add new organism

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add new organism

Quanwei Zhang
Hello:

Thank again for your previous help.

After I run command "apollo run-local", I can open the web page in web browser.  But when I tried to add a new organism, it always reported "Error" or "Failed" message as shown below in blue.

The attached file shows the information I put and now it says "processing" for about 20 minutes, but I guess there must be something wrong, because I am just trying to upload 2 reads (with length 80145943bp,10970156bp). The attached figure shows the information I input to add the new organism. As shown in it, the data I generated are under "/Users/qwzhang/Documents/dataAnalysis/BeaverNew/data/Apollo/Apollo2/data.apollo" (with  "seq        trackList.json    tracks        tracks.conf"). I used the following commands to generate the files.

Apollo/jbrowse/bin/prepare-refseqs.pl --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/prepare-refseqs.pl --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/flatfile-to-json.pl --gff ./data.input/Aldh1a1.geneName.gtf --type exon --trackLabel MAKER --out ./data.apollo



Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application

Configuring Shiro ...

Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Server running. Browse to http://localhost:8082/apollo
| Error 2019-01-14 10:22:25,901 [http-nio-8082-exec-9] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,174 [http-nio-8082-exec-4] ERROR apollo.UserController  - User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,209 [http-nio-8082-exec-3] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:26:34,612 [http-nio-8082-exec-7] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.PermissionService  - Failed to authenticate user
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.SecurityFilters  - Authentication failed

Any suggestions. Thanks

Best
Quanwei




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addNewOrganism.pdf (606K) Download Attachment
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Re: add new organism

nathandunn

Looks like everything you are doing SHOULD work.  

Unless you have a lot of scaffolds (>50K) it shouldn’t take longer than a minute.  5K scaffolds takes me roughly 20 seconds to add, so I agree that something is wrong. 


If you don’t see anything produced in your catalina.out (as below) can you send me your javascript console and network output tabs? 

I am surprised you aren’t seeing any type of error on the backend when you click on “add organism” though. 


I think the directory name seems fine assuming you have read access to it.  

Nathan


On Jan 14, 2019, at 7:51 AM, Quanwei Zhang <[hidden email]> wrote:

Hello:

Thank again for your previous help.

After I run command "apollo run-local", I can open the web page in web browser.  But when I tried to add a new organism, it always reported "Error" or "Failed" message as shown below in blue.

The attached file shows the information I put and now it says "processing" for about 20 minutes, but I guess there must be something wrong, because I am just trying to upload 2 reads (with length 80145943bp,10970156bp). The attached figure shows the information I input to add the new organism. As shown in it, the data I generated are under "/Users/qwzhang/Documents/dataAnalysis/BeaverNew/data/Apollo/Apollo2/data.apollo" (with  "seq        trackList.json    tracks        tracks.conf"). I used the following commands to generate the files.

Apollo/jbrowse/bin/prepare-refseqs.pl --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/prepare-refseqs.pl --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/flatfile-to-json.pl --gff ./data.input/Aldh1a1.geneName.gtf --type exon --trackLabel MAKER --out ./data.apollo



Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application

Configuring Shiro ...

Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Server running. Browse to http://localhost:8082/apollo
| Error 2019-01-14 10:22:25,901 [http-nio-8082-exec-9] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,174 [http-nio-8082-exec-4] ERROR apollo.UserController  - User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,209 [http-nio-8082-exec-3] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:26:34,612 [http-nio-8082-exec-7] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.PermissionService  - Failed to authenticate user
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.SecurityFilters  - Authentication failed

Any suggestions. Thanks

Best
Quanwei
<addNewOrganism.pdf>


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Re: add new organism

Quanwei Zhang
Dear Nathan:

Thank you for your reply.
(1) In my example, I have only two sequences (with length 80145943bp,10970156bp) to upload.
(2) I did not get new information in catalina.out.
(3) For "javascript console" did you mean what shown in the attached file? In this example, I just add the sequence (no gff).
(4) Would you please explain what do you mean by "network output tabs"?

Besides the information I gave, do I need to provide information for "Search database"?

Many thanks

Best
Quanwei

Nathan Dunn <[hidden email]> 于2019年1月14日周一 下午1:15写道:

Looks like everything you are doing SHOULD work.  

Unless you have a lot of scaffolds (>50K) it shouldn’t take longer than a minute.  5K scaffolds takes me roughly 20 seconds to add, so I agree that something is wrong. 


If you don’t see anything produced in your catalina.out (as below) can you send me your javascript console and network output tabs? 

I am surprised you aren’t seeing any type of error on the backend when you click on “add organism” though. 


I think the directory name seems fine assuming you have read access to it.  

Nathan


On Jan 14, 2019, at 7:51 AM, Quanwei Zhang <[hidden email]> wrote:

Hello:

Thank again for your previous help.

