Error "ambiguous method overloading"

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Error "ambiguous method overloading"

Monica Poelchau
Hi Nathan,

Versions:
  • Version: 2.1.1-SNAPSHOT
  • Grails version: 2.5.5
  • Groovy version: 2.4.4
  • JVM version: 1.8.0_212
  • Servlet Container Version: Apache Tomcat/8.5.23

I'm stumped. I've set up a new organism, and I can't create any 2-tier annotations (gene, pseudogene, etc) from any of the gffs that I've loaded. I've attached a screenshot of the error, a reference fasta and gff example. Also below is what catalina.out tells me.

I can create repeat_region and transposable_element annotations.

I don't see this behavior on any of the other organisms that we have loaded.

Any ideas?

Thank you!

Monica

2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - CAUGHT ERROR through websocket call: java.lang.reflect.InvocationTargetException

2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - THROWING PARENT ERROR instead through reflection: groovy.lang.GroovyRuntimeException: Ambiguous method overloading for method java.lang.Integer#div.

Cannot resolve which method to invoke for [null] due to overlapping prototypes between:

        [class java.lang.Character]

        [class java.lang.Number]

2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - exception groovy.lang.GroovyRuntimeException: Ambiguous method overloading for method java.lang.Integer#div.

Cannot resolve which method to invoke for [null] due to overlapping prototypes between:

        [class java.lang.Character]

        [class java.lang.Number]

2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - exception message Ambiguous method overloading for method java.lang.Integer#div.

Cannot resolve which method to invoke for [null] due to overlapping prototypes between:

        [class java.lang.Character]

        [class java.lang.Number]

2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - username [hidden email]

2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - error destination message: /topic/AnnotationNotification/user/[hidden email]

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Screen Shot 2019-04-26 at 10.12.26.png (62K) Download Attachment
LSTR012198-5.gff (1K) Download Attachment
QKKF02000013.fna (103K) Download Attachment
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Re: Error "ambiguous method overloading"

nathandunn

On the development version of Apollo , I uploaded the GFF3 and it appeared fine. 

I know that different overlapping bugs have been fixed in versions subsequent to 2.1 (I think that 2.3.1 is the most recent version). 





##gff-version 3
##sequence-region QKKF02000013.1 1 102964
QKKF02000013.1 . gene 31291 55870 . - . [hidden email];ID=485eaf9f-4d9f-4d16-ae2f-d0b87736e19e;date_last_modified=2019-04-26;Name=LSTR012198-RA;date_creation=2019-04-26
QKKF02000013.1 . mRNA 31291 55870 . - . [hidden email];Parent=485eaf9f-4d9f-4d16-ae2f-d0b87736e19e;ID=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;orig_id=LSTR012198-RA;date_last_modified=2019-04-26;Name=LSTR012198-RA-00001;date_creation=2019-04-26
QKKF02000013.1 . exon 49015 49835 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=ca466041-66e9-459c-97cb-d23a940470d1;Name=ca466041-66e9-459c-97cb-d23a940470d1
QKKF02000013.1 . exon 55552 55870 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=b8ba1328-b0ec-4334-9975-ed9cb4b08eb6;Name=b8ba1328-b0ec-4334-9975-ed9cb4b08eb6
QKKF02000013.1 . exon 44400 44486 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=a31d0041-e0df-4b86-be1f-0517198ccc89;Name=a31d0041-e0df-4b86-be1f-0517198ccc89
QKKF02000013.1 . exon 37971 38177 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=8f4161f8-0cec-443e-9f60-d369e75fa8c1;Name=8f4161f8-0cec-443e-9f60-d369e75fa8c1
QKKF02000013.1 . exon 32789 32970 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=8c1f0b7c-c17c-4b88-b73d-123a801f0cf7;Name=8c1f0b7c-c17c-4b88-b73d-123a801f0cf7
QKKF02000013.1 . exon 36489 36669 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=78e74d1a-5852-45fa-9409-612375a2c0da;Name=78e74d1a-5852-45fa-9409-612375a2c0da
QKKF02000013.1 . exon 31291 31674 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=2b265504-4db0-4cef-980e-59d0c67549ff;Name=2b265504-4db0-4cef-980e-59d0c67549ff
QKKF02000013.1 . exon 52673 52990 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=d98c511f-fe78-427d-bdec-701242fe1f05;Name=d98c511f-fe78-427d-bdec-701242fe1f05
QKKF02000013.1 . exon 46553 46729 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=083cfc73-a436-41a7-9002-064e0039aa2d;Name=083cfc73-a436-41a7-9002-064e0039aa2d
QKKF02000013.1 . exon 43387 43469 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=12b15f0e-afef-4ccd-b17c-75177ede0017;Name=12b15f0e-afef-4ccd-b17c-75177ede0017
QKKF02000013.1 . CDS 55552 55612 . - 0 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 52673 52990 . - 2 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 49015 49835 . - 2 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 46553 46729 . - 0 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 44400 44486 . - 0 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 43387 43469 . - 0 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 37971 38177 . - 1 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 36489 36669 . - 1 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 32789 32970 . - 0 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 31494 31674 . - 1 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
###



