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[Gmod-ajax] JBrowse refseq names

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Devin Strickland

[Gmod-ajax] JBrowse refseq names

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

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Ke Jiang

Re: JBrowse refseq names

Have you tried deleting all the browser caches and history?

On Friday, September 9, 2016, Devin Strickland <[hidden email]> wrote:

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

Devin Strickland

Re: JBrowse refseq names

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]]
Sent: Friday, September 09, 2016 5:00 PM
To: Devin Strickland <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] JBrowse refseq names

Have you tried deleting all the browser caches and history?

On Friday, September 9, 2016, Devin Strickland <[hidden email]> wrote:

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

------------------------------------------------------------------------------
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]
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Ke Jiang

Re: JBrowse refseq names

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.

On Mon, Sep 12, 2016 at 12:12 PM, Devin Strickland <[hidden email]> wrote:

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]]
Sent: Friday, September 09, 2016 5:00 PM
To: Devin Strickland <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] JBrowse refseq names

Have you tried deleting all the browser caches and history?

On Friday, September 9, 2016, Devin Strickland <[hidden email]> wrote:

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

Devin Strickland

Re: JBrowse refseq names

Didn’t help. It was happening before I loaded the NGS tracks anyway.

From: Ke Jiang [mailto:[hidden email]]
Sent: Monday, September 12, 2016 9:50 AM
To: Devin Strickland <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] JBrowse refseq names

On Mon, Sep 12, 2016 at 12:12 PM, Devin Strickland <[hidden email]> wrote:

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:

[hidden email] 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]]
Sent: Friday, September 09, 2016 5:00 PM
To: Devin Strickland <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] JBrowse refseq names

Have you tried deleting all the browser caches and history?

On Friday, September 9, 2016, Devin Strickland <[hidden email]> wrote:

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

Colin

Re: JBrowse refseq names

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:

Didn’t help. It was happening before I loaded the NGS tracks anyway.

From: Ke Jiang [mailto:[hidden email]]
Sent: Monday, September 12, 2016 9:50 AM
To: Devin Strickland <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] JBrowse refseq names

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:

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:

[hidden email] 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]]
Sent: Friday, September 09, 2016 5:00 PM
To: Devin Strickland <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] JBrowse refseq names

Have you tried deleting all the browser caches and history?

On Friday, September 9, 2016, Devin Strickland <[hidden email]> wrote:

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

------------------------------------------------------------------------------
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]
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Devin Strickland

Re: JBrowse refseq names

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]]
Sent: Monday, September 12, 2016 10:34 AM
To: Devin Strickland <[hidden email]>
Cc: [hidden email]; Ke Jiang <[hidden email]>
Subject: Re: [Gmod-ajax] JBrowse refseq names

-Colin

On Sep 12, 2016 1:07 PM, "Devin Strickland" <[hidden email]> wrote:

Didn’t help. It was happening before I loaded the NGS tracks anyway.

From: Ke Jiang [mailto:[hidden email]]
Sent: Monday, September 12, 2016 9:50 AM
To: Devin Strickland <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] JBrowse refseq names

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:

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:

[hidden email] 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]]
Sent: Friday, September 09, 2016 5:00 PM
To: Devin Strickland <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] JBrowse refseq names

Have you tried deleting all the browser caches and history?

On Friday, September 9, 2016, Devin Strickland <[hidden email]> wrote:

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

------------------------------------------------------------------------------
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