Sequence length != multiple of 3 for some CDS

[U201412486]

Hi,
Why is the sequence length not multiple of 3 for some CDS in the output?
Is it normal?

Thanks,

[brianjohnhaas]

Hi, If it's a partial sequence that begins or runs off the end of a contig, then it could include a partial codon and hence won't be divisible by 3.

…

On Sun, Apr 5, 2020 at 5:07 AM U201412486 ***@***.***> wrote: Hi, Why is the sequence length not multiple of 3 for some CDS in the output? Is it normal? Thanks, — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX2VTHP447AUQ7WK37LRLBC5ZANCNFSM4MAOORPA> .

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[U201412486]

Thanks for your answer.
And When I run the code EvmUtils/gff3_file_to_proteins.pl annotaion.gff3 genome.fasta CDS >cds.fasta ,It report the error below
Out of memory!
It is due to the big file of annotaion.gff3.How can I solve it?

[brianjohnhaas]

I wonder if there's a problem with the annotation.gff3 file. Where did it come from? If you can share the inputs with me privately, I could try to debug the issue. [email protected] best, ~brian

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On Tue, Apr 7, 2020 at 7:54 AM U201412486 ***@***.***> wrote: Thanks for your answer. And When I run the code EvmUtils/gff3_file_to_proteins.pl annotaion.gff3 genome.fasta CDS >cds.fasta ,It report the error below Out of memory! It is due to the big file of annotaion.gff3.How can I solve it? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX7BFEE5YFXUJZNAQW3RLMH5XANCNFSM4MAOORPA> .

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[U201412486]

Sorry,I have tried for a long time. I can not success in sending my inputs to you according to your email "[email protected]" by my private email.
It reports it below.
SMTP error, DOT: Host broadinstitute.org(108.177.97.27) DOT said 552-5.2.3 Your message exceeded Google's message size limits. Please visit 552-5.2.3 https://support.google.com/mail/?p=MaxSizeError to view our size 552 5.2.3 guidelines. lt19si490524pjb.31 - gsmtp
Thanks,

[brianjohnhaas]

Hi, Can you reproduce the error using a small subset of your data? If you could send me a smaller data set, that would be best.

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On Sat, Apr 11, 2020 at 9:54 AM U201412486 ***@***.***> wrote: Sorry,I have tried for a long time. I can not success in sending my inputs to you according to your email ***@***.***" by my private email. It reports it below. SMTP error, DOT: Host broadinstitute.org(108.177.97.27) DOT said 552-5.2.3 Your message exceeded Google's message size limits. Please visit 552-5.2.3 https://support.google.com/mail/?p=MaxSizeError to view our size 552 5.2.3 guidelines. lt19si490524pjb.31 - gsmtp Thanks, — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX3C5JBKQZOX7WYS5KLRMBY7RANCNFSM4MAOORPA> .

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[U201412486]

Hi,I have solved this problem. It is my fault.
Thank you.

[sunnycqcn]

Hi, If it's a partial sequence that begins or runs off the end of a contig, then it could include a partial codon and hence won't be divisible by 3.
…
On Sun, Apr 5, 2020 at 5:07 AM U201412486 @.***> wrote: Hi, Why is the sequence length not multiple of 3 for some CDS in the output? Is it normal? Thanks, — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX2VTHP447AUQ7WK37LRLBC5ZANCNFSM4MAOORPA .
-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

Hi Brain,
Do you have any suggestions for improve this problem or remove this problem?
Thanks,
Fuyou

[brianjohnhaas]

Hi Fuyou, I figured it was more of a feature than a problem. It's just the way it works. Is it causing trouble with downstream applications?

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On Thu, Feb 3, 2022 at 6:11 PM sunnycqcn ***@***.***> wrote: Hi, If it's a partial sequence that begins or runs off the end of a contig, then it could include a partial codon and hence won't be divisible by 3. … <#m_-7139601121663882012_> On Sun, Apr 5, 2020 at 5:07 AM U201412486 *@*.***> wrote: Hi, Why is the sequence length not multiple of 3 for some CDS in the output? Is it normal? Thanks, — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1 <#1>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX2VTHP447AUQ7WK37LRLBC5ZANCNFSM4MAOORPA . -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas Hi Brain, Do you have any suggestions for improve this problem or remove this problem? Thanks, Fuyou — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX3W3AIXK45PRQRWQU3UZMDSNANCNFSM4MAOORPA> . 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 commented.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[sunnycqcn]

