gem-pasteur PanACoTA issues

gem-pasteur / PanACoTA

PANgenome with Annotations, COre identification, Tree and corresponding Alignments

GNU Affero General Public License v3.0

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issues

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Conda installation conflict

#48 ASUQ opened 4 months ago
0
ERROR ERROR: Your list file 'Examples/input_files/list_genomes.lst' does not exist. Please provide a list file.

#47 asershova opened 4 months ago
1
Could not determine version of cmpress - please install version 1.1 or higher

#46 octolis closed 2 months ago
1
[Enhancement] using bakta instead of prokka

#45 rdenise opened 7 months ago
1
PanACoTA align There is not any protein for genome X

#44 AlperYurtseven closed 9 months ago
5
>mash sketch error

#43 sujeetpowar closed 9 months ago
3
PanACoTA prepare command download from NCBI error

#42 lear-711 closed 1 year ago
2
running only formating of annotation step

#41 aymericola closed 1 year ago
3
Error while trying to run prokka on

#40 aymericola closed 1 year ago
2
Alignment fails when using gembase format

#39 jeanrjc closed 1 year ago
1
Broken in conda with python > 3.6

#38 psydvl closed 1 year ago
1
cpu count vs available cpus

#37 EricDeveaud closed 1 year ago
3
No distance matrix in output of FastME tree building

#36 rasedb00 closed 2 years ago
3
Protein ortho for separate branch

#35 RedSnail closed 2 years ago
0
Error at alignment

#34 ryobon-dev closed 12 months ago
4
L90 filtering

#33 Sirbius closed 2 years ago
1
Issue 31

#32 asetGem closed 2 years ago
1
Protein ortho

#30 RedSnail closed 2 years ago
4
Add a Gitter chat badge to README.md

#29 gitter-badger closed 3 years ago
0
The prepare step misses genomes

#24 asetGem closed 3 years ago
0
The prepare step misses genomes

#20 RedSnail closed 3 years ago
3
Prokka error

#19 ryobon-dev closed 3 years ago
4
Feature: passing strains list to ncbi-genome-download

#18 oxygen311 closed 3 years ago
4
Feature request: pass `-S/--strains` to `ncbi-genome-download`

#17 oxygen311 closed 3 years ago
11
Bootstrapping with `PanACoTA all`

#16 oxygen311 closed 3 years ago
2
the error about "The core genome contains 0 families"

#15 albertzhuo closed 1 year ago
6
Problem with mmseq

#14 yoshikal closed 3 years ago
5
Problem with iqtree2

#13 genomesandMGEs closed 3 years ago
6
Combining step1 and step2 on the prepare module

#12 genomesandMGEs closed 3 years ago
2
PanACoTA all skips cutn parametr

#11 oxygen311 closed 3 years ago
5
query/target coverage

#10 ramiroricardo closed 3 years ago
1
prokka installed with PanACoTA under conda environment did not work for me.

#9 Happyalisa closed 3 years ago
5
IQtree error: -quiet does not exist

#8 IsabelFE closed 3 years ago
2
Download individual assemblies with prepare

#7 IsabelFE closed 3 years ago
5
'utf-8' codec can't decode byte 0x80 in position 3131: invalid start byte

#6 IsabelFE closed 3 years ago
15
Combining genomes from several sources in one analysis

#5 IsabelFE closed 3 years ago
5
Choosing assembly level in `prepare` module

#4 oxygen311 closed 3 years ago
1
annotate error: Uh oh! Sequence file 'XXXXX_genomic.fna_prepare-split5N.fna' contains duplicate sequence ID

#3 IsabelFE closed 3 years ago
5
Error using annotate: unexpected keyword argument 'max_value'

#2 IsabelFE closed 3 years ago
22
Logger Error

#1 TorresRC closed 3 years ago
5