py", line 365, in wait_for_all_jobs
    result.get()
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/multiprocessing/pool.py", line 644, in get
    raise self._value
sepp.scheduler.JobError: The following execution failed:
/home/dylan/miniconda3/envs/qiime2-2020.11/bin/pplacer --out-dir /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_15 -j 1 -r /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_15/pplacer.backbone.wqff6xyc.fasta -s /tmp/qiime2-archive-n4nno1to/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt -t /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_15/pplacer.tree.plwylyww.tre --groups 10 /tmp/tmp.YE7eIK5BTh/sepp-tempssd-3NqyBhHOxi/q2-fragment-insertion.nufc1fbf/root/P_15/pplacer.extended.0.plzerdgy.fasta
No error messages available
=====================================================================
Traceback (most recent call last):
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/commands.py", line 329, in __call__
    results = action(**arguments)
  File "<decorator-gen-303>", line 2, in sepp
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
    output_types, provenance)
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 77, in sepp
    debug)
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 53, in _run
    subprocess.run(cmd, check=True, cwd=cwd)
  File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/subprocess.py", line 438, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run-sepp.sh', '/tmp/qiime2-archive-avho24u1/75746a5b-c9d7-49b8-8e44-683cb7c80ca2/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '3', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-n4nno1to/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-n4nno1to/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2-archive-n4nno1to/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt', '-b', '1']' returned non-zero exit status 1.

Plugin error from fragment-insertion:

  Command '['run-sepp.sh', '/tmp/qiime2-archive-avho24u1/75746a5b-c9d7-49b8-8e44-683cb7c80ca2/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '3', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-n4nno1to/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-n4nno1to/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2-archive-n4nno1to/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt', '-b', '1']' returned non-zero exit status 1.

See above for debug info.

```

---

<div class="post-metadata">

### Author: ![Stefan](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/s/bbce88/32.png) [@Stefan](https://forum.qiime2.org/u/Stefan)
#### Post date: [January 22, 2021, 4:02pm UTC](https://forum.qiime2.org/t/fragment-insertion-sepp-debug-help/18178/6 "2021-01-22T16:02:57Z")

</div>

would you be willing to send me your reduced `representative_sequences.qza` file, such that I can take a look myself?

---

<div class="post-metadata">

### Author: ![dylan](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/d/e95f7d/32.png) [@dylan](https://forum.qiime2.org/u/dylan)
#### Post date: [January 24, 2021, 2:12am UTC](https://forum.qiime2.org/t/fragment-insertion-sepp-debug-help/18178/7 "2021-01-24T02:12:33Z")

</div>

For posterity:

@Stefan was able to successfully execute the command on his end. I continued to encounter an error even in a fresh conda environment. I also experienced an error when trying on my laptop, again with a clean conda install.

However, I installed Ubuntu and was able to successfully execute the command on test sequences in that OS, so this issue may be related to WSL.

Thanks to both @Stefan and @thermokarst for their help.

---

<div class="post-metadata">

### Author: ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [January 24, 2021, 8:17pm UTC](https://forum.qiime2.org/t/fragment-insertion-sepp-debug-help/18178/8 "2021-01-24T20:17:54Z")

</div>

> [@dylan](#):
>
> I continued to encounter an error even in a fresh conda environment.

Yes, that is what I expected, I just needed to be sure that there wasn't an _additional_ error caused by your manual edits to the environment, make sense? As I mentioned above, this is important for diagnosis, it was not intended as a _fix_ for your problem (this is an important distinction to make for any future readers of this thread).

> [@dylan](#):
>
> so this issue may be related to WSL.

Sounds to me like maybe you didn't have enough memory allocated in WSL, I'll leave it to @Stefan to follow up with his thoughts.

---

<div class="post-metadata">

### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [February 25, 2021, 2:17am UTC](https://forum.qiime2.org/t/fragment-insertion-sepp-debug-help/18178/9 "2021-02-25T02:17:56Z")

</div>

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