Errors after installing JBrowse

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Errors after installing JBrowse

sanjeevs
Dear developers,

We are still facing issues in installing jbrowse (JBrowse version: JBrowse-1.11.3-devon our server. we have followed all the posts related to jbrowse installation errors and tried using the below mentioned commands:

1) nohup ./setup.sh &

2)bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa

3) bin/prepare-refseqs.pl --conf docs/tutorial/conf_files/volvox.json
I got warnings after running the above command:
WARNING: multiple reference sequences found named 'ctgB', using only the first one.
WARNING: multiple reference sequences found named 'ctgA', using only the first one.

However, we didn't get any library (@INC...., etc) or installation related errors.

when we try to view volvox sample data on our server, it didn't display any track(s). Also, reference sequence is not being displayed. http://gbrowse2014.biology.gatech.edu/

We tried to hard code the url (below URL) where sample volvox data is provided by jbrowse.org to check if we are missing something related to path and we are able to view the sample volvox data.

http://jbrowse.org/code/JBrowse-1.11.3/index.html?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A20003..30108&tracks=DNA%2Cvolvox-paired_bam&highlight=

our server url: 
http://gbrowse2014.biology.gatech.edu/index.html?data=sample_data%2Fjson%2Fvolvox%2F&loc=ctgB%3A1806..1849&tracks=DNA%2Cvolvox_microarray.wig%2Cvolvox-sorted_bam_coverage%2CEST%2Cmalformed_alignments&highlight=

We are still confused where are we missing the actual path so that we can view the volvox data without any hard coding.
I am attaching 2 jpeg files:
1) default:default server URL 
2) error_install: hard coded URL


Let me know if any further details are required on files, installation or server from my side.
Looking forward for help from you. 


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nohup.out (732 bytes) Download Attachment
setup.log (521K) Download Attachment
error_install.JPG (185K) Download Attachment
default.JPG (96K) Download Attachment
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Re: Errors after installing JBrowse

Scott Cain
Hi Sanjeev,

JBrowse has a separate mailing list, [hidden email]; I'm cc'ing it here (the list was named before JBrowse was).

I haven't looked at your error logs, but I'm a little concerned about your GFF file: the message about there being multiple references sequences with the same name makes me wonder if the rest of your GFF is OK.

Scott



On Sat, Mar 29, 2014 at 1:12 AM, Sanjeev Sariya <[hidden email]> wrote:
Dear developers,

We are still facing issues in installing jbrowse (JBrowse version: JBrowse-1.11.3-devon our server. we have followed all the posts related to jbrowse installation errors and tried using the below mentioned commands:

1) nohup ./setup.sh &

2)bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa

3) bin/prepare-refseqs.pl --conf docs/tutorial/conf_files/volvox.json
I got warnings after running the above command:
WARNING: multiple reference sequences found named 'ctgB', using only the first one.
WARNING: multiple reference sequences found named 'ctgA', using only the first one.

However, we didn't get any library (@INC...., etc) or installation related errors.

when we try to view volvox sample data on our server, it didn't display any track(s). Also, reference sequence is not being displayed. http://gbrowse2014.biology.gatech.edu/

We tried to hard code the url (below URL) where sample volvox data is provided by jbrowse.org to check if we are missing something related to path and we are able to view the sample volvox data.


our server url: 

We are still confused where are we missing the actual path so that we can view the volvox data without any hard coding.
I am attaching 2 jpeg files:
1) default:default server URL 
2) error_install: hard coded URL


Let me know if any further details are required on files, installation or server from my side.
Looking forward for help from you. 


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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: [Gmod-ajax] Errors after installing JBrowse

Colin
Thanks for forwarding the message Scott. I didn't get the attachments, but I am able to access your server. I think most of the tracks look fine on the Volvox sample_data, but it looks like some tracks (the raw files) are looking in the wrong place. For example, the raw files like bigwig,bam,vcf produce 404 errors. They seem to be looking for the files in paths such as  http://gbrowse2014.biology.gatech.edu/sample_data/json/raw/volvox/volvox_sine.bw
On a standard installation,the raw files are stored at sample_data/raw/volvox/volvox_microarray.bw
Did the hardcoding of the paths cause any problem here? And are there any other problems that i'm not seeing? If not the jbrowse instance outside of the sample_data might be fine to use now.
Thanks,
-Colin


On Mon, Mar 31, 2014 at 9:44 AM, Scott Cain <[hidden email]> wrote:
Hi Sanjeev,

JBrowse has a separate mailing list, [hidden email]; I'm cc'ing it here (the list was named before JBrowse was).

I haven't looked at your error logs, but I'm a little concerned about your GFF file: the message about there being multiple references sequences with the same name makes me wonder if the rest of your GFF is OK.

Scott



On Sat, Mar 29, 2014 at 1:12 AM, Sanjeev Sariya <[hidden email]> wrote:
Dear developers,

We are still facing issues in installing jbrowse (JBrowse version: JBrowse-1.11.3-devon our server. we have followed all the posts related to jbrowse installation errors and tried using the below mentioned commands:

1) nohup ./setup.sh &

2)bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa

3) bin/prepare-refseqs.pl --conf docs/tutorial/conf_files/volvox.json
I got warnings after running the above command:
WARNING: multiple reference sequences found named 'ctgB', using only the first one.
WARNING: multiple reference sequences found named 'ctgA', using only the first one.

However, we didn't get any library (@INC...., etc) or installation related errors.

when we try to view volvox sample data on our server, it didn't display any track(s). Also, reference sequence is not being displayed. http://gbrowse2014.biology.gatech.edu/

We tried to hard code the url (below URL) where sample volvox data is provided by jbrowse.org to check if we are missing something related to path and we are able to view the sample volvox data.


our server url: 

We are still confused where are we missing the actual path so that we can view the volvox data without any hard coding.
I am attaching 2 jpeg files:
1) default:default server URL 
2) error_install: hard coded URL


Let me know if any further details are required on files, installation or server from my side.
Looking forward for help from you. 


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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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