On Apr 26, 2019, at 11:16 AM, Monica Poelchau <[hidden email]> wrote:

Hi Nathan,

Versions:
  • Version: 2.1.1-SNAPSHOT
  • Grails version: 2.5.5
  • Groovy version: 2.4.4
  • JVM version: 1.8.0_212
  • Servlet Container Version: Apache Tomcat/8.5.23

I'm stumped. I've set up a new organism, and I can't create any 2-tier annotations (gene, pseudogene, etc) from any of the gffs that I've loaded. I've attached a screenshot of the error, a reference fasta and gff example. Also below is what catalina.out tells me.

I can create repeat_region and transposable_element annotations.

I don't see this behavior on any of the other organisms that we have loaded.

Any ideas?

Thank you!

Monica

2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - CAUGHT ERROR through websocket call: java.lang.reflect.InvocationTargetException
2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - THROWING PARENT ERROR instead through reflection: groovy.lang.GroovyRuntimeException: Ambiguous method overloading for method java.lang.Integer#div.
Cannot resolve which method to invoke for [null] due to overlapping prototypes between:
        [class java.lang.Character]
        [class java.lang.Number]
2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - exception groovy.lang.GroovyRuntimeException: Ambiguous method overloading for method java.lang.Integer#div.
Cannot resolve which method to invoke for [null] due to overlapping prototypes between:
        [class java.lang.Character]
        [class java.lang.Number]
2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - exception message Ambiguous method overloading for method java.lang.Integer#div.
Cannot resolve which method to invoke for [null] due to overlapping prototypes between:
        [class java.lang.Character]
        [class java.lang.Number]
2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - username [hidden email]
2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - error destination message: /[hidden email]
<Screen Shot 2019-04-26 at 10.12.26.png><LSTR012198-5.gff><QKKF02000013.fna>

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Re: Error "ambiguous method overloading"

Monica Poelchau
Thanks for the feedback, Nathan!

Looks like this issue was already reported and fixed: https://github.com/GMOD/Apollo/issues/2065

Unfortunately we can't move to Apollo 2.3 yet, since we're having issues with the track styles (introns not showing up). In the meantime, I'm just not using the index option for the reference fasta - that seems to take care of the problem.

Monica

On Fri, Apr 26, 2019 at 3:19 PM Nathan Dunn <[hidden email]> wrote:

On the development version of Apollo , I uploaded the GFF3 and it appeared fine. 

I know that different overlapping bugs have been fixed in versions subsequent to 2.1 (I think that 2.3.1 is the most recent version). 