After I run command "apollo run-local", I can open the web page in web browser.  But when I tried to add a new organism, it always reported "Error" or "Failed" message as shown below in blue.

The attached file shows the information I put and now it says "processing" for about 20 minutes, but I guess there must be something wrong, because I am just trying to upload 2 reads (with length 80145943bp,10970156bp). The attached figure shows the information I input to add the new organism. As shown in it, the data I generated are under "/Users/qwzhang/Documents/dataAnalysis/BeaverNew/data/Apollo/Apollo2/data.apollo" (with  "seq        trackList.json    tracks        tracks.conf"). I used the following commands to generate the files.

Apollo/jbrowse/bin/prepare-refseqs.pl --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/prepare-refseqs.pl --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/flatfile-to-json.pl --gff ./data.input/Aldh1a1.geneName.gtf --type exon --trackLabel MAKER --out ./data.apollo



Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application

Configuring Shiro ...

Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Server running. Browse to http://localhost:8082/apollo
| Error 2019-01-14 10:22:25,901 [http-nio-8082-exec-9] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,174 [http-nio-8082-exec-4] ERROR apollo.UserController  - User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,209 [http-nio-8082-exec-3] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:26:34,612 [http-nio-8082-exec-7] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.PermissionService  - Failed to authenticate user
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.SecurityFilters  - Authentication failed

Any suggestions. Thanks

Best
Quanwei
<addNewOrganism.pdf>


This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





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NewExample.pdf (1M) Download Attachment
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Re: add new organism

nathandunn

That’s exactly right.  It looks like its getting unparseable data (just a guess).  If you click on the tab you can see what the query is and click on the query preview (and copy and paste the response, as well) and hopefully we can see what’s wrong. 

Nathan






On Jan 14, 2019, at 12:40 PM, Quanwei Zhang <[hidden email]> wrote:

Dear Nathan:

Thank you for your reply.
(1) In my example, I have only two sequences (with length 80145943bp,10970156bp) to upload.
(2) I did not get new information in catalina.out.
(3) For "javascript console" did you mean what shown in the attached file? In this example, I just add the sequence (no gff).
(4) Would you please explain what do you mean by "network output tabs"?

Besides the information I gave, do I need to provide information for "Search database"?

Many thanks

Best
Quanwei

Nathan Dunn <[hidden email]> 于2019年1月14日周一 下午1:15写道:

Looks like everything you are doing SHOULD work.  

Unless you have a lot of scaffolds (>50K) it shouldn’t take longer than a minute.  5K scaffolds takes me roughly 20 seconds to add, so I agree that something is wrong. 


If you don’t see anything produced in your catalina.out (as below) can you send me your javascript console and network output tabs? 

I am surprised you aren’t seeing any type of error on the backend when you click on “add organism” though. 


I think the directory name seems fine assuming you have read access to it.  

Nathan


On Jan 14, 2019, at 7:51 AM, Quanwei Zhang <[hidden email]> wrote:

Hello:

Thank again for your previous help.

After I run command "apollo run-local", I can open the web page in web browser.  But when I tried to add a new organism, it always reported "Error" or "Failed" message as shown below in blue.

The attached file shows the information I put and now it says "processing" for about 20 minutes, but I guess there must be something wrong, because I am just trying to upload 2 reads (with length 80145943bp,10970156bp). The attached figure shows the information I input to add the new organism. As shown in it, the data I generated are under "/Users/qwzhang/Documents/dataAnalysis/BeaverNew/data/Apollo/Apollo2/data.apollo" (with  "seq        trackList.json    tracks        tracks.conf"). I used the following commands to generate the files.

Apollo/jbrowse/bin/prepare-refseqs.pl --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/prepare-refseqs.pl --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/flatfile-to-json.pl --gff ./data.input/Aldh1a1.geneName.gtf --type exon --trackLabel MAKER --out ./data.apollo



Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application

Configuring Shiro ...

Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Server running. Browse to http://localhost:8082/apollo
| Error 2019-01-14 10:22:25,901 [http-nio-8082-exec-9] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,174 [http-nio-8082-exec-4] ERROR apollo.UserController  - User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,209 [http-nio-8082-exec-3] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:26:34,612 [http-nio-8082-exec-7] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.PermissionService  - Failed to authenticate user
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.SecurityFilters  - Authentication failed

Any suggestions. Thanks

Best
Quanwei
<addNewOrganism.pdf>


This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

<NewExample.pdf>


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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: add new organism

Quanwei Zhang
Dear Nathan:

Thanks. Now I can upload some data. But it seems there may be still some error. Please see the attached figures for "Console" and "Network".

