BLAT error

[kediza]

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]

Hi,

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

Benoit

[kediza]

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?

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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 — Reply to this email directly, view it on GitHub <#11 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIVAKUA23L7RCRGQXH65UXLWSEG5LANCNFSM6AAAAAAT2ECM5Q> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[bvalot]

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

[kediza]

both for now if possible

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On Fri, Jan 13, 2023 at 10:56 AM bvalot ***@***.***> wrote: It depends the phylogeny you want to do? Maximum likelihood or allelic distance? — Reply to this email directly, view it on GitHub <#11 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIVAKUFHW4XPZFGZPRIACJ3WSEKCXANCNFSM6AAAAAAT2ECM5Q> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[bvalot]

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

[kediza]

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

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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 — Reply to this email directly, view it on GitHub <#11 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIVAKUCJ4MNDUWC5ELG4KALWSEPOHANCNFSM6AAAAAAT2ECM5Q> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[bvalot]

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

[kediza]

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

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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 — Reply to this email directly, view it on GitHub <#11 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIVAKUCSTLSRBNHEY76OBWLWSERAHANCNFSM6AAAAAAT2ECM5Q> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[bvalot]

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]

Thanks a lot.

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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 — Reply to this email directly, view it on GitHub <#11 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIVAKUBIWRNGB7UG7RMIM7TWSFZNTANCNFSM6AAAAAAT2ECM5Q> . You are receiving this because you authored the thread.Message ID: ***@***.***>