Re: Gff import issues in jbrowse

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Re: Gff import issues in jbrowse

Scott Cain
Hi Sheri,

I'm cc'ing this to the JBrowse mailing list; please keep it cc'ed when you reply.

When asking for help of this sort, it's really helpful to know what the exact command you used was and a sample of the GFF file you were process.  You might also want to check out the JBrowse FAQ: http://gmod.org/wiki/JBrowse_FAQ and make sure you clear you cache when adding data or changing the config files, since browsers tend to "strongly" cache things like javascript and config files.

Scott


On Tue, Sep 20, 2016 at 5:11 PM, Sanders, Sheri <[hidden email]> wrote:

I'm embarking on producing a genome browser for a group here at IU. I ran into issues using tripal,  and began working on jbrowse directly.   However,  now I cannot load a gff3 track.

I tried using the flatfile-to-json.pl utility, which takes the data and loads happily.  However,  on the browser,  it won't display, it just says html unspecified error.  I can get the tutorial to work, so it doesn't appear to be my perl, system settings,  etc.   My gff3 file has nine columns, but i don't know what other things to look for in that arena.  I've tried  a bunch of options, json or conf files,  etc. To no avail.

Any suggestions? I could include the head of my file if that helps (tomorrow when I can access that vm again).

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.



--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Gff import issues in jbrowse

ssanders

​Thanks for forwarding my plea for help!  I was in a conference, so I didn't have my files with me.  Here are more details.  Thank you to everyone in advance for the help!


#What I am trying to do

I am tasked with creating a genome browser for a lab here at Indiana University.  I will likely be doing more, so I want to understand how this software works.  My immediate problem is the that I cannot seem to load a gff3 file.  I am doing all of this on a Ubuntu 16.04 virtual machine.


#What I have as input

1)This is the first 10 lines of the real data gff:

<gff3 real>

##gff-version 3

scaffold1039_len3753 . contig 1 3752 . . . ID=scaffold1039_len3753;Name=scaffold1039_len3753

###

scaffold1039_len3753 repeatmasker match 933 967 12 + . ID=scaffold1039_len3753:hit:551560:1.3.0.0;Name=species:%28AACA%29n|genus:Simple_repeat;Target=species:%28AACA%29n|genus:Simple_repeat 1 35 +

scaffold1039_len3753 repeatmasker match_part 933 967 12 + . ID=scaffold1039_len3753:hsp:1576442:1.3.0.0;Parent=scaffold1039_len3753:hit:551560:1.3.0.0;Target=species:%2528AACA%2529n|genus:Simple_repeat 1 35 +

###

scaffold134_len380039 . contig 1 380038 . . . ID=scaffold134_len380039;Name=scaffold134_len380039

scaffold134_len380039 maker gene 67 7814 . + . ID=maker-scaffold134_len380039-exonerate_est2genome-gene-0.0;Name=maker-scaffold134_len380039-exonerate_est2genome-gene-0.0

scaffold134_len380039 maker mRNA 67 7814 4193 + . ID=maker-scaffold134_len380039-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-scaffold134_len380039-exonerate_est2genome-gene-0.0;Name=maker-scaffold134_len380039-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.03;_eAED=0.04;_QI=133|1|1|1|0|0|26|895|1054

scaffold134_len380039 maker mRNA 218 7814 4266 + . ID=maker-scaffold134_len380039-exonerate_est2genome-gene-0.0-mRNA-2;Parent=maker-scaffold134_len380039-exonerate_est2genome-gene-0.0;Name=maker-scaffold134_len380039-exonerate_est2genome-gene-0.0-mRNA-2;_AED=0.03;_eAED=0.03;_QI=206|1|1|1|0|0|25|895|1054


2)This is the first 10 lines of a simplified gff that I have been using to narrow down the issue: 

<gff3 simplified - the one I used>

##gff-version 3

scaffold134 . contig 1 3752 . . . ID=scaffold134;Name=scaffold134

scaffold134 . contig 1 380038 . . . ID=scaffold134;Name=scaffold134

scaffold134 maker gene 67 7814 . + . ID=gene0.0;Name=gene0.0

scaffold134 maker mRNA 67 7814 4193 + . ID=mRNA-1;Name=mRNA-1;Parent=gene0.0

scaffold134 maker mRNA 218 7814 4266 + . ID=mRNA-2;Name=mRNA-1;Parent=gene0.0

scaffold134 maker mRNA 67 4870 3151 + . ID=mRNA-3;Name=mRNA-1;Parent=gene0.0

scaffold134 maker mRNA 67 4225 2710 + . ID=mRNA-4;Name=mRNA-1;Parent=gene0.0

scaffold134 maker exon 67 186 . + . ID=exon:84824;Name=exon:84824;Parent=mRNA-1

scaffold134 maker exon 411 583 . + . ID=exon:84825;Name=exon:84825;Parent=mRNA-1


#Initial thoughts and Command I use

Since I can run the tutorial data, with the track popping up beautifully, I don’t believe this is an issue with the browser itself or anything within the top level .conf files.  Maybe I’m wrong here, but the input doesn’t seem to be importing correctly.  As such, here is the most recent command I was using.  I have tried many things, but this one matches the output below: 


pwd -> /var/www/jbrowse/JBrowse-1.12.1

bin/flatfile-to-json.pl --gff test_data/raw/PA42/tmp --out test_data/json/ --trackType CanvasFeatures --trackLabel test


#output I have

When I check the browser on private (non-caching) browser window, I see the following less than helpful error:

<see attached image>


Other output includes the changes to the trackData.json, trackList.json, and tracks.conf.  The trackData.json does not appear to be filling in the same way as the example, furthering my thoughts that it is an input issue.