Before I "add the new organism", I used the following command to prepare the data. Then I provide the directory of data.apollo when I "add the new organism". But I can only see the sequence file, no gene structure information from GFF. Isn't this something abnormal? Data under ./data.apollo include "seq        trackList.json    tracks        tracks.conf".

jbrowse/bin/prepare-refseqs.pl --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
jbrowse/bin/prepare-refseqs.pl --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
jbrowse/bin/flatfile-to-json.pl --gff ./data.input/Aldh1a1.geneName.gtf --type exon --trackLabel MAKER --out ./data.apollo


##the GFF file are in the following format including information for exons and CDS
Contig2667      maker   exon    11929   11954   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    12150   12251   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    12872   12979   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    13499   13569   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    14822   14955   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    15404   15498   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    21086   21187   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    21808   21915   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    22435   22505   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    23706   23839   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    24286   24380   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    29579   29680   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    30301   30408   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    30928   31036   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     11929   11954   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     12150   12251   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     12872   12979   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     13499   13569   .       -       1       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     14822   14955   .       -       0       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     15404   15498   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     21086   21187   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     21808   21915   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     22435   22505   .       -       1       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     23706   23839   .       -       0       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     24286   24380   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     29579   29680   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     30301   30408   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     30928   31036   .       -       0       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    154799  154971  .       +       .       transcript_id "UNKNOWN_1066"; gene_id "UNKNOWN_1066"; gene_name "UNKNOWN_1066";


Thanks

Best
Quanwei


Nathan Dunn <[hidden email]> 于2019年1月14日周一 下午7:53写道:

That’s exactly right.  It looks like its getting unparseable data (just a guess).  If you click on the tab you can see what the query is and click on the query preview (and copy and paste the response, as well) and hopefully we can see what’s wrong. 

Nathan






On Jan 14, 2019, at 12:40 PM, Quanwei Zhang <[hidden email]> wrote:

Dear Nathan:

Thank you for your reply.
(1) In my example, I have only two sequences (with length 80145943bp,10970156bp) to upload.
(2) I did not get new information in catalina.out.
(3) For "javascript console" did you mean what shown in the attached file? In this example, I just add the sequence (no gff).
(4) Would you please explain what do you mean by "network output tabs"?

Besides the information I gave, do I need to provide information for "Search database"?

Many thanks

Best
Quanwei

Nathan Dunn <[hidden email]> 于2019年1月14日周一 下午1:15写道:

Looks like everything you are doing SHOULD work.  

Unless you have a lot of scaffolds (>50K) it shouldn’t take longer than a minute.  5K scaffolds takes me roughly 20 seconds to add, so I agree that something is wrong. 


If you don’t see anything produced in your catalina.out (as below) can you send me your javascript console and network output tabs? 

I am surprised you aren’t seeing any type of error on the backend when you click on “add organism” though. 


I think the directory name seems fine assuming you have read access to it.  

Nathan


On Jan 14, 2019, at 7:51 AM, Quanwei Zhang <[hidden email]> wrote:

Hello:

Thank again for your previous help.

After I run command "apollo run-local", I can open the web page in web browser.  But when I tried to add a new organism, it always reported "Error" or "Failed" message as shown below in blue.

The attached file shows the information I put and now it says "processing" for about 20 minutes, but I guess there must be something wrong, because I am just trying to upload 2 reads (with length 80145943bp,10970156bp). The attached figure shows the information I input to add the new organism. As shown in it, the data I generated are under "/Users/qwzhang/Documents/dataAnalysis/BeaverNew/data/Apollo/Apollo2/data.apollo" (with  "seq        trackList.json    tracks        tracks.conf"). I used the following commands to generate the files.

Apollo/jbrowse/bin/prepare-refseqs.pl --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/prepare-refseqs.pl --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/flatfile-to-json.pl --gff ./data.input/Aldh1a1.geneName.gtf --type exon --trackLabel MAKER --out ./data.apollo



Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application

Configuring Shiro ...

Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Server running. Browse to http://localhost:8082/apollo
| Error 2019-01-14 10:22:25,901 [http-nio-8082-exec-9] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,174 [http-nio-8082-exec-4] ERROR apollo.UserController  - User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,209 [http-nio-8082-exec-3] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:26:34,612 [http-nio-8082-exec-7] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.PermissionService  - Failed to authenticate user
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.SecurityFilters  - Authentication failed

Any suggestions. Thanks

Best
Quanwei
<addNewOrganism.pdf>


This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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<NewExample.pdf>


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Re: add new organism

nathandunn

It should produce a tracks directory with that label in the directory provided (and added to the trackList.json). 

That being said, at a minimum you should have transcript data in your GFF3.  Typically I would use type of mRNA or transcript to process the GFF3. 

Also, there is a maker2jbrowse command in JBrowse (I have not tried it), that might simplify this, as well.   



