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ssolo / ALE

Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.
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Error, file 1000 does not seem accessible. #37

Closed Biscuite-wzy closed 1 year ago

Biscuite-wzy commented 2 years ago

Hi, I am using the program ALEobserve to create a geneFamily.ale file with example data. My comand is: docker run -v $PWD:$PWD -w $PWD boussau/alesuite ALEobserve $PWD/HBG745965_real.1.treelist 1000. However, I met a error, i.e. Error, file 1000 does not seem accessible. How can I discard the first 1000 trees as burnin? I hope I can get your help. Thanks.

ssolo commented 2 years ago

Like so:

~/src/ALE/build/bin/ALEobserve ~/src/ALE/example_data/HBG745965_real.1.treelist burnin=1000

Best,

Gergely

On 29 Sep 2022, at 10:55, SuperY @.***> wrote:

Hi, I am using the program ALEobserve to create a geneFamily.ale file with example data. My comand is: docker run -v $PWD:$PWD -w $PWD boussau/alesuite ALEobserve $PWD/HBG745965_real.1.treelist 1000. However, I met a error, i.e. Error, file 1000 does not seem accessible. How can I discard the first 1000 trees as burnin? I hope I can get your help. Thanks.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.

Dr. Gergely J Szöllősi

MTA-ELTE ,,Lendület” Evolutionary Genomics Research Group ERC “GENECLOCKS” Research Group head researcher http://ssolo.web.elte.hu Tel: 00 36 30 725 35 32

Biscuite-wzy commented 2 years ago

Hi,

I wonder how to use Docker to  discard the first 1000 trees as burnin. I hope I can get your help. Thanks.

787117923 @.***

 

------------------ 原始邮件 ------------------ 发件人: "ssolo/ALE" @.>; 发送时间: 2022年9月29日(星期四) 晚上7:00 @.>; @.**@.>; 主题: Re: [ssolo/ALE] Error, file 1000 does not seem accessible. (Issue #37)

Like so:

~/src/ALE/build/bin/ALEobserve ~/src/ALE/example_data/HBG745965_real.1.treelist burnin=1000

Best,

Gergely

> On 29 Sep 2022, at 10:55, SuperY @.***> wrote: > > > Hi, > I am using the program ALEobserve to create a geneFamily.ale file with example data. My comand is: > docker run -v $PWD:$PWD -w $PWD boussau/alesuite ALEobserve $PWD/HBG745965_real.1.treelist 1000. > However, I met a error, i.e. Error, file 1000 does not seem accessible. How can I discard the first 1000 trees as burnin? I hope I can get your help. Thanks. > > — > Reply to this email directly, view it on GitHub, or unsubscribe. > You are receiving this because you are subscribed to this thread. >

Dr. Gergely J Szöllősi

MTA-ELTE ,,Lendület” Evolutionary Genomics Research Group ERC “GENECLOCKS” Research Group head researcher http://ssolo.web.elte.hu Tel: 00 36 30 725 35 32

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>