pomoxis

pomoxis copied to clipboard

Hi, I had an issue regarding the use of assem_assembly command using the medaka_walkthrough (https://github.com/nanoporetech/medaka/blob/master/docs/walkthrough.rst) Run into error where the command split_fastx was not found even though the script has...

tweilin

Large chromosomes cannot be indexed using `bai` indices, so a `csi `index is created here. This is useful for many plants and other organisms with long chr. This is important...

colindaven

Assess_assembly Documentation

5

It would be really nice if the documentation provided some explanation of the output files. Specifically these two table types. # Percentage Errors name mean q10 q50 q90 err_ont 1.609%...

nhartwic

I want to compare assembly results from three assembly tools 1. I concat three assembly fasta to one; 2. running `intersect_assembly_errors ` with cmd ``` intersect_assembly_errors -r ref.fasta -i ./all_assm.fa...

yipukangda

Got this error when trying to build pomoxis. Seems to be an issue when fetching the minimap2 source. Please advise. ``` (medaka) $:~/medaka_walkthrough$ cd pomoxis && make install && cd...

CFmicro

mini_assemble empty target sequences error

3

Dear nanopore devs, I'm having issues getting mini_assemble to run on human (HG001/NA12978) data. I've successfully ran it on smaller assemblies before, but a ~30x human genome seems to be...

kautto

Python 3.7?

4

Just tried to install this using conda, and the install failed because it was "incompatible with the existing python installation in your environment". Here is the error: ``` Specifications: -...

BrianaGross

mini_assemble core dump

1

Hi, I've tried to run several versions of pomoxis (the info is from v. 0.3.2), on a linux compute cluster in an sbatch script. The command I use is: mini_assemble...

ccbruels

Tracing issues with racon after running mini_assemble

6

Is there any way of tracking/ tracing issues with racon thats included in Pomoxis? I'm getting "[racon::Polisher::initialize] error: empty target sequences set!" after running mini_assemble.

beasty1711

Installation error

1

Hi, I wanted to install the Pomoxis package, and followed the installation instructions. All pre-requested packages are installed, but still I get the following error during installation. ...

JesseBNL