Phylogenetic Tree

[Sveta-user]

Greetings -
I've started 4 phylogenetic trees in the morning today, Feb 24th (10 hours ago) . One of them worked well and fast, but 3 others are not done still. Is it possible to find out why they are not working? Is there anything wrong with specific genomes in these trees?
Will really appreciate your advice!

[mshukla1]

Are they still running or failed?

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Sent from my iPhone On Feb 24, 2022, at 8:40 PM, Sveta-user ***@***.***> wrote:  Greetings - I've started 4 phylogenetic trees in the morning today, Feb 24th (10 hours ago) . One of them worked well and fast, but 3 others are not done still. Is it possible to find out why they are not working? Is there anything wrong with specific genomes in these trees? Will really appreciate your advice! — Reply to this email directly, view it on GitHub<#2428>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAJN333YKQPUAQH7GJJTIMTU43TZHANCNFSM5PJCII7A>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Sveta-user]

Still running - since 11 am

[Sveta-user]

Hi Maulik! Thank you for looking into this. I found a way to check if the genomes were a problem. I just ran the same trees with much smaller number of core genes (100 instead of 500) - and all 3 trees finished successfully. So good news: (i) Tree service works ; (ii) all my genomes are acceptable by this service. It just takes longer . Case closed ;))

[ARWattam]

Sveta, you can also use the protein family sorter to examine your group. Load them in, using the PGFams, and then click perfect protein families.

This will tell you how many protein families can be used with your particular group. If you don't have any, or have too few, you can use the Allow deletions or Allow duplications functions.

You can check out this video that shows you how to do it:
https://docs.patricbrc.org/videos/phylogenetic_codon_tree.html#codon6

Rebecca

[olsonanl]

Just wanted to note the original set of trees did finish after 17 hours:

[Sveta-user]

Greeting! Many thanks for all your advice. All 4 trees worked. I should have been more patient :) Sorry for bothering you . I know Patric Tree service takes time (and is worth the wait). But this time 1 of 4 trees finished in less than a hour. so I assumed that you guys must have recently upgraded the Tree tool, made it faster, but in the process the old problem with including private genomes in trees came back . Glad that was not the case. Thanks again!