<trackList.json>

{"formatVersion":1,"featureCount":3,"histograms":{"meta":[{"basesPerBin":"500000","arrayParams":{"urlTemplate":"hist-500000-{Chunk}.json","chunkSize":10000,"length":1}}],"stats":[{"mean":3,"basesPerBin":"500000","max":3}]},"intervals":{"urlTemplate":"lf-{Chunk}.json","classes":[{"attributes":["Start","End","Strand","Id","Seq_id","Type","Name"],"isArrayAttr":{}},{"attributes":["Start","End","Strand","Seq_id","Type","Name","Id"],"isArrayAttr":{}},{"isArrayAttr":{"Subfeatures":1},"attributes":["Start","End","Strand","Type","Subfeatures","Seq_id","Source","Id","Name"]},{"isArrayAttr":{"Subfeatures":1},"attributes":["Start","End","Strand","Seq_id","Subfeatures","Type","Id","Source","Score","Name"]},{"attributes":["Start","End","Strand","Seq_id","Type","Id","Source","Name"],"isArrayAttr":{}},{"attributes":["Start","End","Strand","Source","Id","Name","Type","Seq_id"],"isArrayAttr":{}},{"attributes":["Start","End","Strand","Type","Seq_id","Score","Source","Id","Name"],"isArrayAttr":{}},{"attributes":["Start","End","Strand","Name","Source","Score","Id","Type","Seq_id"],"isArrayAttr":{}},{"attributes":["Start","End","Strand","Seq_id","Type","Name","Id","Source","Score"],"isArrayAttr":{}},{"isArrayAttr":{"Sublist":1},"attributes":["Start","End","Chunk"]}],"count":3,"maxEnd":380038,"nclist":[[1,0,380038,0,"scaffold134","contig","scaffold134","scaffold134",{"Sublist":[[0,0,3752,0,"scaffold134","scaffold134","contig","scaffold134"],[2,66,7814,1,"gene",[[3,66,7814,1,"scaffold134",[[4,66,186,1,"scaffold134","exon","exon:84824","maker","exon:84824"],[5,410,583,1,"maker","exon:84825","exon:84825","exon","scaffold134"]],"mRNA","mRNA-1","maker",4193,"mRNA-1"],[6,217,7814,1,"mRNA","scaffold134",4266,"maker","mRNA-2","mRNA-1"],[7,66,4870,1,"mRNA-1","maker",3151,"mRNA-3","mRNA","scaffold134"],[8,66,4225,1,"scaffold134","mRNA","mRNA-1","mRNA-4","maker",2710]],"scaffold134","maker","gene0.0","gene0.0"]]}]],"lazyClass":9,"minStart":0}}


<trackList.json>

{

   "formatVersion" : 1,

   "tracks" : [

      {

         "chunkSize" : 20000,

         "type" : "SequenceTrack",

         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",

         "label" : "DNA",

         "key" : "Reference sequence",

         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",

         "category" : "Reference sequence"

      },

      {

         "trackType" : "CanvasFeatures",

         "style" : {

            "className" : "feature"

         },

         "storeClass" : "JBrowse/Store/SeqFeature/NCList",

         "label" : "test",

         "compress" : 0,

         "type" : "CanvasFeatures",

         "key" : "test",

         "urlTemplate" : "tracks/test/{refseq}/trackData.json"

      }

   ]

}


<tracks.conf>

#Empty



Insights?



Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

From: Scott Cain <[hidden email]>
Sent: Wednesday, September 21, 2016 12:06 PM
To: Sanders, Sheri; [hidden email]
Subject: Re: Gff import issues in jbrowse
 
Hi Sheri,

I'm cc'ing this to the JBrowse mailing list; please keep it cc'ed when you reply.

When asking for help of this sort, it's really helpful to know what the exact command you used was and a sample of the GFF file you were process.  You might also want to check out the JBrowse FAQ: http://gmod.org/wiki/JBrowse_FAQ and make sure you clear you cache when adding data or changing the config files, since browsers tend to "strongly" cache things like javascript and config files.

Scott


On Tue, Sep 20, 2016 at 5:11 PM, Sanders, Sheri <[hidden email]> wrote:

I'm embarking on producing a genome browser for a group here at IU. I ran into issues using tripal,  and began working on jbrowse directly.   However,  now I cannot load a gff3 track.

