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3/22/24

EVM support discontinued

Hi all - I'm cutting back on the number of projects I'm going to support moving forward, and

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EVM support discontinued

Hi all - I'm cutting back on the number of projects I'm going to support moving forward, and

3/22/24

kevin wang, Brian Haas2

3/31/23

write_EVM_commands.pl

Hi, It looks like it's not finding the file: partition_EVM_inputs.out perhaps you missed an

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write_EVM_commands.pl

Hi, It looks like it's not finding the file: partition_EVM_inputs.out perhaps you missed an

3/31/23

Krešimir Križanović, Brian Haas4

2/16/23

Using miniprot output with EVM

Hi Kresimir, responses below On Thu, Feb 16, 2023 at 3:49 AM Krešimir Križanović <kkrizanovic@

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Using miniprot output with EVM

Hi Kresimir, responses below On Thu, Feb 16, 2023 at 3:49 AM Krešimir Križanović <kkrizanovic@

2/16/23

1/17/23

Announcement: EVM Release v2.0.0

Greetings all. We have a new release for EVM available (v2.0.0): https://github.com/EVidenceModeler/

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Announcement: EVM Release v2.0.0

Greetings all. We have a new release for EVM available (v2.0.0): https://github.com/EVidenceModeler/

1/17/23

Brian Haas, Alessandro de Mello Varani3

1/15/23

Announcement: EVM documentation migration to wiki format

Yes, good idea. I'm way overdue for a new release. I'll make it more turn-key including

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Announcement: EVM documentation migration to wiki format

Yes, good idea. I'm way overdue for a new release. I'll make it more turn-key including

1/15/23

Marco Sollitto, 戴睿紘2

3/28/22

EvidenceModeler output

Hi there, I also have this problem. My braker's BUSCO reached 92% and Maker's BUSCO is 80%.

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EvidenceModeler output

Hi there, I also have this problem. My braker's BUSCO reached 92% and Maker's BUSCO is 80%.

3/28/22

Chaiwat Naktang

4/30/21

Error, no asmbl_id from gene_obj

Hi everyone After I got the result from Augustus, then I use augustus_GFF3_to_EVM_GFF3.pl to chnge

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Error, no asmbl_id from gene_obj

Hi everyone After I got the result from Augustus, then I use augustus_GFF3_to_EVM_GFF3.pl to chnge

4/30/21

12/28/20

how to run evidence_modeler.pl without partition

I used this codes on my pc ``` ~/EVidenceModeler-1.1.1/EvmUtils/partition_EVM_inputs.pl ``` It went

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how to run evidence_modeler.pl without partition

I used this codes on my pc ``` ~/EVidenceModeler-1.1.1/EvmUtils/partition_EVM_inputs.pl ``` It went

12/28/20

Alessandro de Mello Varani, Brian Haas2

9/28/20

EVM and BRAKER gene prediction

Hi, Note, EVM is meant to tackle a set of gene predictions, which means folding in Braker results

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EVM and BRAKER gene prediction

Hi, Note, EVM is meant to tackle a set of gene predictions, which means folding in Braker results

9/28/20

Jon Palmer, … Brian Haas4

9/15/20

Should I be worried about this error? Error with prediction: Augustus lend_intergenic:.....

hi, normally I wouldn't worry about the gene overlap issue as long as the genes do actually

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Should I be worried about this error? Error with prediction: Augustus lend_intergenic:.....

hi, normally I wouldn't worry about the gene overlap issue as long as the genes do actually

9/15/20

Chaiwat Naktang, Brian Haas2

8/6/20

how to know number of transcript in each gene

Hi, EVM only provides a single prediction per genomic locus. For alt splicing annotations based on

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how to know number of transcript in each gene

Hi, EVM only provides a single prediction per genomic locus. For alt splicing annotations based on

8/6/20

Sisi Yuan, Brian Haas2

7/15/20

GeMoMa as ABINITO PREDICTION or OTHER PREDICTION

Basically, if the complete gene prediction is derived from a protein alignment, then you would use

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GeMoMa as ABINITO PREDICTION or OTHER PREDICTION

Basically, if the complete gene prediction is derived from a protein alignment, then you would use

7/15/20

John Martinson, Brian Haas4

7/7/20

Is this protein sequence in the output from EVidenceModeler wrong?

Sure, I'll log it. You can just retranslate it given the outputted gff3 file using a tool

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Is this protein sequence in the output from EVidenceModeler wrong?