##gff-version 3
##sequence-region QKKF02000013.1 1 102964
QKKF02000013.1 . gene 31291 55870 . - . [hidden email];ID=485eaf9f-4d9f-4d16-ae2f-d0b87736e19e;date_last_modified=2019-04-26;Name=LSTR012198-RA;date_creation=2019-04-26
QKKF02000013.1 . mRNA 31291 55870 . - . [hidden email];Parent=485eaf9f-4d9f-4d16-ae2f-d0b87736e19e;ID=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;orig_id=LSTR012198-RA;date_last_modified=2019-04-26;Name=LSTR012198-RA-00001;date_creation=2019-04-26
QKKF02000013.1 . exon 49015 49835 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=ca466041-66e9-459c-97cb-d23a940470d1;Name=ca466041-66e9-459c-97cb-d23a940470d1
QKKF02000013.1 . exon 55552 55870 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=b8ba1328-b0ec-4334-9975-ed9cb4b08eb6;Name=b8ba1328-b0ec-4334-9975-ed9cb4b08eb6
QKKF02000013.1 . exon 44400 44486 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=a31d0041-e0df-4b86-be1f-0517198ccc89;Name=a31d0041-e0df-4b86-be1f-0517198ccc89
QKKF02000013.1 . exon 37971 38177 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=8f4161f8-0cec-443e-9f60-d369e75fa8c1;Name=8f4161f8-0cec-443e-9f60-d369e75fa8c1
QKKF02000013.1 . exon 32789 32970 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=8c1f0b7c-c17c-4b88-b73d-123a801f0cf7;Name=8c1f0b7c-c17c-4b88-b73d-123a801f0cf7
QKKF02000013.1 . exon 36489 36669 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=78e74d1a-5852-45fa-9409-612375a2c0da;Name=78e74d1a-5852-45fa-9409-612375a2c0da
QKKF02000013.1 . exon 31291 31674 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=2b265504-4db0-4cef-980e-59d0c67549ff;Name=2b265504-4db0-4cef-980e-59d0c67549ff
QKKF02000013.1 . exon 52673 52990 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=d98c511f-fe78-427d-bdec-701242fe1f05;Name=d98c511f-fe78-427d-bdec-701242fe1f05
QKKF02000013.1 . exon 46553 46729 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=083cfc73-a436-41a7-9002-064e0039aa2d;Name=083cfc73-a436-41a7-9002-064e0039aa2d
QKKF02000013.1 . exon 43387 43469 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=12b15f0e-afef-4ccd-b17c-75177ede0017;Name=12b15f0e-afef-4ccd-b17c-75177ede0017
QKKF02000013.1 . CDS 55552 55612 . - 0 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 52673 52990 . - 2 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 49015 49835 . - 2 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 46553 46729 . - 0 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 44400 44486 . - 0 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 43387 43469 . - 0 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 37971 38177 . - 1 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 36489 36669 . - 1 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 32789 32970 . - 0 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 31494 31674 . - 1 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
###



On Apr 26, 2019, at 11:16 AM, Monica Poelchau <[hidden email]> wrote:

Hi Nathan,

Versions:
  • Version: 2.1.1-SNAPSHOT
  • Grails version: 2.5.5
  • Groovy version: 2.4.4
  • JVM version: 1.8.0_212
  • Servlet Container Version: Apache Tomcat/8.5.23

I'm stumped. I've set up a new organism, and I can't create any 2-tier annotations (gene, pseudogene, etc) from any of the gffs that I've loaded. I've attached a screenshot of the error, a reference fasta and gff example. Also below is what catalina.out tells me.

I can create repeat_region and transposable_element annotations.

I don't see this behavior on any of the other organisms that we have loaded.

Any ideas?

Thank you!