I tried using the flatfile-to-json.pl utility, which takes the data and loads happily.  However,  on the browser,  it won't display, it just says html unspecified error.  I can get the tutorial to work, so it doesn't appear to be my perl, system settings,  etc.   My gff3 file has nine columns, but i don't know what other things to look for in that arena.  I've tried  a bunch of options, json or conf files,  etc. To no avail.

Any suggestions? I could include the head of my file if that helps (tomorrow when I can access that vm again).

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Gff import issues in jbrowse

Ke Jiang
In reply to this post by Scott Cain
Flatfile-to-json.pl didn't throw any error?

On Wednesday, September 21, 2016, Scott Cain <[hidden email]> wrote:
Hi Sheri,

I'm cc'ing this to the JBrowse mailing list; please keep it cc'ed when you reply.

When asking for help of this sort, it's really helpful to know what the exact command you used was and a sample of the GFF file you were process.  You might also want to check out the JBrowse FAQ: http://gmod.org/wiki/JBrowse_FAQ and make sure you clear you cache when adding data or changing the config files, since browsers tend to "strongly" cache things like javascript and config files.

Scott


On Tue, Sep 20, 2016 at 5:11 PM, Sanders, Sheri <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;ss93@iu.edu&#39;);" target="_blank">ss93@...> wrote:

I'm embarking on producing a genome browser for a group here at IU. I ran into issues using tripal,  and began working on jbrowse directly.   However,  now I cannot load a gff3 track.

I tried using the flatfile-to-json.pl utility, which takes the data and loads happily.  However,  on the browser,  it won't display, it just says html unspecified error.  I can get the tutorial to work, so it doesn't appear to be my perl, system settings,  etc.   My gff3 file has nine columns, but i don't know what other things to look for in that arena.  I've tried  a bunch of options, json or conf files,  etc. To no avail.

Any suggestions? I could include the head of my file if that helps (tomorrow when I can access that vm again).

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Gff import issues in jbrowse

ssanders
No error from flatfile-to-json.pl.  Really having a hard time troubleshooting this one,  with the only error being "HTML unspecified error"!

S

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

________________________________________
From: Ke Jiang [[hidden email]]
Sent: Wednesday, September 21, 2016 9:11 PM
To: Scott Cain
Cc: Sanders, Sheri; [hidden email]
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse

Flatfile-to-json.pl didn't throw any error?

On Wednesday, September 21, 2016, Scott Cain <[hidden email]<mailto:[hidden email]>> wrote:
Hi Sheri,

I'm cc'ing this to the JBrowse mailing list; please keep it cc'ed when you reply.

When asking for help of this sort, it's really helpful to know what the exact command you used was and a sample of the GFF file you were process.  You might also want to check out the JBrowse FAQ: http://gmod.org/wiki/JBrowse_FAQ and make sure you clear you cache when adding data or changing the config files, since browsers tend to "strongly" cache things like javascript and config files.

Scott


On Tue, Sep 20, 2016 at 5:11 PM, Sanders, Sheri <[hidden email]> wrote:

I'm embarking on producing a genome browser for a group here at IU. I ran into issues using tripal,  and began working on jbrowse directly.   However,  now I cannot load a gff3 track.

I tried using the flatfile-to-json.pl<http://flatfile-to-json.pl> utility, which takes the data and loads happily.  However,  on the browser,  it won't display, it just says html unspecified error.  I can get the tutorial to work, so it doesn't appear to be my perl, system settings,  etc.   My gff3 file has nine columns, but i don't know what other things to look for in that arena.  I've tried  a bunch of options, json or conf files,  etc. To no avail.

Any suggestions? I could include the head of my file if that helps (tomorrow when I can access that vm again).

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Gff import issues in jbrowse

Scott Cain
Hi Sheri,

It looks like your GFF came from MAKER--isn't there a maker2jbrowse script that will automate this for you?

If not, or you want to go a different route, please open the javascript console to see what it says; presumably it will be more than a "unspecified error" :-)

Scott

On Thu, Sep 22, 2016 at 9:36 AM, Sanders, Sheri <[hidden email]> wrote:
No error from flatfile-to-json.pl.  Really having a hard time troubleshooting this one,  with the only error being "HTML unspecified error"!

S

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

________________________________________
From: Ke Jiang [[hidden email]]
Sent: Wednesday, September 21, 2016 9:11 PM
To: Scott Cain
Cc: Sanders, Sheri; [hidden email]
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse

Flatfile-to-json.pl didn't throw any error?

On Wednesday, September 21, 2016, Scott Cain <[hidden email]<mailto:[hidden email]>> wrote:
Hi Sheri,

I'm cc'ing this to the JBrowse mailing list; please keep it cc'ed when you reply.

When asking for help of this sort, it's really helpful to know what the exact command you used was and a sample of the GFF file you were process.  You might also want to check out the JBrowse FAQ: http://gmod.org/wiki/JBrowse_FAQ and make sure you clear you cache when adding data or changing the config files, since browsers tend to "strongly" cache things like javascript and config files.

