GeneRax
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BenoitMorel
Termination of Gene tree Reconciliation
Hi there!
I am having an issue with achieving the duplication and loss rates for my dataset. I have 7-10 distantly related species (>200 MYA divergence time) for each and I am analyzing 8 genes for each. Everything was working fine up until recently when I began to receive the following message in my output file:
[00:00:00] Optimizing the phylogenetic likelihood... [00:00:00] Reconciling gene trees with the species tree... [00:00:00] Terminating the instance..
[00:00:00] DT rates: D=0.0925951 L= 0.152956 [00:00:00] Reconciliation likelihood: -30.1332 [00:00:00] Results directory: Mala_GeneRax_RESULTS [00:00:00] End of GeneRax execution
How can I resolve this, so I have access to the duplication and loss rates of each gene?
Thank you!
Olivia Waldridge
Hi Olivia, Can you send me the command line that you are using? Are you using the option "--per-family-rates"? Best, Benoit
Le mer. 3 janv. 2024 à 22:13, omwa227 @.***> a écrit :
Hi there!
I am having an issue with achieving the duplication and loss rates for my dataset. I have 7-10 distantly related species (>200 MYA divergence time) for each and I am analyzing 8 genes for each. Everything was working fine up until recently when I began to receive the following message in my output file:
[00:00:00] Optimizing the phylogenetic likelihood... [00:00:00] Reconciling gene trees with the species tree... [00:00:00] Terminating the instance..
[00:00:00] DT rates: D=0.0925951 L= 0.152956 [00:00:00] Reconciliation likelihood: -30.1332 [00:00:00] Results directory: Mala_GeneRax_RESULTS [00:00:00] End of GeneRax execution
How can I resolve this, so I have access to the duplication and loss rates of each gene?
Thank you!
Olivia Waldridge
— Reply to this email directly, view it on GitHub https://github.com/BenoitMorel/GeneRax/issues/73, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJJ3UPFOY36OIOXKLAEW5DYMXCYLAVCNFSM6AAAAABBL74Z2CVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3DINRVGU2DEOA . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Yes of course! Here it is:
generax --families Info_file_CHORDATES --species-tree Chordates_SP_tree.nwk --rec-model UndatedDL --prefix Op_RESULTS_Chordates_GeneRax --strategy EVAL --per-family-rates
Upon further inspection, the termination may be referring to the species tree estimate (which I have disabled as I am giving the program a species tree to work from). Attached are the last few lines of the output file. Do you think this is the case or is this a separate issue?
[00:00:00] Optimizing DTL rates before the reconciliation... [00:00:00] Optimizing the phylogenetic likelihood... [00:00:02] Reconciling gene trees with the species tree... [00:00:04] Terminating the instance..
[00:00:04] Reconciliation likelihood: -1223.76 [00:00:04] Results directory: Op_RESULTS_Chordates_GeneRax [00:00:04] End of GeneRax execution
Thank you so much for your help,
Olivia
Olivia Waldridge (she/her)
Biology Graduate Student
BGSA Outreach Co-Chair
Cassone Lab
THM 302B
College of Arts & Sciences
University of Kentucky
From: BenoitMorel @.> Sent: Monday, January 8, 2024 4:30 AM To: BenoitMorel/GeneRax @.> Cc: Waldridge, Olivia M. @.>; Author @.> Subject: Re: [BenoitMorel/GeneRax] Termination of Gene tree Reconciliation (Issue #73)
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Hi Olivia, Can you send me the command line that you are using? Are you using the option "--per-family-rates"? Best, Benoit
Le mer. 3 janv. 2024 à 22:13, omwa227 @.***> a écrit :
Hi there!
I am having an issue with achieving the duplication and loss rates for my dataset. I have 7-10 distantly related species (>200 MYA divergence time) for each and I am analyzing 8 genes for each. Everything was working fine up until recently when I began to receive the following message in my output file:
[00:00:00] Optimizing the phylogenetic likelihood... [00:00:00] Reconciling gene trees with the species tree... [00:00:00] Terminating the instance..