Monica

2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - CAUGHT ERROR through websocket call: java.lang.reflect.InvocationTargetException
2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - THROWING PARENT ERROR instead through reflection: groovy.lang.GroovyRuntimeException: Ambiguous method overloading for method java.lang.Integer#div.
Cannot resolve which method to invoke for [null] due to overlapping prototypes between:
        [class java.lang.Character]
        [class java.lang.Number]
2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - exception groovy.lang.GroovyRuntimeException: Ambiguous method overloading for method java.lang.Integer#div.
Cannot resolve which method to invoke for [null] due to overlapping prototypes between:
        [class java.lang.Character]
        [class java.lang.Number]
2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - exception message Ambiguous method overloading for method java.lang.Integer#div.
Cannot resolve which method to invoke for [null] due to overlapping prototypes between:
        [class java.lang.Character]
        [class java.lang.Number]
2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - username [hidden email]
2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - error destination message: /[hidden email]
<Screen Shot 2019-04-26 at 10.12.26.png><LSTR012198-5.gff><QKKF02000013.fna>

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Re: Error "ambiguous method overloading"

nathandunn


On Apr 30, 2019, at 1:26 PM, Monica Poelchau <[hidden email]> wrote:

Thanks for the feedback, Nathan!

Looks like this issue was already reported and fixed: https://github.com/GMOD/Apollo/issues/2065

Glad to hear it. 

Unfortunately we can't move to Apollo 2.3 yet, since we're having issues with the track styles (introns not showing up).

I think this is tractable.  My understanding is that there is some custom CSS that needs to be modified to use namespaces properly in the newer JBrowse.

In the meantime, I'm just not using the index option for the reference fasta - that seems to take care of the problem.

Sounds good. 

Nathan



Monica

On Fri, Apr 26, 2019 at 3:19 PM Nathan Dunn <[hidden email]> wrote:

On the development version of Apollo , I uploaded the GFF3 and it appeared fine. 

I know that different overlapping bugs have been fixed in versions subsequent to 2.1 (I think that 2.3.1 is the most recent version). 




<PastedGraphic-1.png>

##gff-version 3
##sequence-region QKKF02000013.1 1 102964
QKKF02000013.1 . gene 31291 55870 . - . [hidden email];ID=485eaf9f-4d9f-4d16-ae2f-d0b87736e19e;date_last_modified=2019-04-26;Name=LSTR012198-RA;date_creation=2019-04-26
QKKF02000013.1 . mRNA 31291 55870 . - . [hidden email];Parent=485eaf9f-4d9f-4d16-ae2f-d0b87736e19e;ID=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;orig_id=LSTR012198-RA;date_last_modified=2019-04-26;Name=LSTR012198-RA-00001;date_creation=2019-04-26
QKKF02000013.1 . exon 49015 49835 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=ca466041-66e9-459c-97cb-d23a940470d1;Name=ca466041-66e9-459c-97cb-d23a940470d1
QKKF02000013.1 . exon 55552 55870 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=b8ba1328-b0ec-4334-9975-ed9cb4b08eb6;Name=b8ba1328-b0ec-4334-9975-ed9cb4b08eb6
QKKF02000013.1 . exon 44400 44486 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=a31d0041-e0df-4b86-be1f-0517198ccc89;Name=a31d0041-e0df-4b86-be1f-0517198ccc89
QKKF02000013.1 . exon 37971 38177 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=8f4161f8-0cec-443e-9f60-d369e75fa8c1;Name=8f4161f8-0cec-443e-9f60-d369e75fa8c1
QKKF02000013.1 . exon 32789 32970 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=8c1f0b7c-c17c-4b88-b73d-123a801f0cf7;Name=8c1f0b7c-c17c-4b88-b73d-123a801f0cf7
QKKF02000013.1 . exon 36489 36669 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=78e74d1a-5852-45fa-9409-612375a2c0da;Name=78e74d1a-5852-45fa-9409-612375a2c0da
QKKF02000013.1 . exon 31291 31674 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=2b265504-4db0-4cef-980e-59d0c67549ff;Name=2b265504-4db0-4cef-980e-59d0c67549ff
QKKF02000013.1 . exon 52673 52990 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=d98c511f-fe78-427d-bdec-701242fe1f05;Name=d98c511f-fe78-427d-bdec-701242fe1f05
QKKF02000013.1 . exon 46553 46729 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=083cfc73-a436-41a7-9002-064e0039aa2d;Name=083cfc73-a436-41a7-9002-064e0039aa2d
QKKF02000013.1 . exon 43387 43469 . - . Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=12b15f0e-afef-4ccd-b17c-75177ede0017;Name=12b15f0e-afef-4ccd-b17c-75177ede0017
QKKF02000013.1 . CDS 55552 55612 . - 0 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 52673 52990 . - 2 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 49015 49835 . - 2 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 46553 46729 . - 0 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 44400 44486 . - 0 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 43387 43469 . - 0 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 37971 38177 . - 1 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 36489 36669 . - 1 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 32789 32970 . - 0 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
QKKF02000013.1 . CDS 31494 31674 . - 1 Parent=7c9a71df-51be-4d92-a2fa-cc37ba9841a6;ID=c7d255eb-7382-4515-ae81-571ee58fd7b6;Name=c7d255eb-7382-4515-ae81-571ee58fd7b6
###



