jbrowse not working

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jbrowse not working

Emmanuel Nnadi
Please,
I ran the command line

maker2jbrowse muc1_genome_snap2.all.gff


The command created some folders. However, at the end it read
No reference sequences defined in configuration, nothing to do.

Please what does it mean? How can I view it in jbrowse. 

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.

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Re: jbrowse not working

Carson Holt-2
Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of the file? That can happen if you use the -n option with gff3_merge. Alternatively it’s possible one of the individual contig gff3 used to build the merged gff3 is truncated. If that is the case then gff3_merge should have thrown some sort of error or warning when you run it.

Thanks,
Carson




On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <[hidden email]> wrote:

Please,
I ran the command line

maker2jbrowse muc1_genome_snap2.all.gff

The command created some folders. However, at the end it read
No reference sequences defined in configuration, nothing to do.

Please what does it mean? How can I view it in jbrowse. 

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.


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Re: jbrowse not working

Emmanuel Nnadi
Hi Carson
Thanks for the reply

I generated the off with this command gff3_merge –d dpp_contig.maker.output/dpp_contig_master_datastore_index.log

I had to rerun browse with the following command

maker2jbrowse /Users/emmannaemeka/desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2.functional_blast.gff\maker2jbrowse -d /Users/emmannaemeka/Desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2_master_datastore_index.log \-out /Library/WebServer/Documents/JBrowse-1.12.1/muc/muc_jb


Although its showing


WARNING: No matching features found for mRNA I don't know what it means


I don't understand what it means



Successfully, I was able to setup the jbrowse local host. I had to move the jbrowse folder to my local host


The jbrowse is up and running however, I have about 18488 contigs only 31 contigs are showing, how can i make all my contigs to show on jbrowse?




Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.

On Tue, Oct 10, 2017 at 1:35 AM, Carson Holt <[hidden email]> wrote:
Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of the file? That can happen if you use the -n option with gff3_merge. Alternatively it’s possible one of the individual contig gff3 used to build the merged gff3 is truncated. If that is the case then gff3_merge should have thrown some sort of error or warning when you run it.

Thanks,
Carson




On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <[hidden email]> wrote:

Please,
I ran the command line

maker2jbrowse muc1_genome_snap2.all.gff

The command created some folders. However, at the end it read
No reference sequences defined in configuration, nothing to do.

Please what does it mean? How can I view it in jbrowse. 

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.



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Re: jbrowse not working

Carson Holt-2
The master_datastore_index.log file has a list of failed and finished contigs.  You can grep the file contents for FAILED or DIED to see if any contigs are not finished. Finished contigs will be listed as FINISHED in the file.

Also note that if you have errors with the jbrowse build, you have to start over (i.e. wipe out old build). Rerunning the command over a failed build will try and insert again which can generate it’s own errors. If gff3_merge was run without the -n option then you need to see if one of the GFF3 files being used is truncated (possibly dew to an IO error - not uncommon on NFS storage).

You will need to see if you can identify which contig file is truncated and rerun it.

—Carson






On Oct 9, 2017, at 10:42 PM, Emmanuel Nnadi <[hidden email]> wrote:

Hi Carson
Thanks for the reply

I generated the off with this command gff3_merge –d dpp_contig.maker.output/dpp_contig_master_datastore_index.log

I had to rerun browse with the following command

maker2jbrowse /Users/emmannaemeka/desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2.functional_blast.gff\maker2jbrowse -d /Users/emmannaemeka/Desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2_master_datastore_index.log \-out /Library/WebServer/Documents/JBrowse-1.12.1/muc/muc_jb

Although its showing

WARNING: No matching features found for mRNA I don't know what it means

I don't understand what it means


Successfully, I was able to setup the jbrowse local host. I had to move the jbrowse folder to my local host


The jbrowse is up and running however, I have about 18488 contigs only 31 contigs are showing, how can i make all my contigs to show on jbrowse?




Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.

On Tue, Oct 10, 2017 at 1:35 AM, Carson Holt <[hidden email]> wrote:
Is muc1_genome_snap2.all.gff missing embedded fasta entries at the end of the file? That can happen if you use the -n option with gff3_merge. Alternatively it’s possible one of the individual contig gff3 used to build the merged gff3 is truncated. If that is the case then gff3_merge should have thrown some sort of error or warning when you run it.

Thanks,
Carson




On Oct 7, 2017, at 3:34 PM, Emmanuel Nnadi <[hidden email]> wrote:

Please,
I ran the command line

maker2jbrowse muc1_genome_snap2.all.gff

The command created some folders. However, at the end it read
No reference sequences defined in configuration, nothing to do.

Please what does it mean? How can I view it in jbrowse. 

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.




_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org