Unable to run successfully

[cht-jk]

Dear Armando, In my own data.map file, there are 1812799 SNPs on chromosome 1, out of a total of 40 chromosomes and 8495844 SNPs. Is this data not runnable?

[armando-caballero]

Please see tutorial for maximum numbers of SNPs

[cht-jk]

Dear Armando, I filtered out the data of chromosome 40 for the experiment based on the limitations described in the tutorial, but the following error still occurred during operation. Additionally, the test data has been uploaded： example.zip

$bash script_GONE.sh 40 DIVIDE .ped AND .map FILES IN CHROMOSOMES RUNNING ANALYSIS OF CHROMOSOMES ... CHROMOSOME ANALYSES took 0 seconds Running GONE Format error in file Format error in file Format error in file Format error in file Format error in file outfileLDoutfileLD Format error in file outfileLDoutfileLD

outfileLD

outfileLD

Format error in file outfileLD Format error in file Format error in file Format error in file outfileLDoutfileLD Format error in file Format error in file outfileLD Format error in file outfileLDoutfileLD

outfileLD

Format error in file outfileLD Format error in file Format error in file outfileLD outfileLD Format error in file outfileLD Format error in file outfileLD Format error in file outfileLD Format error in file outfileLD Format error in file Format error in file outfileLD outfileLD Format error in file outfileLD Format error in file Format error in file outfileLDoutfileLD

Format error in file outfileLD Format error in file Format error in file outfileLD Format error in file Format error in file outfileLDoutfileLD Format error in file outfileLD Format error in file outfileLD Format error in file Format error in file outfileLD outfileLD Format error in file outfileLD Format error in file Format error in file Format error in file Format error in file outfileLD outfileLD

outfileLDoutfileLD Format error in file outfileLD

outfileLD

Error opening file outfileLD_TEMP/outfileLD_1_GONE_Nebest END OF ALL PROCESSES GONE run took 0 seconds END OF ANALYSES mv: cannot stat ‘outfileLD_Ne_estimates’: No such file or directory mv: cannot stat ‘outfileLD_d2_sample’: No such file or directory

[armando-caballero]

I do not understand. If you analise a single chromosome, the map file shuld have a first column with "1" not "40". Armando,

[cht-jk]

Dear Armando, I have changed all the first columns in 40. map to 1, but after running it, there is still an error message: Single strip.zip

—————————————————————————————— $bash script_GONE.sh 40 DIVIDE .ped AND .map FILES IN CHROMOSOMES RUNNING ANALYSIS OF CHROMOSOMES ... CHROMOSOME ANALYSES took 0 seconds Running GONE Format error in file Format error in file Format error in file Format error in file Format error in file Format error in file outfileLDoutfileLDoutfileLD Format error in file outfileLD Format error in file outfileLD Format error in file Format error in file Format error in file outfileLDoutfileLD Format error in file Format error in file

Format error in file outfileLD

outfileLD Format error in file Format error in file outfileLD Format error in file outfileLD Format error in file outfileLDoutfileLDoutfileLD outfileLD outfileLD Format error in file outfileLD Format error in file outfileLD Format error in file

outfileLD Format error in file outfileLDoutfileLD outfileLD

Format error in file outfileLD Format error in file outfileLD Format error in file Format error in file Format error in file Format error in file Format error in file Format error in file Format error in file outfileLDoutfileLDoutfileLDoutfileLDoutfileLDoutfileLDoutfileLD

Format error in file outfileLD Format error in file outfileLD Format error in file outfileLD Format error in file outfileLD Format error in file Format error in file outfileLD Format error in file Format error in file outfileLDoutfileLDoutfileLD

Format error in file outfileLD Error opening file outfileLD_TEMP/outfileLD_1_GONE_Nebest END OF ALL PROCESSES GONE run took 0 seconds END OF ANALYSES mv: cannot stat ‘outfileLD_Ne_estimates’: No such file or directory mv: cannot stat ‘outfileLD_d2_sample’: No such file or directory

[cht-jk]

Dear Armando, The problem has been solved. The data in column 6 of the. med file needs to be modified to -9. Additionally, I have a question. Can GONE only infer the history of one group, or can it infer multiple groups simultaneously? Thank you. Best wishes

[armando-caballero]

Only one group. Armando

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De: cht-jk @.> Enviado: martes, 20 de agosto de 2024 5:14 Para: esrud/GONE @.> Cc: Armando Caballero Rúa @.>; Comment @.> Asunto: Re: [esrud/GONE] Unable to run successfully (Issue #46)

Dear Armando, The problem has been solved. The data in column 6 of the. med file needs to be modified to -9. Additionally, I have a question. Can GONE only infer the history of one group, or can it infer multiple groups simultaneously? Thank you. Best wishes

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[cht-jk]

Dear Armando, After I successfully run GONE, I will get the result files I want: Output_Ce_example and Outputd_d_example. What software should I use to visualize the above results, just like in your published article? Thank you, good wishes.

[armando-caballero]

Anyone to plot a line.