Scott


On Tue, Sep 20, 2016 at 5:11 PM, Sanders, Sheri <[hidden email]> wrote:

I'm embarking on producing a genome browser for a group here at IU. I ran into issues using tripal,  and began working on jbrowse directly.   However,  now I cannot load a gff3 track.

I tried using the flatfile-to-json.pl<http://flatfile-to-json.pl> utility, which takes the data and loads happily.  However,  on the browser,  it won't display, it just says html unspecified error.  I can get the tutorial to work, so it doesn't appear to be my perl, system settings,  etc.   My gff3 file has nine columns, but i don't know what other things to look for in that arena.  I've tried  a bunch of options, json or conf files,  etc. To no avail.

Any suggestions? I could include the head of my file if that helps (tomorrow when I can access that vm again).

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Gff import issues in jbrowse

Ke Jiang
In reply to this post by ssanders
Can you clear the caches and history, then try turning on the track. When the error replicates, take a look at the httpd error log? Sometimes maybe a clue over there?

On Thu, Sep 22, 2016 at 9:36 AM, Sanders, Sheri <[hidden email]> wrote:
No error from flatfile-to-json.pl.  Really having a hard time troubleshooting this one,  with the only error being "HTML unspecified error"!

S

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

________________________________________
From: Ke Jiang [[hidden email]]
Sent: Wednesday, September 21, 2016 9:11 PM
To: Scott Cain
Cc: Sanders, Sheri; [hidden email]
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse

Flatfile-to-json.pl didn't throw any error?

On Wednesday, September 21, 2016, Scott Cain <[hidden email]<mailto:[hidden email]>> wrote:
Hi Sheri,

I'm cc'ing this to the JBrowse mailing list; please keep it cc'ed when you reply.

When asking for help of this sort, it's really helpful to know what the exact command you used was and a sample of the GFF file you were process.  You might also want to check out the JBrowse FAQ: http://gmod.org/wiki/JBrowse_FAQ and make sure you clear you cache when adding data or changing the config files, since browsers tend to "strongly" cache things like javascript and config files.

Scott


On Tue, Sep 20, 2016 at 5:11 PM, Sanders, Sheri <[hidden email]> wrote:

I'm embarking on producing a genome browser for a group here at IU. I ran into issues using tripal,  and began working on jbrowse directly.   However,  now I cannot load a gff3 track.

I tried using the flatfile-to-json.pl<http://flatfile-to-json.pl> utility, which takes the data and loads happily.  However,  on the browser,  it won't display, it just says html unspecified error.  I can get the tutorial to work, so it doesn't appear to be my perl, system settings,  etc.   My gff3 file has nine columns, but i don't know what other things to look for in that arena.  I've tried  a bunch of options, json or conf files,  etc. To no avail.

Any suggestions? I could include the head of my file if that helps (tomorrow when I can access that vm again).

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
Ontario Institute for Cancer Research


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Re: Gff import issues in jbrowse

Colin
This is the line of code that produces this message

src/JBrowse/Store/SeqFeature/NCList.js: thisB._failAllDeferred( "Server returned an HTTP " + error.response.status + " error" );

The fact that this status code is "undefined" makes me think perhaps jbrowse is being loaded via file:/// or not a proper http server? A http server would have a status code I think


-Colin


On Thu, Sep 22, 2016 at 9:42 AM, Ke Jiang <[hidden email]> wrote:
Can you clear the caches and history, then try turning on the track. When the error replicates, take a look at the httpd error log? Sometimes maybe a clue over there?

On Thu, Sep 22, 2016 at 9:36 AM, Sanders, Sheri <[hidden email]> wrote:
No error from flatfile-to-json.pl.  Really having a hard time troubleshooting this one,  with the only error being "HTML unspecified error"!

S

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

________________________________________
From: Ke Jiang [[hidden email]]
Sent: Wednesday, September 21, 2016 9:11 PM
To: Scott Cain
Cc: Sanders, Sheri; [hidden email]
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse

Flatfile-to-json.pl didn't throw any error?

On Wednesday, September 21, 2016, Scott Cain <[hidden email]<mailto:[hidden email]>> wrote:
Hi Sheri,

I'm cc'ing this to the JBrowse mailing list; please keep it cc'ed when you reply.

When asking for help of this sort, it's really helpful to know what the exact command you used was and a sample of the GFF file you were process.  You might also want to check out the JBrowse FAQ: http://gmod.org/wiki/JBrowse_FAQ and make sure you clear you cache when adding data or changing the config files, since browsers tend to "strongly" cache things like javascript and config files.

Scott


On Tue, Sep 20, 2016 at 5:11 PM, Sanders, Sheri <[hidden email]> wrote:

I'm embarking on producing a genome browser for a group here at IU. I ran into issues using tripal,  and began working on jbrowse directly.   However,  now I cannot load a gff3 track.

I tried using the flatfile-to-json.pl<http://flatfile-to-json.pl> utility, which takes the data and loads happily.  However,  on the browser,  it won't display, it just says html unspecified error.  I can get the tutorial to work, so it doesn't appear to be my perl, system settings,  etc.   My gff3 file has nine columns, but i don't know what other things to look for in that arena.  I've tried  a bunch of options, json or conf files,  etc. To no avail.

