Termination of Gene tree Reconciliation

[omwa227]

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

[BenoitMorel]

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 <#73>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJJ3UPFOY36OIOXKLAEW5DYMXCYLAVCNFSM6AAAAABBL74Z2CVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3DINRVGU2DEOA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[omwa227]

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 <#73>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJJ3UPFOY36OIOXKLAEW5DYMXCYLAVCNFSM6AAAAABBL74Z2CVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3DINRVGU2DEOA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

— Reply to this email directly, view it on GitHub<#73 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BAZOTMMFGCDMP73JK2VV33LYNO4EVAVCNFSM6AAAAABBL74Z2CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBQGY2DKOBSGA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[BenoitMorel]

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 :

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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 > <#73>, or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ADJJ3UPFOY36OIOXKLAEW5DYMXCYLAVCNFSM6AAAAABBL74Z2CVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3DINRVGU2DEOA> > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> > — Reply to this email directly, view it on GitHub< #73 (comment)>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/BAZOTMMFGCDMP73JK2VV33LYNO4EVAVCNFSM6AAAAABBL74Z2CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBQGY2DKOBSGA>. You are receiving this because you authored the thread.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub <#73 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJJ3UNPYTEICT33KXLGZXLYNQEGTAVCNFSM6AAAAABBL74Z2CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBRGIYDANBVGU> . You are receiving this because you commented.Message ID: ***@***.***>