Re: [Gmod-ajax] [apollo] add new organism

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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:

http://gmod.org/wiki/JBrowse_FAQ#How_do_I_setup_a_GFF_track.3F <http://gmod.org/wiki/JBrowse_FAQ#How_do_I_setup_a_GFF_track.3F>
http://gmod.827538.n3.nabble.com/JBrowse-Support-f815920.html <http://gmod.827538.n3.nabble.com/JBrowse-Support-f815920.html>

As well as the tutorial:  http://jbrowse.org/docs/tutorial_classic.html <http://jbrowse.org/docs/tutorial_classic.html> 
http://gmod.org/wiki/JBrowse_Tutorial#Features_from_GFF3_or_BED_files <http://gmod.org/wiki/JBrowse_Tutorial#Features_from_GFF3_or_BED_files>

Hope this helps,

Nathan

> On Jan 15, 2019, at 7:08 AM, Quanwei Zhang <qwz...@gm...> 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 <http://prepare-refseqs.pl/> --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo 
> jbrowse/bin/prepare-refseqs.pl <http://prepare-refseqs.pl/> --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
> jbrowse/bin/flatfile-to-json.pl <http://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 <nat...@lb... <mailto:nat...@lb...>> 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 <qwz...@gm... <mailto:qwz...@gm...>> 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 <nat...@lb... <mailto:nat...@lb...>> 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 <qwz...@gm... <mailto:qwz...@gm...>> 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 <http://prepare-refseqs.pl/> --fasta  ./data.input/Aldh1a1.folded.fasta --out ./data.apollo 
>>> Apollo/jbrowse/bin/prepare-refseqs.pl <http://prepare-refseqs.pl/> --indexed_fasta ./data.input/Aldh1a1.folded.fasta --out ./data.apollo
>>> Apollo/jbrowse/bin/flatfile-to-json.pl <http://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 <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/ <http://genomearchitect.org/>
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>>> 
>> 
>> 
>> 
>> 
>> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
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>> 
>> <NewExample.pdf>
>> 
>> 
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>> 
> 
> 
> 
> 
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <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 sy...@li... <mailto:sy...@li...> | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 
> 
> <Console.pdf><Network.pdf>
> 
> 
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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> 