Any suggestions? I could include the head of my file if that helps (tomorrow when I can access that vm again).

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Gff import issues in jbrowse

ssanders

Thanks everyone for the help thus far.  Here are some responses to suggestions:


maker2json.pl ​- errored out with unreadable text. One readable part stated the program failed with an exit status if 512 in line 452 of FormatSequences.pm.  I used the command: bin/maker2json.pl path/to/file/test.gff and with the --out option.  Both failed.  


This browser is being loaded via file:/// and not a proper http server at this point.  I did the same for the example and it works fine.  Should I be doing something different?  


Thanks for the help as I learn.  Did not expect gff to give me so much trouble!!


Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

From: Colin <[hidden email]>
Sent: Thursday, September 22, 2016 10:26 AM
To: Ke Jiang
Cc: Sanders, Sheri; [hidden email]
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse
 
This is the line of code that produces this message

src/JBrowse/Store/SeqFeature/NCList.js: thisB._failAllDeferred( "Server returned an HTTP " + error.response.status + " error" );

The fact that this status code is "undefined" makes me think perhaps jbrowse is being loaded via file:/// or not a proper http server? A http server would have a status code I think


-Colin


On Thu, Sep 22, 2016 at 9:42 AM, Ke Jiang <[hidden email]> wrote:
Can you clear the caches and history, then try turning on the track. When the error replicates, take a look at the httpd error log? Sometimes maybe a clue over there?

On Thu, Sep 22, 2016 at 9:36 AM, Sanders, Sheri <[hidden email]> wrote:
No error from flatfile-to-json.pl.  Really having a hard time troubleshooting this one,  with the only error being "HTML unspecified error"!

S

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

________________________________________
From: Ke Jiang [[hidden email]]
Sent: Wednesday, September 21, 2016 9:11 PM
To: Scott Cain
Cc: Sanders, Sheri; [hidden email]
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse

Flatfile-to-json.pl didn't throw any error?

On Wednesday, September 21, 2016, Scott Cain <[hidden email]<mailto:[hidden email]>> wrote:
Hi Sheri,

I'm cc'ing this to the JBrowse mailing list; please keep it cc'ed when you reply.

When asking for help of this sort, it's really helpful to know what the exact command you used was and a sample of the GFF file you were process.  You might also want to check out the JBrowse FAQ: http://gmod.org/wiki/JBrowse_FAQ and make sure you clear you cache when adding data or changing the config files, since browsers tend to "strongly" cache things like javascript and config files.

Scott


On Tue, Sep 20, 2016 at 5:11 PM, Sanders, Sheri <[hidden email]> wrote:

I'm embarking on producing a genome browser for a group here at IU. I ran into issues using tripal,  and began working on jbrowse directly.   However,  now I cannot load a gff3 track.

I tried using the flatfile-to-json.pl<http://flatfile-to-json.pl> utility, which takes the data and loads happily.  However,  on the browser,  it won't display, it just says html unspecified error.  I can get the tutorial to work, so it doesn't appear to be my perl, system settings,  etc.   My gff3 file has nine columns, but i don't know what other things to look for in that arena.  I've tried  a bunch of options, json or conf files,  etc. To no avail.

Any suggestions? I could include the head of my file if that helps (tomorrow when I can access that vm again).

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="&#43;12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Gff import issues in jbrowse

Colin

Here is a jbrowse FAQ entry about the webserver needed

http://gmod.org/wiki/JBrowse_FAQ#What_webserver_is_needed_for_JBrowse

It mentions some of the limitations with just using file:/// and alternatives

-Colin


On Sep 22, 2016 10:51 AM, "Sanders, Sheri" <[hidden email]> wrote:

Thanks everyone for the help thus far.  Here are some responses to suggestions:


maker2json.pl ​- errored out with unreadable text. One readable part stated the program failed with an exit status if 512 in line 452 of FormatSequences.pm.  I used the command: bin/maker2json.pl path/to/file/test.gff and with the --out option.  Both failed.  


This browser is being loaded via file:/// and not a proper http server at this point.  I did the same for the example and it works fine.  Should I be doing something different?  


Thanks for the help as I learn.  Did not expect gff to give me so much trouble!!


Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

From: Colin <[hidden email]>
Sent: Thursday, September 22, 2016 10:26 AM
To: Ke Jiang
Cc: Sanders, Sheri; [hidden email]
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse
 
This is the line of code that produces this message

src/JBrowse/Store/SeqFeature/NCList.js: thisB._failAllDeferred( "Server returned an HTTP " + error.response.status + " error" );

The fact that this status code is "undefined" makes me think perhaps jbrowse is being loaded via file:/// or not a proper http server? A http server would have a status code I think


-Colin


On Thu, Sep 22, 2016 at 9:42 AM, Ke Jiang <[hidden email]> wrote:
Can you clear the caches and history, then try turning on the track. When the error replicates, take a look at the httpd error log? Sometimes maybe a clue over there?

