Hi, I’ve been working with a JBrowse installation for about a month. I set it up using a provisional set of refseqs (named Scaffold1, Scaffold2, …) and it was working fine. However, we have a better assembly of the genome and I would like to
replace the old data with the new. The new refseqs are named CONTIG_1, CONTIG_2, … which will be important later. Basically, I’ve tried a lot of things including deleting and completely reinstalling the JBrowse directory. However, no matter what I do I can’t get the new refseqs to show up and the pull-down menu still says Scaffold1, Scaffold2, …. The
search bar is also indexed for annotations from the previous installation, even though I haven’t added those to the new installation and I ran generate-names.pl on the new installation. I have no idea how these names are being retained.
I’m installing into the a directory JBrowse-1.12.1/strain_r. I have been able to install the updated refseqs into a separate directory called strain_r_new, but this isn’t ideal because it doesn’t really allow the data to be updated in the
future without changing URLs all over the place. Any ideas what can be going on here? Thanks for the help. Devin ------------------------------------------------------------------------------ _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
Have you tried deleting all the browser caches and history?
On Friday, September 9, 2016, Devin Strickland <[hidden email]> wrote:
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Hi, I did this and it seems to have solved the immediate problem. However, now I’m getting “Error reading from name store.” I tried several of the fixes listed in
the FAQ without success: mg-admin@laptop-VM:/var/www/html/JBrowse-1.12.1$ bin/generate-names.pl --hashBits 16 --out strain_r/ --completionLimit 0 --verbose Tracks: DNA ngs_reads WARNING: No feature names found for indexing, only reference sequence names will be indexed. Sampled input stats: operation stream estimated count 0 avg record text bytes 16 namerecs buffered 222 namerecs converted to operations 222 total input bytes 0 operations made 222 total namerec bytes 3552 record stream estimated count 0 name input records 222 Removing existing contents of target dir strain_r/names Hash store cache size: 2684 buckets Using 2 chars for sort log names (256 sort logs) Any ideas? Thanks again! Devin From: Ke Jiang [mailto:[hidden email]]
Have you tried deleting all the browser caches and history?
------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
Can you try taking out the ngs_reads out of the indexing process, only indexing the "DNA" track? I have never indexed read names before but I suspect that the large number of reads may hurt the indexing process? Let me know how this goes. KeOn Mon, Sep 12, 2016 at 12:12 PM, Devin Strickland <[hidden email]> wrote:
------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
Didn’t help. It was happening before I loaded the NGS tracks anyway. From: Ke Jiang [mailto:[hidden email]]
Can you try taking out the ngs_reads out of the indexing process, only indexing the "DNA" track? I have never indexed read names before but I suspect that the large number of reads may hurt the indexing process?
Let me know how this goes. Ke On Mon, Sep 12, 2016 at 12:12 PM, Devin Strickland <[hidden email]> wrote:
------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
I've seen that message when the "refseq names only" are indexed. It might be worth adding other features if you have them and rerunning generate-names because it just seems to get confused if only refseq names are indexed (and if you don't have other features, not really necessary to use generate-names). Btw bam file reads don't get indexed by generate-names. Vcf.gz files do get indexed though -Colin On Sep 12, 2016 1:07 PM, "Devin Strickland" <[hidden email]> wrote:
------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
Thanks. That’s good to know. I am still waiting on features for this assembly, so I will try re-running when I have them. Best, Devin From: Colin [mailto:[hidden email]]
I've seen that message when the "refseq names only" are indexed. It might be worth adding other features if you have them and rerunning generate-names because it just seems to get confused if only refseq names are indexed (and if you don't have other features,
not really necessary to use generate-names). Btw bam file reads don't get indexed by generate-names. Vcf.gz files do get indexed though -Colin On Sep 12, 2016 1:07 PM, "Devin Strickland" <[hidden email]> wrote:
------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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