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bvalot / pyMLST

whole genome MLST analysis
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BLAT error #11

Open kediza opened 1 year ago

kediza commented 1 year ago

I am adding species to the database and im getting the error

[ERROR: 2023-01-13 10:12:02,702] End of file reading 4 bytes Error: An error occurred while running BLAT

Kindly assist

bvalot commented 1 year ago

Hi,

It is a classical problems with a database with no sequence. How do you constructed your database?

Benoit

kediza commented 1 year ago

Thanks for your response, I managed to redownload the database and is now working. other issues is the workflow I have contigs files which were assembled from raw reads and I will 'like to do pymlst on the genes and do phylogeny. The workflow on the github is not that clear. kindly assist?

On Fri, Jan 13, 2023 at 10:29 AM bvalot @.***> wrote:

Hi,

It is a classical problems with a database with no sequence. How do you constructed your database?

Benoit

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bvalot commented 1 year ago

It depends the phylogeny you want to do? Maximum likelihood or allelic distance?

kediza commented 1 year ago

both for now if possible

On Fri, Jan 13, 2023 at 10:56 AM bvalot @.***> wrote:

It depends the phylogeny you want to do? Maximum likelihood or allelic distance?

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bvalot commented 1 year ago

What i propose to you is:

kediza commented 1 year ago

Thanks a lot, when I add the samples do I do it with/without the strain? because it gives me this error wgMLST add -s Senegal s.enterica contigs.fa Error: Strain Senegal already present in the base. Most samples have the same strain

On Fri, Jan 13, 2023 at 11:41 AM bvalot @.***> wrote:

What i propose to you is:

  • ADD all your samples in the database
  • STRAIN with -c to check if some strain are not good (lower gene detected)
  • DISTANCE with appropriate -m option to have matrix of alleluic difference then make bioNJ on it or Minimum Spanning Tree
  • GENE with appropriate -m option to extract variable genes that are coregenom of your analysis
  • MSA to build you alignment with the gene list previously selected, then used it with FASTTREE

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bvalot commented 1 year ago

The problem is that you need to add your samples sequentially and give them different names with the option -s

kediza commented 1 year ago

thanks, but the add option only include -s which is a strain , will you kindly assist with the command for samples and strain addititon

On Fri, Jan 13, 2023 at 11:55 AM bvalot @.***> wrote:

The problem is that you add your sample sequentially and give them different names with the option -s

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bvalot commented 1 year ago 
wgMLST add -s strainA  s.enterica.db strainA.fa
wgMLST add -s strainB  s.enterica.db strainB.fa
wgMLST add -s strainC  s.enterica.db strainC.fa

where strainA.fa, strainB.fa... is assembly genome on contigs for each of this strains

kediza commented 1 year ago

Thanks a lot.

On Fri, Jan 13, 2023 at 5:40 PM bvalot @.***> wrote:

wgMLST add -s strainA s.enterica.db strainA.fa wgMLST add -s strainB s.enterica.db strainB.fa wgMLST add -s strainC s.enterica.db strainC.fa

where strainA.fa, strainB.fa... is assembly genome on contigs for each of this strains

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