On Thu, Sep 22, 2016 at 9:36 AM, Sanders, Sheri <[hidden email]> wrote:
No error from flatfile-to-json.pl.  Really having a hard time troubleshooting this one,  with the only error being "HTML unspecified error"!

S

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

________________________________________
From: Ke Jiang [[hidden email]]
Sent: Wednesday, September 21, 2016 9:11 PM
To: Scott Cain
Cc: Sanders, Sheri; [hidden email]
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse

Flatfile-to-json.pl didn't throw any error?

On Wednesday, September 21, 2016, Scott Cain <[hidden email]<mailto:[hidden email]>> wrote:
Hi Sheri,

I'm cc'ing this to the JBrowse mailing list; please keep it cc'ed when you reply.

When asking for help of this sort, it's really helpful to know what the exact command you used was and a sample of the GFF file you were process.  You might also want to check out the JBrowse FAQ: http://gmod.org/wiki/JBrowse_FAQ and make sure you clear you cache when adding data or changing the config files, since browsers tend to "strongly" cache things like javascript and config files.

Scott


On Tue, Sep 20, 2016 at 5:11 PM, Sanders, Sheri <[hidden email]> wrote:

I'm embarking on producing a genome browser for a group here at IU. I ran into issues using tripal,  and began working on jbrowse directly.   However,  now I cannot load a gff3 track.

I tried using the flatfile-to-json.pl<http://flatfile-to-json.pl> utility, which takes the data and loads happily.  However,  on the browser,  it won't display, it just says html unspecified error.  I can get the tutorial to work, so it doesn't appear to be my perl, system settings,  etc.   My gff3 file has nine columns, but i don't know what other things to look for in that arena.  I've tried  a bunch of options, json or conf files,  etc. To no avail.

Any suggestions? I could include the head of my file if that helps (tomorrow when I can access that vm again).

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Gff import issues in jbrowse

ssanders

Thanks for the tip on running it on a webserver.  I moved to working from the http server.  Now, I just get a blank track.  I still think it has something to do with the inporting only partially working.  It doesn't give an error, but it doesn't display either.


Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

From: Colin <[hidden email]>
Sent: Thursday, September 22, 2016 11:09 AM
To: Sanders, Sheri
Cc: [hidden email]; Ke Jiang
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse
 

Here is a jbrowse FAQ entry about the webserver needed

http://gmod.org/wiki/JBrowse_FAQ#What_webserver_is_needed_for_JBrowse

It mentions some of the limitations with just using file:/// and alternatives

-Colin


On Sep 22, 2016 10:51 AM, "Sanders, Sheri" <[hidden email]> wrote:

Thanks everyone for the help thus far.  Here are some responses to suggestions:


maker2json.pl ​- errored out with unreadable text. One readable part stated the program failed with an exit status if 512 in line 452 of FormatSequences.pm.  I used the command: bin/maker2json.pl path/to/file/test.gff and with the --out option.  Both failed.  


This browser is being loaded via file:/// and not a proper http server at this point.  I did the same for the example and it works fine.  Should I be doing something different?  


Thanks for the help as I learn.  Did not expect gff to give me so much trouble!!


Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

From: Colin <[hidden email]>
Sent: Thursday, September 22, 2016 10:26 AM
To: Ke Jiang
Cc: Sanders, Sheri; [hidden email]
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse
 
This is the line of code that produces this message

src/JBrowse/Store/SeqFeature/NCList.js: thisB._failAllDeferred( "Server returned an HTTP " + error.response.status + " error" );

The fact that this status code is "undefined" makes me think perhaps jbrowse is being loaded via file:/// or not a proper http server? A http server would have a status code I think


-Colin


On Thu, Sep 22, 2016 at 9:42 AM, Ke Jiang <[hidden email]> wrote:
Can you clear the caches and history, then try turning on the track. When the error replicates, take a look at the httpd error log? Sometimes maybe a clue over there?

On Thu, Sep 22, 2016 at 9:36 AM, Sanders, Sheri <[hidden email]> wrote:
No error from flatfile-to-json.pl.  Really having a hard time troubleshooting this one,  with the only error being "HTML unspecified error"!

S

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

________________________________________
From: Ke Jiang [[hidden email]]
Sent: Wednesday, September 21, 2016 9:11 PM
To: Scott Cain
Cc: Sanders, Sheri; [hidden email]
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse

Flatfile-to-json.pl didn't throw any error?

On Wednesday, September 21, 2016, Scott Cain <[hidden email]<mailto:[hidden email]>> wrote:
Hi Sheri,

I'm cc'ing this to the JBrowse mailing list; please keep it cc'ed when you reply.

When asking for help of this sort, it's really helpful to know what the exact command you used was and a sample of the GFF file you were process.  You might also want to check out the JBrowse FAQ: http://gmod.org/wiki/JBrowse_FAQ and make sure you clear you cache when adding data or changing the config files, since browsers tend to "strongly" cache things like javascript and config files.

