GetOrganelle

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get_organelle_from_assembly.py: no slimmed_assembly_graph found

11

hi everyone, i'm trying to evaluate the mithocondrial DNA of my sample (fusarium sp.); i performed the assembly with flye tool on galaxy.eu and use the fastg file produced by...

LucaD91

ERROR: Blast is not available!

4

#ERROR: Blast is not available! This is an issue for setting up GetOrganelle Database using "get_organelle_config.py" .

wbyu

fix a bug: summary_get_organelle_output.py does not recognize degenerate/ambiguous bases #279

JianjunJin

Discrepancy between get_organelle_from_reads and summary_get_organelle_output logs

1

**First check** - [X] I used the GitHub search to find a similar issue and didn't find it. - [X] I searched [GetOrganelle.wiki](https://github.com/Kinggerm/GetOrganelle/wiki) context, especially the [FAQ](https://github.com/Kinggerm/GetOrganelle/wiki/FAQ) and browsed the...

marcelglueck

Problems with canu-produced gfa processing

1

Describe the bug I am using getorganelle for obtaining a circular mitochondria and I am getting this message. The gfa is from a canu assembly. Could you help me please?...

Hoberti

ERROR: Assembling failed due to SPAdes failure

4

I installed the last version of getorganelle: 1.7.7.0, and then it would not work with Spades as many have pointed out. Thus I downloaded the dependencies from the authors (GetOrganelleDep),...

njbayonav

Error with OS return value: 22; Can anyone please help me with a solution ?

5

023-03-15 15:07:43,679 - INFO: Separating extended fastq file ... 2023-03-15 15:07:43,763 - INFO: Setting '-k 21,55,85,115' 2023-03-15 15:07:43,763 - INFO: Assembling using SPAdes ... 2023-03-15 15:07:43,787 - INFO: spades.py -t...

avvypaks

error using different seed

1

I read that your tool was used also to assemble the rDNA locus. I would like to assemble long reads from a single specific gene locus (human) coming from a...

ilenia6

Incompatible glibc on conda install

4

HI! I am having a problem install GetOrganelle from conda. When I run ```conda install -c bioconda getorganelle``` I get the following error during installation: ``` Collecting package metadata (current_repodata.json):...

McAllister-NOAA

Error assembling the Arabidopsis test dataset (SPAdes errors)

6

Hello, I am attempting to assemble the _Arabidopsis_ plastome using the provided test dataset (simulated _Arabidopsis thaliana_ WGS dataset). After (i) installing/updating GetOrganelle, (ii) initializing the organelle type, and (iii)...

jsmillergh