[00:00:00] DT rates: D=0.0925951 L= 0.152956 [00:00:00] Reconciliation likelihood: -30.1332 [00:00:00] Results directory: Mala_GeneRax_RESULTS [00:00:00] End of GeneRax execution
How can I resolve this, so I have access to the duplication and loss rates of each gene?
Thank you!
Olivia Waldridge
— Reply to this email directly, view it on GitHub https://github.com/BenoitMorel/GeneRax/issues/73, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJJ3UPFOY36OIOXKLAEW5DYMXCYLAVCNFSM6AAAAABBL74Z2CVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3DINRVGU2DEOA . You are receiving this because you are subscribed to this thread.Message ID: @.***>
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In your second message, the logs seem to be ok (I would think that the per-family rates have been estimated). Have you checked the output files? It should be the stats.txt files (see https://github.com/BenoitMorel/GeneRax/wiki/GeneRax#outputs)
Le lun. 8 janv. 2024 à 16:12, omwa227 @.***> a écrit :
Yes of course! Here it is:
generax --families Info_file_CHORDATES --species-tree Chordates_SP_tree.nwk --rec-model UndatedDL --prefix Op_RESULTS_Chordates_GeneRax --strategy EVAL --per-family-rates
Upon further inspection, the termination may be referring to the species tree estimate (which I have disabled as I am giving the program a species tree to work from). Attached are the last few lines of the output file. Do you think this is the case or is this a separate issue?
[00:00:00] Optimizing DTL rates before the reconciliation... [00:00:00] Optimizing the phylogenetic likelihood... [00:00:02] Reconciling gene trees with the species tree... [00:00:04] Terminating the instance..
[00:00:04] Reconciliation likelihood: -1223.76 [00:00:04] Results directory: Op_RESULTS_Chordates_GeneRax [00:00:04] End of GeneRax execution
Thank you so much for your help,
Olivia
Olivia Waldridge (she/her)
Biology Graduate Student
BGSA Outreach Co-Chair
Cassone Lab
THM 302B
College of Arts & Sciences
University of Kentucky
From: BenoitMorel @.> Sent: Monday, January 8, 2024 4:30 AM To: BenoitMorel/GeneRax @.> Cc: Waldridge, Olivia M. @.>; Author @.> Subject: Re: [BenoitMorel/GeneRax] Termination of Gene tree Reconciliation (Issue #73)
You don't often get email from @.*** Learn why this is important< https://aka.ms/LearnAboutSenderIdentification> CAUTION: External Sender
Hi Olivia, Can you send me the command line that you are using? Are you using the option "--per-family-rates"? Best, Benoit
Le mer. 3 janv. 2024 à 22:13, omwa227 @.***> a écrit :
Hi there!
I am having an issue with achieving the duplication and loss rates for my dataset. I have 7-10 distantly related species (>200 MYA divergence time) for each and I am analyzing 8 genes for each. Everything was working fine up until recently when I began to receive the following message in my output file:
[00:00:00] Optimizing the phylogenetic likelihood... [00:00:00] Reconciling gene trees with the species tree... [00:00:00] Terminating the instance..
[00:00:00] DT rates: D=0.0925951 L= 0.152956 [00:00:00] Reconciliation likelihood: -30.1332 [00:00:00] Results directory: Mala_GeneRax_RESULTS [00:00:00] End of GeneRax execution
How can I resolve this, so I have access to the duplication and loss rates of each gene?
Thank you!
Olivia Waldridge
— Reply to this email directly, view it on GitHub https://github.com/BenoitMorel/GeneRax/issues/73, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ADJJ3UPFOY36OIOXKLAEW5DYMXCYLAVCNFSM6AAAAABBL74Z2CVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3DINRVGU2DEOA>
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