But depending on what you want, you are now more in the JBrowse realm and I am going to cross-post you there.  

Might be worth perusing the FAQ and a few other docs:



Hope this helps,

Nathan


On Jan 15, 2019, at 7:08 AM, Quanwei Zhang <[hidden email]> wrote:

Dear Nathan:

Thanks. Now I can upload some data. But it seems there may be still some error. Please see the attached figures for "Console" and "Network".

Before I "add the new organism", I used the following command to prepare the data. Then I provide the directory of data.apollo when I "add the new organism". But I can only see the sequence file, no gene structure information from GFF. Isn't this something abnormal? Data under ./data.apollo include "seq        trackList.json    tracks        tracks.conf".

jbrowse/bin/prepare-refseqs.pl --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
jbrowse/bin/prepare-refseqs.pl --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
jbrowse/bin/flatfile-to-json.pl --gff ./data.input/Aldh1a1.geneName.gtf --type exon --trackLabel MAKER --out ./data.apollo


##the GFF file are in the following format including information for exons and CDS
Contig2667      maker   exon    11929   11954   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    12150   12251   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    12872   12979   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    13499   13569   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    14822   14955   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    15404   15498   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    21086   21187   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    21808   21915   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    22435   22505   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    23706   23839   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    24286   24380   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    29579   29680   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    30301   30408   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    30928   31036   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     11929   11954   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     12150   12251   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     12872   12979   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     13499   13569   .       -       1       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     14822   14955   .       -       0       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     15404   15498   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     21086   21187   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     21808   21915   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     22435   22505   .       -       1       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     23706   23839   .       -       0       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     24286   24380   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     29579   29680   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     30301   30408   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     30928   31036   .       -       0       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    154799  154971  .       +       .       transcript_id "UNKNOWN_1066"; gene_id "UNKNOWN_1066"; gene_name "UNKNOWN_1066";


Thanks

Best
Quanwei


Nathan Dunn <[hidden email]> 于2019年1月14日周一 下午7:53写道:

That’s exactly right.  It looks like its getting unparseable data (just a guess).  If you click on the tab you can see what the query is and click on the query preview (and copy and paste the response, as well) and hopefully we can see what’s wrong. 

Nathan


<Edited.png>

<Screen Shot 2019-01-14 at 4.51.18 PM.png><Screen Shot 2019-01-14 at 4.51.22 PM.png>



On Jan 14, 2019, at 12:40 PM, Quanwei Zhang <[hidden email]> wrote:

Dear Nathan:

Thank you for your reply.
(1) In my example, I have only two sequences (with length 80145943bp,10970156bp) to upload.
(2) I did not get new information in catalina.out.
(3) For "javascript console" did you mean what shown in the attached file? In this example, I just add the sequence (no gff).
(4) Would you please explain what do you mean by "network output tabs"?

Besides the information I gave, do I need to provide information for "Search database"?

Many thanks

Best
Quanwei

Nathan Dunn <[hidden email]> 于2019年1月14日周一 下午1:15写道:

Looks like everything you are doing SHOULD work.  

Unless you have a lot of scaffolds (>50K) it shouldn’t take longer than a minute.  5K scaffolds takes me roughly 20 seconds to add, so I agree that something is wrong. 


If you don’t see anything produced in your catalina.out (as below) can you send me your javascript console and network output tabs? 

I am surprised you aren’t seeing any type of error on the backend when you click on “add organism” though. 


I think the directory name seems fine assuming you have read access to it.  

Nathan


On Jan 14, 2019, at 7:51 AM, Quanwei Zhang <[hidden email]> wrote:

Hello:

Thank again for your previous help.

After I run command "apollo run-local", I can open the web page in web browser.  But when I tried to add a new organism, it always reported "Error" or "Failed" message as shown below in blue.

The attached file shows the information I put and now it says "processing" for about 20 minutes, but I guess there must be something wrong, because I am just trying to upload 2 reads (with length 80145943bp,10970156bp). The attached figure shows the information I input to add the new organism. As shown in it, the data I generated are under "/Users/qwzhang/Documents/dataAnalysis/BeaverNew/data/Apollo/Apollo2/data.apollo" (with  "seq        trackList.json    tracks        tracks.conf"). I used the following commands to generate the files.

Apollo/jbrowse/bin/prepare-refseqs.pl --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/prepare-refseqs.pl --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/flatfile-to-json.pl --gff ./data.input/Aldh1a1.geneName.gtf --type exon --trackLabel MAKER --out ./data.apollo



Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application

Configuring Shiro ...

Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Server running. Browse to http://localhost:8082/apollo
| Error 2019-01-14 10:22:25,901 [http-nio-8082-exec-9] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,174 [http-nio-8082-exec-4] ERROR apollo.UserController  - User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,209 [http-nio-8082-exec-3] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:26:34,612 [http-nio-8082-exec-7] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.PermissionService  - Failed to authenticate user
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.SecurityFilters  - Authentication failed

Any suggestions. Thanks

Best
Quanwei
<addNewOrganism.pdf>


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<NewExample.pdf>


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<Console.pdf><Network.pdf>


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Re: add new organism

Loraine Guéguen
Dear Nathan and Quanwei,

Having a quick look at your posts, I see that you try to load a GTF file (and not a GFF file).
See http://jbrowse.org/docs/faq.html#how-do-i-convert-gtf-to-gff

My 2 cents.

Loraine



Le 15/01/2019 16:26, Nathan Dunn a écrit :

It should produce a tracks directory with that label in the directory provided (and added to the trackList.json). 

That being said, at a minimum you should have transcript data in your GFF3.  Typically I would use type of mRNA or transcript to process the GFF3. 

Also, there is a maker2jbrowse command in JBrowse (I have not tried it), that might simplify this, as well.   



But depending on what you want, you are now more in the JBrowse realm and I am going to cross-post you there.  

Might be worth perusing the FAQ and a few other docs:



Hope this helps,

Nathan


On Jan 15, 2019, at 7:08 AM, Quanwei Zhang <[hidden email]> wrote:

Dear Nathan:

Thanks. Now I can upload some data. But it seems there may be still some error. Please see the attached figures for "Console" and "Network".

Before I "add the new organism", I used the following command to prepare the data. Then I provide the directory of data.apollo when I "add the new organism". But I can only see the sequence file, no gene structure information from GFF. Isn't this something abnormal? Data under ./data.apollo include "seq        trackList.json    tracks        tracks.conf".

jbrowse/bin/prepare-refseqs.pl --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
jbrowse/bin/prepare-refseqs.pl --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
jbrowse/bin/flatfile-to-json.pl --gff ./data.input/Aldh1a1.geneName.gtf --type exon --trackLabel MAKER --out ./data.apollo


##the GFF file are in the following format including information for exons and CDS
Contig2667      maker   exon    11929   11954   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    12150   12251   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    12872   12979   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    13499   13569   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    14822   14955   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    15404   15498   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    21086   21187   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    21808   21915   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    22435   22505   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    23706   23839   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    24286   24380   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    29579   29680   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    30301   30408   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    30928   31036   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     11929   11954   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     12150   12251   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     12872   12979   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     13499   13569   .       -       1       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     14822   14955   .       -       0       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     15404   15498   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     21086   21187   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     21808   21915   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     22435   22505   .       -       1       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     23706   23839   .       -       0       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     24286   24380   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     29579   29680   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     30301   30408   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     30928   31036   .       -       0       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    154799  154971  .       +       .       transcript_id "UNKNOWN_1066"; gene_id "UNKNOWN_1066"; gene_name "UNKNOWN_1066";


Thanks

Best
Quanwei


Nathan Dunn <[hidden email]> 于2019年1月14日周一 下午7:53写道:

That’s exactly right.  It looks like its getting unparseable data (just a guess).  If you click on the tab you can see what the query is and click on the query preview (and copy and paste the response, as well) and hopefully we can see what’s wrong. 

Nathan


<Edited.png>

<Screen Shot 2019-01-14 at 4.51.18 PM.png><Screen Shot 2019-01-14 at 4.51.22 PM.png>



On Jan 14, 2019, at 12:40 PM, Quanwei Zhang <[hidden email]> wrote:

Dear Nathan:

Thank you for your reply.
(1) In my example, I have only two sequences (with length 80145943bp,10970156bp) to upload.
(2) I did not get new information in catalina.out.
(3) For "javascript console" did you mean what shown in the attached file? In this example, I just add the sequence (no gff).
(4) Would you please explain what do you mean by "network output tabs"?

Besides the information I gave, do I need to provide information for "Search database"?

Many thanks

Best
Quanwei

Nathan Dunn <[hidden email]> 于2019年1月14日周一 下午1:15写道:

Looks like everything you are doing SHOULD work.  

Unless you have a lot of scaffolds (>50K) it shouldn’t take longer than a minute.  5K scaffolds takes me roughly 20 seconds to add, so I agree that something is wrong. 


If you don’t see anything produced in your catalina.out (as below) can you send me your javascript console and network output tabs? 

I am surprised you aren’t seeing any type of error on the backend when you click on “add organism” though. 


I think the directory name seems fine assuming you have read access to it.  

Nathan


On Jan 14, 2019, at 7:51 AM, Quanwei Zhang <[hidden email]> wrote:

Hello:

Thank again for your previous help.

After I run command "apollo run-local", I can open the web page in web browser.  But when I tried to add a new organism, it always reported "Error" or "Failed" message as shown below in blue.

