# 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:** 1 **Showing post:** 10
### Author: ![TKOneal](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/a9a28c/32.png) [@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! --- _[View the full topic](https://forum.qiime2.org/t/error-when-running-insert-fragment-sequences-using-sepp/9856)._