Hi Brian, Yes. I get some trouble for do KaKS analysis. I know the reason for partial genes using EVM. My mean can we discard them or keep them? Thanks, Fuyou

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On Fri, Feb 4, 2022 at 8:01 AM Brian Haas ***@***.***> wrote: Hi Fuyou, I figured it was more of a feature than a problem. It's just the way it works. Is it causing trouble with downstream applications? On Thu, Feb 3, 2022 at 6:11 PM sunnycqcn ***@***.***> wrote: > Hi, If it's a partial sequence that begins or runs off the end of a > contig, then it could include a partial codon and hence won't be divisible > by 3. > … <#m_-7139601121663882012_> > On Sun, Apr 5, 2020 at 5:07 AM U201412486 *@*.***> wrote: Hi, Why is the > sequence length not multiple of 3 for some CDS in the output? Is it normal? > Thanks, — You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub <#1 > <#1 >>, > or unsubscribe > https://github.com/notifications/unsubscribe-auth/ABZRKX2VTHP447AUQ7WK37LRLBC5ZANCNFSM4MAOORPA > . > -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas > http://broad.mit.edu/~bhaas > > Hi Brain, > Do you have any suggestions for improve this problem or remove this > problem? > Thanks, > Fuyou > > — > Reply to this email directly, view it on GitHub > < #1 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ABZRKX3W3AIXK45PRQRWQU3UZMDSNANCNFSM4MAOORPA > > . > 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 commented.Message ID: > ***@***.***> > -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF3JCKELGWMT2KB5HMKX3SDUZPLZ3ANCNFSM4MAOORPA> . 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 commented.Message ID: ***@***.***>

-- Fuyou Fu, Ph.D. Saskatoon Research Center Agriculture Agri-Food Canada Cananda

[brianjohnhaas]

I see. Updating EVM to work differently here would be a challenge and won't happen any time soon, unfortunately.

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On Fri, Feb 4, 2022 at 9:55 AM sunnycqcn ***@***.***> wrote: Hi Brian, Yes. I get some trouble for do KaKS analysis. I know the reason for partial genes using EVM. My mean can we discard them or keep them? Thanks, Fuyou On Fri, Feb 4, 2022 at 8:01 AM Brian Haas ***@***.***> wrote: > Hi Fuyou, > > I figured it was more of a feature than a problem. It's just the way it > works. Is it causing trouble with downstream applications? > > On Thu, Feb 3, 2022 at 6:11 PM sunnycqcn ***@***.***> wrote: > > > Hi, If it's a partial sequence that begins or runs off the end of a > > contig, then it could include a partial codon and hence won't be > divisible > > by 3. > > … <#m_-7139601121663882012_> > > On Sun, Apr 5, 2020 at 5:07 AM U201412486 *@*.***> wrote: Hi, Why is the > > sequence length not multiple of 3 for some CDS in the output? Is it > normal? > > Thanks, — You are receiving this because you are subscribed to this > thread. > > Reply to this email directly, view it on GitHub <#1 > > <#1 > >>, > > or unsubscribe > > > https://github.com/notifications/unsubscribe-auth/ABZRKX2VTHP447AUQ7WK37LRLBC5ZANCNFSM4MAOORPA > > . > > -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas > > http://broad.mit.edu/~bhaas > > > > Hi Brain, > > Do you have any suggestions for improve this problem or remove this > > problem? > > Thanks, > > Fuyou > > > > — > > Reply to this email directly, view it on GitHub > > < > #1 (comment) > >, > > or unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/ABZRKX3W3AIXK45PRQRWQU3UZMDSNANCNFSM4MAOORPA > > > > . > > 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 commented.Message ID: > > ***@***.***> > > > > > -- > -- > Brian J. Haas > The Broad Institute > http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> > > — > Reply to this email directly, view it on GitHub > < #1 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AF3JCKELGWMT2KB5HMKX3SDUZPLZ3ANCNFSM4MAOORPA > > . > 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 commented.Message ID: > ***@***.***> > -- Fuyou Fu, Ph.D. Saskatoon Research Center Agriculture Agri-Food Canada Cananda — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX7FPKSKO2D3TWQRKSTUZPSGHANCNFSM4MAOORPA> . 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 commented.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>