Scott


On Tue, Sep 20, 2016 at 5:11 PM, Sanders, Sheri <[hidden email]> wrote:

I'm embarking on producing a genome browser for a group here at IU. I ran into issues using tripal,  and began working on jbrowse directly.   However,  now I cannot load a gff3 track.

I tried using the flatfile-to-json.pl<http://flatfile-to-json.pl> utility, which takes the data and loads happily.  However,  on the browser,  it won't display, it just says html unspecified error.  I can get the tutorial to work, so it doesn't appear to be my perl, system settings,  etc.   My gff3 file has nine columns, but i don't know what other things to look for in that arena.  I've tried  a bunch of options, json or conf files,  etc. To no avail.

Any suggestions? I could include the head of my file if that helps (tomorrow when I can access that vm again).

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="&#43;12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Gff import issues in jbrowse

Monica Poelchau
Hi Sheri,

Not sure if this has been covered already - in the screenshot you posted earlier, the scaffold ID is scaffold_134, whereas in test gff that you shared, it's scaffold134. The scaffold IDs need to be identical in the reference fasta and the gff.

Hth,

Monica

On Thu, Sep 22, 2016 at 10:20 AM, Sanders, Sheri <[hidden email]> wrote:

Thanks for the tip on running it on a webserver.  I moved to working from the http server.  Now, I just get a blank track.  I still think it has something to do with the inporting only partially working.  It doesn't give an error, but it doesn't display either.


Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

From: Colin <[hidden email]>
Sent: Thursday, September 22, 2016 11:09 AM
To: Sanders, Sheri
Cc: [hidden email]; Ke Jiang

Subject: Re: [Gmod-ajax] Gff import issues in jbrowse
 

Here is a jbrowse FAQ entry about the webserver needed

http://gmod.org/wiki/JBrowse_FAQ#What_webserver_is_needed_for_JBrowse

It mentions some of the limitations with just using file:/// and alternatives

-Colin


On Sep 22, 2016 10:51 AM, "Sanders, Sheri" <[hidden email]> wrote:

Thanks everyone for the help thus far.  Here are some responses to suggestions:


maker2json.pl ​- errored out with unreadable text. One readable part stated the program failed with an exit status if 512 in line 452 of FormatSequences.pm.  I used the command: bin/maker2json.pl path/to/file/test.gff and with the --out option.  Both failed.  


This browser is being loaded via file:/// and not a proper http server at this point.  I did the same for the example and it works fine.  Should I be doing something different?  


Thanks for the help as I learn.  Did not expect gff to give me so much trouble!!


Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

From: Colin <[hidden email]>
Sent: Thursday, September 22, 2016 10:26 AM
To: Ke Jiang
Cc: Sanders, Sheri; [hidden email]
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse
 
This is the line of code that produces this message

src/JBrowse/Store/SeqFeature/NCList.js: thisB._failAllDeferred( "Server returned an HTTP " + error.response.status + " error" );

The fact that this status code is "undefined" makes me think perhaps jbrowse is being loaded via file:/// or not a proper http server? A http server would have a status code I think


-Colin


On Thu, Sep 22, 2016 at 9:42 AM, Ke Jiang <[hidden email]> wrote:
Can you clear the caches and history, then try turning on the track. When the error replicates, take a look at the httpd error log? Sometimes maybe a clue over there?

On Thu, Sep 22, 2016 at 9:36 AM, Sanders, Sheri <[hidden email]> wrote:
No error from flatfile-to-json.pl.  Really having a hard time troubleshooting this one,  with the only error being "HTML unspecified error"!

S

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

________________________________________
From: Ke Jiang [[hidden email]]
Sent: Wednesday, September 21, 2016 9:11 PM
To: Scott Cain
Cc: Sanders, Sheri; [hidden email]
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse

Flatfile-to-json.pl didn't throw any error?

On Wednesday, September 21, 2016, Scott Cain <[hidden email]<mailto:[hidden email]>> wrote:
Hi Sheri,

I'm cc'ing this to the JBrowse mailing list; please keep it cc'ed when you reply.

When asking for help of this sort, it's really helpful to know what the exact command you used was and a sample of the GFF file you were process.  You might also want to check out the JBrowse FAQ: http://gmod.org/wiki/JBrowse_FAQ and make sure you clear you cache when adding data or changing the config files, since browsers tend to "strongly" cache things like javascript and config files.

Scott


On Tue, Sep 20, 2016 at 5:11 PM, Sanders, Sheri <[hidden email]> wrote:

I'm embarking on producing a genome browser for a group here at IU. I ran into issues using tripal,  and began working on jbrowse directly.   However,  now I cannot load a gff3 track.

I tried using the flatfile-to-json.pl<http://flatfile-to-json.pl> utility, which takes the data and loads happily.  However,  on the browser,  it won't display, it just says html unspecified error.  I can get the tutorial to work, so it doesn't appear to be my perl, system settings,  etc.   My gff3 file has nine columns, but i don't know what other things to look for in that arena.  I've tried  a bunch of options, json or conf files,  etc. To no avail.

Any suggestions? I could include the head of my file if that helps (tomorrow when I can access that vm again).