Sure, I'll log it. You can just retranslate it given the outputted gff3 file using a tool

7/7/20

jeremy le luyer, … Brian Haas5

6/28/20

excessive RAM use after splitting partitions

Hi, Do you have a small example you can share with me that reproduces the problem? My guess is that

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excessive RAM use after splitting partitions

Hi, Do you have a small example you can share with me that reproduces the problem? My guess is that

6/28/20

Paolo, Brian Haas4

11/12/19

EVM with no ab initio models

Sure thing. I'd suggest working with the transcript data first, then have a look at cases where

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EVM with no ab initio models

Sure thing. I'd suggest working with the transcript data first, then have a look at cases where

11/12/19

9/26/19

AAT package output to EVM

Hi, I tried to combine the output of AAT package in EVM using following command: .AAT_btab_to_gff3.pl

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AAT package output to EVM

Hi, I tried to combine the output of AAT package in EVM using following command: .AAT_btab_to_gff3.pl

9/26/19

Chaiwat Naktang, … Brian Haas6

7/12/19

error in partition step

Hi It looks like it's related to the genome scaffold identifiers. If you remove the pipe symbol

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error in partition step

Hi It looks like it's related to the genome scaffold identifiers. If you remove the pipe symbol

7/12/19

Jon Lerga Jaso, Brian Haas3

3/12/19

EVM does not produce the consensus gene structure of a gene with very clear hints

Excellent, I will try that. Many thanks! El martes, 12 de marzo de 2019, 11:57:07 (UTC+1), Brian Haas

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EVM does not produce the consensus gene structure of a gene with very clear hints

Excellent, I will try that. Many thanks! El martes, 12 de marzo de 2019, 11:57:07 (UTC+1), Brian Haas

3/12/19

John Martinson, Brian Haas4

2/23/19

Question regarding CDS frame

Sure thing. Thanks for mentioning this. I need to move the documentation over to the wiki format and

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Question regarding CDS frame

Sure thing. Thanks for mentioning this. I need to move the documentation over to the wiki format and

2/23/19

mtbr...@ucdavis.edu, Brian Haas3

1/30/19

errors in evm.out.log files

Hi Monica, You've stumped me on this one. I haven't seen this before and it's not obvious

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errors in evm.out.log files

Hi Monica, You've stumped me on this one. I haven't seen this before and it's not obvious

1/30/19

alyssa....@uconn.edu, Brian Haas5

12/5/18

Dropping Gene Models

I am trying to use EVM to resolve fragmentation in the annotation of a conifer species (douglas fir).

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Dropping Gene Models

I am trying to use EVM to resolve fragmentation in the annotation of a conifer species (douglas fir).

12/5/18

peachan...@gmail.com, … Brian Haas5

10/19/18

EVM super-beginner

Sounds neat! Uses much of my tool stack. 🤗 -Brian (by iPhone) On Oct 19, 2018, at 3:31 PM, Craig

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EVM super-beginner

Sounds neat! Uses much of my tool stack. 🤗 -Brian (by iPhone) On Oct 19, 2018, at 3:31 PM, Craig

10/19/18

Monica Poelchau

8/13/18

question about CDS phase in gff3 output

Hi there EVM group, I have a question about the gff3 output from the EVM program - specifically about

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question about CDS phase in gff3 output

Hi there EVM group, I have a question about the gff3 output from the EVM program - specifically about

8/13/18

Mirian TN Tsuchiya

2/13/18

SNAP to GFF3 error

Hi, I'm trying to run the SNAP_to_GFF3.pl script but I get the following error every time: Error,

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SNAP to GFF3 error

Hi, I'm trying to run the SNAP_to_GFF3.pl script but I get the following error every time: Error,

2/13/18

Matthew MacManes, Brian Haas2

12/21/17

Hi Matt, Do you know if it's partitioning the target data? It usually splits things up into

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Hi Matt, Do you know if it's partitioning the target data? It usually splits things up into

12/21/17

falinor181, Brian Haas6

10/18/17

Troubleshooting tandem fused genes

Hi Tim, For ABINITIO_PREDICTION, the intergenic regions are inferred as the regions between

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Troubleshooting tandem fused genes

Hi Tim, For ABINITIO_PREDICTION, the intergenic regions are inferred as the regions between

10/18/17

Bas Verbruggen, … Brian Haas8

9/21/17

Combining predictions doesn't yield any output

This should be fine as long as the 2nd column of the gff3 file matched up with the prediction type in

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Combining predictions doesn't yield any output

This should be fine as long as the 2nd column of the gff3 file matched up with the prediction type in

9/21/17

Juan O A, Brian Haas5

7/27/17

Use of several gene predictors

Hi, best thing to do is to compare your alignment formatting to what's in the example data

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Use of several gene predictors

Hi, best thing to do is to compare your alignment formatting to what's in the example data

7/27/17

5/11/17

How can I transfer the genewise gff format output into the alignments gff3 format that EVM can use?

Sorry, the script might be wrong. Maybe try this: $cat genewise.gff.best|perl -lane 'next unless

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How can I transfer the genewise gff format output into the alignments gff3 format that EVM can use?

Sorry, the script might be wrong. Maybe try this: $cat genewise.gff.best|perl -lane 'next unless

5/11/17

Ana Nascimento, Brian Haas3

4/28/17

Converting blast tabular results in gff3

ty :) Em quarta-feira, 26 de abril de 2017 21:07:06 UTC-3, Brian Haas escreveu: Hi Ana, For

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Converting blast tabular results in gff3

ty :) Em quarta-feira, 26 de abril de 2017 21:07:06 UTC-3, Brian Haas escreveu: Hi Ana, For

4/28/17

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