The attached file shows the information I put and now it says "processing" for about 20 minutes, but I guess there must be something wrong, because I am just trying to upload 2 reads (with length 80145943bp,10970156bp). The attached figure shows the information I input to add the new organism. As shown in it, the data I generated are under "/Users/qwzhang/Documents/dataAnalysis/BeaverNew/data/Apollo/Apollo2/data.apollo" (with  "seq        trackList.json    tracks        tracks.conf"). I used the following commands to generate the files.

Apollo/jbrowse/bin/prepare-refseqs.pl --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/prepare-refseqs.pl --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/flatfile-to-json.pl --gff ./data.input/Aldh1a1.geneName.gtf --type exon --trackLabel MAKER --out ./data.apollo



Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application

Configuring Shiro ...

Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Server running. Browse to http://localhost:8082/apollo
| Error 2019-01-14 10:22:25,901 [http-nio-8082-exec-9] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,174 [http-nio-8082-exec-4] ERROR apollo.UserController  - User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,209 [http-nio-8082-exec-3] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:26:34,612 [http-nio-8082-exec-7] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.PermissionService  - Failed to authenticate user
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.SecurityFilters  - Authentication failed

Any suggestions. Thanks

Best
Quanwei
<addNewOrganism.pdf>


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<Console.pdf><Network.pdf>


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-- 
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS | Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





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Re: add new organism

Quanwei Zhang
Thank you all. I will try it!

Best
Quanwei

Loraine Guéguen <[hidden email]> 于2019年1月15日周二 上午10:44写道:
Dear Nathan and Quanwei,

Having a quick look at your posts, I see that you try to load a GTF file (and not a GFF file).
See http://jbrowse.org/docs/faq.html#how-do-i-convert-gtf-to-gff

My 2 cents.

Loraine



Le 15/01/2019 16:26, Nathan Dunn a écrit :

It should produce a tracks directory with that label in the directory provided (and added to the trackList.json). 

That being said, at a minimum you should have transcript data in your GFF3.  Typically I would use type of mRNA or transcript to process the GFF3. 

Also, there is a maker2jbrowse command in JBrowse (I have not tried it), that might simplify this, as well.   



But depending on what you want, you are now more in the JBrowse realm and I am going to cross-post you there.  

Might be worth perusing the FAQ and a few other docs:



Hope this helps,

Nathan


On Jan 15, 2019, at 7:08 AM, Quanwei Zhang <[hidden email][hidden email]> wrote:

Dear Nathan:

Thanks. Now I can upload some data. But it seems there may be still some error. Please see the attached figures for "Console" and "Network".

Before I "add the new organism", I used the following command to prepare the data. Then I provide the directory of data.apollo when I "add the new organism". But I can only see the sequence file, no gene structure information from GFF. Isn't this something abnormal? Data under ./data.apollo include "seq        trackList.json    tracks        tracks.conf".

jbrowse/bin/prepare-refseqs.pl --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
jbrowse/bin/prepare-refseqs.pl --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
jbrowse/bin/flatfile-to-json.pl --gff ./data.input/Aldh1a1.geneName.gtf --type exon --trackLabel MAKER --out ./data.apollo


##the GFF file are in the following format including information for exons and CDS
Contig2667      maker   exon    11929   11954   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    12150   12251   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    12872   12979   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    13499   13569   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    14822   14955   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    15404   15498   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    21086   21187   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    21808   21915   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    22435   22505   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    23706   23839   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    24286   24380   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    29579   29680   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    30301   30408   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    30928   31036   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     11929   11954   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     12150   12251   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     12872   12979   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     13499   13569   .       -       1       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     14822   14955   .       -       0       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     15404   15498   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     21086   21187   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     21808   21915   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     22435   22505   .       -       1       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     23706   23839   .       -       0       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     24286   24380   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     29579   29680   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     30301   30408   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     30928   31036   .       -       0       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    154799  154971  .       +       .       transcript_id "UNKNOWN_1066"; gene_id "UNKNOWN_1066"; gene_name "UNKNOWN_1066";


Thanks

Best
Quanwei


Nathan Dunn <[hidden email][hidden email]> 于2019年1月14日周一 下午7:53写道:

That’s exactly right.  It looks like its getting unparseable data (just a guess).  If you click on the tab you can see what the query is and click on the query preview (and copy and paste the response, as well) and hopefully we can see what’s wrong. 

Nathan


<Edited.png>

<Screen Shot 2019-01-14 at 4.51.18 PM.png><Screen Shot 2019-01-14 at 4.51.22 PM.png>



On Jan 14, 2019, at 12:40 PM, Quanwei Zhang <[hidden email]> wrote:

Dear Nathan:

Thank you for your reply.
(1) In my example, I have only two sequences (with length 80145943bp,10970156bp) to upload.
(2) I did not get new information in catalina.out.
(3) For "javascript console" did you mean what shown in the attached file? In this example, I just add the sequence (no gff).
(4) Would you please explain what do you mean by "network output tabs"?