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Gff import issues in jbrowse

ssanders

​You know, I figured the answer would be this dumb.  THANK YOU.  I had already edited the file to not have extra information after then name (had length tagged on there too), but missed the "_".  Still getting some weird import issues, but at least I can get things to show up now!


Lesson learned!


Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

From: Monica Poelchau <[hidden email]>
Sent: Thursday, September 22, 2016 1:00 PM
To: Sanders, Sheri
Cc: Colin; [hidden email]
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse
 
Hi Sheri,

Not sure if this has been covered already - in the screenshot you posted earlier, the scaffold ID is scaffold_134, whereas in test gff that you shared, it's scaffold134. The scaffold IDs need to be identical in the reference fasta and the gff.

Hth,

Monica

On Thu, Sep 22, 2016 at 10:20 AM, Sanders, Sheri <[hidden email]> wrote:

Thanks for the tip on running it on a webserver.  I moved to working from the http server.  Now, I just get a blank track.  I still think it has something to do with the inporting only partially working.  It doesn't give an error, but it doesn't display either.


Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

From: Colin <[hidden email]>
Sent: Thursday, September 22, 2016 11:09 AM
To: Sanders, Sheri
Cc: [hidden email]; Ke Jiang

Subject: Re: [Gmod-ajax] Gff import issues in jbrowse
 

Here is a jbrowse FAQ entry about the webserver needed

http://gmod.org/wiki/JBrowse_FAQ#What_webserver_is_needed_for_JBrowse

It mentions some of the limitations with just using file:/// and alternatives

-Colin


On Sep 22, 2016 10:51 AM, "Sanders, Sheri" <[hidden email]> wrote:

Thanks everyone for the help thus far.  Here are some responses to suggestions:


maker2json.pl ​- errored out with unreadable text. One readable part stated the program failed with an exit status if 512 in line 452 of FormatSequences.pm.  I used the command: bin/maker2json.pl path/to/file/test.gff and with the --out option.  Both failed.  


This browser is being loaded via file:/// and not a proper http server at this point.  I did the same for the example and it works fine.  Should I be doing something different?  


Thanks for the help as I learn.  Did not expect gff to give me so much trouble!!


Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

From: Colin <[hidden email]>
Sent: Thursday, September 22, 2016 10:26 AM
To: Ke Jiang
Cc: Sanders, Sheri; [hidden email]
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse
 
This is the line of code that produces this message

src/JBrowse/Store/SeqFeature/NCList.js: thisB._failAllDeferred( "Server returned an HTTP " + error.response.status + " error" );

The fact that this status code is "undefined" makes me think perhaps jbrowse is being loaded via file:/// or not a proper http server? A http server would have a status code I think


-Colin


On Thu, Sep 22, 2016 at 9:42 AM, Ke Jiang <[hidden email]> wrote:
Can you clear the caches and history, then try turning on the track. When the error replicates, take a look at the httpd error log? Sometimes maybe a clue over there?

On Thu, Sep 22, 2016 at 9:36 AM, Sanders, Sheri <[hidden email]> wrote:
No error from flatfile-to-json.pl.  Really having a hard time troubleshooting this one,  with the only error being "HTML unspecified error"!

S

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.

________________________________________
From: Ke Jiang [[hidden email]]
Sent: Wednesday, September 21, 2016 9:11 PM
To: Scott Cain
Cc: Sanders, Sheri; [hidden email]
Subject: Re: [Gmod-ajax] Gff import issues in jbrowse

Flatfile-to-json.pl didn't throw any error?

On Wednesday, September 21, 2016, Scott Cain <[hidden email]<mailto:[hidden email]>> wrote:
Hi Sheri,

I'm cc'ing this to the JBrowse mailing list; please keep it cc'ed when you reply.

When asking for help of this sort, it's really helpful to know what the exact command you used was and a sample of the GFF file you were process.  You might also want to check out the JBrowse FAQ: http://gmod.org/wiki/JBrowse_FAQ and make sure you clear you cache when adding data or changing the config files, since browsers tend to "strongly" cache things like javascript and config files.

Scott


On Tue, Sep 20, 2016 at 5:11 PM, Sanders, Sheri <[hidden email]> wrote:

I'm embarking on producing a genome browser for a group here at IU. I ran into issues using tripal,  and began working on jbrowse directly.   However,  now I cannot load a gff3 track.

I tried using the flatfile-to-json.pl<http://flatfile-to-json.pl> utility, which takes the data and loads happily.  However,  on the browser,  it won't display, it just says html unspecified error.  I can get the tutorial to work, so it doesn't appear to be my perl, system settings,  etc.   My gff3 file has nine columns, but i don't know what other things to look for in that arena.  I've tried  a bunch of options, json or conf files,  etc. To no avail.

Any suggestions? I could include the head of my file if that helps (tomorrow when I can access that vm again).

Sheri Sanders
Bioinformatic Analyst
National Center for Genome Analysis and Support (NCGAS)

NCGAS is part of the Research Technologies division of UITS; Research Technologies is a PTI Cyberinfrastructure & Service Center.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="&#43;12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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