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Packaged pplacer produces segmentation fault

2

I'm running sepp, through busco and am currently experiencing the following with the included pplacer: ``` pplacer Segmentation fault ``` If I install the latest version of pplacer from bioconda,...

rpetit3

Unable to configure sepp ?

3

Unable to install sepp, configuration error. Suggestions. python setup.py install --user running install running bdist_egg running egg_info writing sepp.egg-info/PKG-INFO writing dependency_links to sepp.egg-info/dependency_links.txt writing requirements to sepp.egg-info/requires.txt writing top-level names...

sunnyEV

In https://github.com/smirarab/sepp/blob/654a181565ba497fd79160ed74b1d22d1d4e2577/sepp/alignment.py#L29 `Mapping` is imported directly from `collections`. This has been deprecated since python 3.3: ``` # python3 Python 3.8.10 (default, Nov 26 2021, 20:14:08) [GCC 9.3.0] on linux Type...

panlinux

Depends on python=3.1 ?

4

Hello, I keep having the following error installing sepp from its conda recipe: ResolvePackageNotFound: - python=3.1 Is this really the case? that is a pretty old version...

geboro

fragment-insertion via sept in latest QIIME release requires a single SeppReferenceDatabase artifact, this tutorial outputs 3 files

5

Hi @smirarab, some of my labmates have followed the instructions here to make a reference database of our own, which resulted in the 3 files you describe: original alignment, final...

jgrembi

Log the following: - Input size - Output size - All input parameters, including those in config files. - Number of threads used

smirarab

Is there a reason SEPP would need HMMER 3.1b2 specifically ?

23

Hi, SEPP is now a dependency for installing the latest version of QIIME2 via conda (v2019.10, https://data.qiime2.org/distro/core/qiime2-2019.10-py36-linux-conda.yml). The bioconda recipe for SEPP 4.3.10 (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/sepp/meta.yaml) calls for a very specific dependency...

ppericard

TIPP2 doesn't work with SEPP bioconda recipe

6

The TIPP2 readme states that SEPP must be installed to run TIPP2 (but doesn't list SEPP in the requirements). I installed SEPP via bioconda (it's the best approach, given that...

nick-youngblut

AttributeError: 'Namespace' object has no attribute 'pasta'

4

Hi, I`ve installed sepp and pasta from bioconda and have been trying to execute run_upp.py under conda environment, but I get the following error: [10:38:24] config.py (line 349): INFO: Seed...

Omdeno

DON'T MERGE Relax hmmer

2

this is testing if unit tests will also pass, if hmmer version 3.1 is used instead of the bundled binaries. If so, bioconda package should be able to relax dependencies...

sjanssen2