Besides the information I gave, do I need to provide information for "Search database"?

Many thanks

Best
Quanwei

Nathan Dunn <[hidden email][hidden email]> 于2019年1月14日周一 下午1:15写道:

Looks like everything you are doing SHOULD work.  

Unless you have a lot of scaffolds (>50K) it shouldn’t take longer than a minute.  5K scaffolds takes me roughly 20 seconds to add, so I agree that something is wrong. 


If you don’t see anything produced in your catalina.out (as below) can you send me your javascript console and network output tabs? 

I am surprised you aren’t seeing any type of error on the backend when you click on “add organism” though. 


I think the directory name seems fine assuming you have read access to it.  

Nathan


On Jan 14, 2019, at 7:51 AM, Quanwei Zhang <[hidden email][hidden email]> wrote:

Hello:

Thank again for your previous help.

After I run command "apollo run-local", I can open the web page in web browser.  But when I tried to add a new organism, it always reported "Error" or "Failed" message as shown below in blue.

The attached file shows the information I put and now it says "processing" for about 20 minutes, but I guess there must be something wrong, because I am just trying to upload 2 reads (with length 80145943bp,10970156bp). The attached figure shows the information I input to add the new organism. As shown in it, the data I generated are under "/Users/qwzhang/Documents/dataAnalysis/BeaverNew/data/Apollo/Apollo2/data.apollo" (with  "seq        trackList.json    tracks        tracks.conf"). I used the following commands to generate the files.

Apollo/jbrowse/bin/prepare-refseqs.pl --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/prepare-refseqs.pl --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/flatfile-to-json.pl --gff ./data.input/Aldh1a1.geneName.gtf --type exon --trackLabel MAKER --out ./data.apollo



Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application

Configuring Shiro ...

Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Server running. Browse to http://localhost:8082/apollo
| Error 2019-01-14 10:22:25,901 [http-nio-8082-exec-9] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,174 [http-nio-8082-exec-4] ERROR apollo.UserController  - User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,209 [http-nio-8082-exec-3] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:26:34,612 [http-nio-8082-exec-7] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.PermissionService  - Failed to authenticate user
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.SecurityFilters  - Authentication failed

Any suggestions. Thanks

Best
Quanwei
<addNewOrganism.pdf>


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<NewExample.pdf>


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<Console.pdf><Network.pdf>


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-- 
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS | Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





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Re: add new organism

Quanwei Zhang
Dear Loeaine and Nathan:

Thank you for your help. Now it works.
But I have a question about the track of BAM file (read alingments). Now it seems it shows individual reads (with line connecting paired reads that far from each other). Is that correct?
But in some regions there may be thousands of reads mapped, and it seems only  few reads were shown. Can I make it show all the reads in the track? Besides, is there a way to show the pile up coverage of RNA-seq at each positions?

Thanks

Best
Quanwei

Quanwei Zhang <[hidden email]> 于2019年1月15日周二 上午11:09写道:
Thank you all. I will try it!

Best
Quanwei

Loraine Guéguen <[hidden email]> 于2019年1月15日周二 上午10:44写道:
Dear Nathan and Quanwei,

Having a quick look at your posts, I see that you try to load a GTF file (and not a GFF file).
See http://jbrowse.org/docs/faq.html#how-do-i-convert-gtf-to-gff

My 2 cents.

Loraine



Le 15/01/2019 16:26, Nathan Dunn a écrit :

It should produce a tracks directory with that label in the directory provided (and added to the trackList.json). 

That being said, at a minimum you should have transcript data in your GFF3.  Typically I would use type of mRNA or transcript to process the GFF3. 

Also, there is a maker2jbrowse command in JBrowse (I have not tried it), that might simplify this, as well.   



But depending on what you want, you are now more in the JBrowse realm and I am going to cross-post you there.  

Might be worth perusing the FAQ and a few other docs:



Hope this helps,

Nathan


On Jan 15, 2019, at 7:08 AM, Quanwei Zhang <[hidden email][hidden email]> wrote:

Dear Nathan:

Thanks. Now I can upload some data. But it seems there may be still some error. Please see the attached figures for "Console" and "Network".