On Apr 26, 2019, at 11:16 AM, Monica Poelchau <[hidden email]> wrote:

Hi Nathan,

Versions:
  • Version: 2.1.1-SNAPSHOT
  • Grails version: 2.5.5
  • Groovy version: 2.4.4
  • JVM version: 1.8.0_212
  • Servlet Container Version: Apache Tomcat/8.5.23

I'm stumped. I've set up a new organism, and I can't create any 2-tier annotations (gene, pseudogene, etc) from any of the gffs that I've loaded. I've attached a screenshot of the error, a reference fasta and gff example. Also below is what catalina.out tells me.

I can create repeat_region and transposable_element annotations.

I don't see this behavior on any of the other organisms that we have loaded.

Any ideas?

Thank you!

Monica

2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - CAUGHT ERROR through websocket call: java.lang.reflect.InvocationTargetException
2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - THROWING PARENT ERROR instead through reflection: groovy.lang.GroovyRuntimeException: Ambiguous method overloading for method java.lang.Integer#div.
Cannot resolve which method to invoke for [null] due to overlapping prototypes between:
        [class java.lang.Character]
        [class java.lang.Number]
2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - exception groovy.lang.GroovyRuntimeException: Ambiguous method overloading for method java.lang.Integer#div.
Cannot resolve which method to invoke for [null] due to overlapping prototypes between:
        [class java.lang.Character]
        [class java.lang.Number]
2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - exception message Ambiguous method overloading for method java.lang.Integer#div.
Cannot resolve which method to invoke for [null] due to overlapping prototypes between:
        [class java.lang.Character]
        [class java.lang.Number]
2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - username [hidden email]
2019-04-26 13:43:07,643 [Actor Thread 9] ERROR apollo.AnnotationEditorController  - error destination message: /[hidden email]
<Screen Shot 2019-04-26 at 10.12.26.png><LSTR012198-5.gff><QKKF02000013.fna>


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Re: Error "ambiguous method overloading" [EXT]

t.r.stickland@sanger.ac.uk


On 30/04/2019 21:29, Nathan Dunn wrote:
On Apr 30, 2019, at 1:26 PM, Monica Poelchau <[hidden email]> wrote:
Unfortunately we can't move to Apollo 2.3 yet, since we're having issues with the track styles (introns not showing up).

I think this is tractable.  My understanding is that there is some custom CSS that needs to be modified to use namespaces properly in the newer JBrowse.

This sounds like issues we (genedb.org) were having for a while; have a look at https://github.com/GMOD/Apollo/issues/2039

Specifically, it was a really simple fix in the trackList.json files:
TRACK_STYLE_CLASS=org_genedb_www_dummy_style_class
Defining a class there gets jbrowse to use that class, rather than whatever other (presumed problematic) styling would be used.   The class that's defined there doesn't actually have to exist, as web browsers don't object to non-existent classes.  The only purpose is safely to prevent any other style being loaded.  As you probably guessed,  org_genedb_www_dummy_style_class does not exist.

We did have other issues with intron rendering prior to Apollo 2.3 (connected to the NeatHTMLFeatures/NeatCanvasFeatures plugins, which I had to disable for a while), and perhaps you have experienced some of these too -- but these were all fixed with 2.3.

tim

-- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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