Problem with Phylogenetic tree construction

Hello

I want to construct phylogenetic tree for bacterial sequence. I used a reference-based fragment insertion approach.

This is the command I ran

qiime fragment-insertion sepp --i-representative-sequences si_cs.qza --p-threads 40 --p-alignment-subset-size 1000 --p-placement-subset-size 5000 --o-tree Phylogeny[Rooted] --o-placements Placements

This was the error I got

Removing /tmp/tmp.B5onA1CVkA/sepp-tmp-Wrjwf
Traceback (most recent call last):
File “/home/ruthra/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “</home/ruthra/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-290>”, line 2, in sepp
File “/home/ruthra/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/ruthra/miniconda2/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 “/home/ruthra/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py”, line 179, in sepp
reference_alignment, reference_phylogeny, debug)
File “/home/ruthra/miniconda2/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 “/home/ruthra/miniconda2/envs/qiime2-2019.1/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run-sepp.sh’, ‘/tmp/qiime2-archive-nmlejvgb/5addfdcf-d8e1-4d49-9f46-991dd9e237b8/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘40’, ‘-A’, ‘1000’, ‘-P’, ‘5000’]’ returned non-zero exit status 1.

Plugin error from fragment-insertion:

Command ‘[‘run-sepp.sh’, ‘/tmp/qiime2-archive-nmlejvgb/5addfdcf-d8e1-4d49-9f46-991dd9e237b8/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘40’, ‘-A’, ‘1000’, ‘-P’, ‘5000’]’ returned non-zero exit status 1.

See above for debug info.

Could you please help me how to solve this error?

Hi @Asha1,

This might take a bit to troubleshoot, so please be patient with us! Could you please run the command,

locale

and share the result here?

Best,
Justine

Hi Ma’am,

Thank you so much for your prompt reply ma’am.

(qiime2-2019.1) [email protected]:~/miniconda2/envs/qiime2-2019.1/v3-v4_region_result/sp/mo/moraxellaca.taxaplot$ locale
LANG=C.UTF-8
LANGUAGE=
LC_CTYPE=“C.UTF-8”
LC_NUMERIC=“C.UTF-8”
LC_TIME=“C.UTF-8”
LC_COLLATE=“C.UTF-8”
LC_MONETARY=“C.UTF-8”
LC_MESSAGES=“C.UTF-8”
LC_PAPER=“C.UTF-8”
LC_NAME=“C.UTF-8”
LC_ADDRESS=“C.UTF-8”
LC_TELEPHONE=“C.UTF-8”
LC_MEASUREMENT=“C.UTF-8”
LC_IDENTIFICATION=“C.UTF-8”
LC_ALL=

Looking forward to your reply.

Hi @Asha1,

This is an easy fix, then!

Please run

export LC_ALL="en_US.utf-8"
export LANG="en_US.utf-8"
locale

You should see everything set to en_US.utf-8.

If you want to solve the problem forever, on a mac you can add this line to your ~/.bash_profile and on a linux server your ~/.bashrc, which is kind of a master file which tells the system how to configure itself self.

Best,
Justine

Thank you so much ma’am for your reply., I will check once and get back to you.

I ran the commanline as per your suggestion. But, I am getting the same error again.
(qiime2-2019.1) [email protected]:~/miniconda2/envs/qiime2-2019.1/v3-v4_region_result/sp/mo/moraxellaca.taxaplot$ export LC_ALL=“en_US.utf-8”
(qiime2-2019.1) [email protected]:~/miniconda2/envs/qiime2-2019.1/v3-v4_region_result/sp/mo/moraxellaca.taxaplot$ export LANG=“en_US.utf-8”
(qiime2-2019.1) [email protected]:~/miniconda2/envs/qiime2-2019.1/v3-v4_region_result/sp/mo/moraxellaca.taxaplot$ locale
LANG=en_US.utf-8
LANGUAGE=
LC_CTYPE=“en_US.utf-8”
LC_NUMERIC=“en_US.utf-8”
LC_TIME=“en_US.utf-8”
LC_COLLATE=“en_US.utf-8”
LC_MONETARY=“en_US.utf-8”
LC_MESSAGES=“en_US.utf-8”
LC_PAPER=“en_US.utf-8”
LC_NAME=“en_US.utf-8”
LC_ADDRESS=“en_US.utf-8”
LC_TELEPHONE=“en_US.utf-8”
LC_MEASUREMENT=“en_US.utf-8”
LC_IDENTIFICATION=“en_US.utf-8”
LC_ALL=en_US.utf-8
(qiime2-2019.1) [email protected]:~/miniconda2/envs/qiime2-2019.1/v3-v4_region_result/sp/mo/moraxellaca.taxaplot$ qiime fragment-insertion sepp --i-representative-sequences si_cs.qza --p-threads 40 --p-alignmen
t-subset-size 1000 --p-placement-subset-size 5000 --o-tree Phylogeny[Rooted] --o-placements Placements
Plugin error from fragment-insertion:

Command ‘[‘run-sepp.sh’, ‘/tmp/qiime2-archive-q49w7763/d5ce9526-e2a9-4b53-8b72-a37a2c11da39/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘40’, ‘-A’, ‘1000’, ‘-P’, ‘5000’]’ returned non-zero exit status 1.

Debug info has been saved to /tmp/qiime2-q2cli-err-cw12znbe.log
What to do now Ma’am?

Can you please run the command with the --debug flag and post the results?

Best,
Justine

Hi @Asha1,

Based on your other post, is this ITS or 16s? The current fragment insertion doesn’t support ITS.

Best,
Justine