Before I "add the new organism", I used the following command to prepare the data. Then I provide the directory of data.apollo when I "add the new organism". But I can only see the sequence file, no gene structure information from GFF. Isn't this something abnormal? Data under ./data.apollo include "seq        trackList.json    tracks        tracks.conf".

jbrowse/bin/prepare-refseqs.pl --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
jbrowse/bin/prepare-refseqs.pl --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
jbrowse/bin/flatfile-to-json.pl --gff ./data.input/Aldh1a1.geneName.gtf --type exon --trackLabel MAKER --out ./data.apollo


##the GFF file are in the following format including information for exons and CDS
Contig2667      maker   exon    11929   11954   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    12150   12251   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    12872   12979   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    13499   13569   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    14822   14955   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    15404   15498   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    21086   21187   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    21808   21915   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    22435   22505   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    23706   23839   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    24286   24380   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    29579   29680   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    30301   30408   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    30928   31036   .       -       .       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     11929   11954   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     12150   12251   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     12872   12979   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     13499   13569   .       -       1       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     14822   14955   .       -       0       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     15404   15498   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     21086   21187   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     21808   21915   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     22435   22505   .       -       1       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     23706   23839   .       -       0       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     24286   24380   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     29579   29680   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     30301   30408   .       -       2       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   CDS     30928   31036   .       -       0       transcript_id "VEGP1"; gene_id "VEGP1"; gene_name "VEGP1";
Contig2667      maker   exon    154799  154971  .       +       .       transcript_id "UNKNOWN_1066"; gene_id "UNKNOWN_1066"; gene_name "UNKNOWN_1066";


Thanks

Best
Quanwei


Nathan Dunn <[hidden email][hidden email]> 于2019年1月14日周一 下午7:53写道:

That’s exactly right.  It looks like its getting unparseable data (just a guess).  If you click on the tab you can see what the query is and click on the query preview (and copy and paste the response, as well) and hopefully we can see what’s wrong. 

Nathan


<Edited.png>

<Screen Shot 2019-01-14 at 4.51.18 PM.png><Screen Shot 2019-01-14 at 4.51.22 PM.png>



On Jan 14, 2019, at 12:40 PM, Quanwei Zhang <[hidden email]> wrote:

Dear Nathan:

Thank you for your reply.
(1) In my example, I have only two sequences (with length 80145943bp,10970156bp) to upload.
(2) I did not get new information in catalina.out.
(3) For "javascript console" did you mean what shown in the attached file? In this example, I just add the sequence (no gff).
(4) Would you please explain what do you mean by "network output tabs"?

Besides the information I gave, do I need to provide information for "Search database"?

Many thanks

Best
Quanwei

Nathan Dunn <[hidden email][hidden email]> 于2019年1月14日周一 下午1:15写道:

Looks like everything you are doing SHOULD work.  

Unless you have a lot of scaffolds (>50K) it shouldn’t take longer than a minute.  5K scaffolds takes me roughly 20 seconds to add, so I agree that something is wrong. 


If you don’t see anything produced in your catalina.out (as below) can you send me your javascript console and network output tabs? 

I am surprised you aren’t seeing any type of error on the backend when you click on “add organism” though. 


I think the directory name seems fine assuming you have read access to it.  

Nathan


On Jan 14, 2019, at 7:51 AM, Quanwei Zhang <[hidden email][hidden email]> wrote:

Hello:

Thank again for your previous help.

After I run command "apollo run-local", I can open the web page in web browser.  But when I tried to add a new organism, it always reported "Error" or "Failed" message as shown below in blue.

The attached file shows the information I put and now it says "processing" for about 20 minutes, but I guess there must be something wrong, because I am just trying to upload 2 reads (with length 80145943bp,10970156bp). The attached figure shows the information I input to add the new organism. As shown in it, the data I generated are under "/Users/qwzhang/Documents/dataAnalysis/BeaverNew/data/Apollo/Apollo2/data.apollo" (with  "seq        trackList.json    tracks        tracks.conf"). I used the following commands to generate the files.

Apollo/jbrowse/bin/prepare-refseqs.pl --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/prepare-refseqs.pl --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
Apollo/jbrowse/bin/flatfile-to-json.pl --gff ./data.input/Aldh1a1.geneName.gtf --type exon --trackLabel MAKER --out ./data.apollo



Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application

Configuring Shiro ...

Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Server running. Browse to http://localhost:8082/apollo
| Error 2019-01-14 10:22:25,901 [http-nio-8082-exec-9] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,174 [http-nio-8082-exec-4] ERROR apollo.UserController  - User does not have permission for any organisms.
| Error 2019-01-14 10:22:26,209 [http-nio-8082-exec-3] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-14 10:26:34,612 [http-nio-8082-exec-7] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.PermissionService  - Failed to authenticate user
2019-01-14 10:26:34,613 [http-nio-8082-exec-7] WARN  apollo.SecurityFilters  - Authentication failed

Any suggestions. Thanks

Best
Quanwei
<addNewOrganism.pdf>


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<NewExample.pdf>


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<Console.pdf><Network.pdf>


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-- 
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS | Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





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