[Gmod-ajax] MultiVariantViewer plugin problem

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[Gmod-ajax] MultiVariantViewer plugin problem

Ke Jiang
Hi,

Trying to use the MultiVariantViewer plugin, I've got the "Grid" type working but when I try switching to the "LDTrack" type it throws the following error:

Unable to load undefined?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz status 404

If the Grid is working, the location of the vcf.gz should be fine. But looks like the url constructed is not pointing to the right place.

Any thoughts?

Thanks!

Ke

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Re: MultiVariantViewer plugin problem

Colin
Currently, LDTrack requires the "linkage_server" part of the code to be running. To setup, go into the linkage_server folder, run `npm install`, and then `node index.js`, then set the ldviewer config in trackList.json to point to that node.js microservice (default runs on port 4730) 

-Colin

On Thu, May 4, 2017 at 10:39 AM, Ke Jiang <[hidden email]> wrote:
Hi,

Trying to use the MultiVariantViewer plugin, I've got the "Grid" type working but when I try switching to the "LDTrack" type it throws the following error:

Unable to load undefined?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz status 404

If the Grid is working, the location of the vcf.gz should be fine. But looks like the url constructed is not pointing to the right place.

Any thoughts?

Thanks!

Ke

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Re: MultiVariantViewer plugin problem

Ke Jiang
Thanks, Colin! When I read this in the docs, I thought it meant linkage server was an option...

"Optionally, LD can be calculated from the VCF files on the server side using plink and rendered as a classic block view."

This is gonna be hard for me, as I'm not the administrator of the server, but I'll give it a try.

Thanks!

Ke

On Thu, May 4, 2017 at 12:23 PM, Colin <[hidden email]> wrote:
Currently, LDTrack requires the "linkage_server" part of the code to be running. To setup, go into the linkage_server folder, run `npm install`, and then `node index.js`, then set the ldviewer config in trackList.json to point to that node.js microservice (default runs on port 4730) 

-Colin

On Thu, May 4, 2017 at 10:39 AM, Ke Jiang <[hidden email]> wrote:
Hi,

Trying to use the MultiVariantViewer plugin, I've got the "Grid" type working but when I try switching to the "LDTrack" type it throws the following error:

Unable to load undefined?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz status 404

If the Grid is working, the location of the vcf.gz should be fine. But looks like the url constructed is not pointing to the right place.

Any thoughts?

Thanks!

Ke

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Re: MultiVariantViewer plugin problem

Ke Jiang
Hi,

I gave a try with this and got this error:

Unable to load http://localhost:4730?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz status 0

I noticed some output from the linkage_server prompt sating

[khttp_connect_file] fail to open file (HTTP code: 404).
[main] fail to open the data file.

Is this because the server couldn't find the calculated LD data? So where are these data calculated and stored so I could go and take a look?

Thanks!

Ke

On Thu, May 4, 2017 at 1:03 PM, Ke Jiang <[hidden email]> wrote:
Thanks, Colin! When I read this in the docs, I thought it meant linkage server was an option...

"Optionally, LD can be calculated from the VCF files on the server side using plink and rendered as a classic block view."

This is gonna be hard for me, as I'm not the administrator of the server, but I'll give it a try.

Thanks!

Ke

On Thu, May 4, 2017 at 12:23 PM, Colin <[hidden email]> wrote:
Currently, LDTrack requires the "linkage_server" part of the code to be running. To setup, go into the linkage_server folder, run `npm install`, and then `node index.js`, then set the ldviewer config in trackList.json to point to that node.js microservice (default runs on port 4730) 

-Colin

On Thu, May 4, 2017 at 10:39 AM, Ke Jiang <[hidden email]> wrote:
Hi,

Trying to use the MultiVariantViewer plugin, I've got the "Grid" type working but when I try switching to the "LDTrack" type it throws the following error:

Unable to load undefined?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz status 404

If the Grid is working, the location of the vcf.gz should be fine. But looks like the url constructed is not pointing to the right place.

Any thoughts?

Thanks!

Ke

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Re: MultiVariantViewer plugin problem

Colin
The ldserver assumes that it can fetch the tabix VCF similar to how the browser does, so it receives as an argument the URL to the file e.g. the "http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz" part of the request.


For example, in this case, the url (after urldecoding) says http://jbrowse.xxxxx.com/data/json/Gohir_v11//../../raw/Gohir_v11/WGS/ACH1718_d20.vcf.gz, does this file exist if you visit it manually?

-Colin

On Wed, May 10, 2017 at 9:38 AM, Ke Jiang <[hidden email]> wrote:
Hi,

I gave a try with this and got this error:

Unable to load http://localhost:4730?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz status 0

I noticed some output from the linkage_server prompt sating

[khttp_connect_file] fail to open file (HTTP code: 404).
[main] fail to open the data file.

Is this because the server couldn't find the calculated LD data? So where are these data calculated and stored so I could go and take a look?

Thanks!

Ke

On Thu, May 4, 2017 at 1:03 PM, Ke Jiang <[hidden email]> wrote:
Thanks, Colin! When I read this in the docs, I thought it meant linkage server was an option...

"Optionally, LD can be calculated from the VCF files on the server side using plink and rendered as a classic block view."

This is gonna be hard for me, as I'm not the administrator of the server, but I'll give it a try.

Thanks!

Ke

On Thu, May 4, 2017 at 12:23 PM, Colin <[hidden email]> wrote:
Currently, LDTrack requires the "linkage_server" part of the code to be running. To setup, go into the linkage_server folder, run `npm install`, and then `node index.js`, then set the ldviewer config in trackList.json to point to that node.js microservice (default runs on port 4730) 

-Colin

On Thu, May 4, 2017 at 10:39 AM, Ke Jiang <[hidden email]> wrote:
Hi,

Trying to use the MultiVariantViewer plugin, I've got the "Grid" type working but when I try switching to the "LDTrack" type it throws the following error:

Unable to load undefined?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz status 404

If the Grid is working, the location of the vcf.gz should be fine. But looks like the url constructed is not pointing to the right place.

Any thoughts?

Thanks!

Ke

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Re: MultiVariantViewer plugin problem

Colin
cc list resolved


-Colin

On Wed, May 10, 2017 at 10:56 AM, Ke Jiang <[hidden email]> wrote:
Hi, Colin,

You were absolutely right. The plink in the system is not called plink2 but simply plink. Now I put the full path to plink in the index.js and seems it's working now.

Thank you very much for the help!

Ke

On Wed, May 10, 2017 at 10:42 AM, Colin <[hidden email]> wrote:
Hehe I always say, a new error message is better than the same one over and over again (I am sure that type of thinking is crazy though)


ENOENT is a "No such file or directory"

Is plink2 installed? I think it would give that if it tried to run plink2 and it failed. You can customize the path to the plink exe in the ldserver/index.js too if needed (e.g. it might not be called plink2 on your system) 


-Colin

On Wed, May 10, 2017 at 10:37 AM, Ke Jiang <[hidden email]> wrote:
OK. I moved the vcf.gz and tbi to jbrowse_folder/data/json/Gohir_v11, so I can download the vcf at this url directly:


And changed the configuration accordingly. I'm still getting the "unable to load" error:

Unable to load http://localhost:4730?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2FACH1718_d20.vcf.gz status 0

The linkage server prompt said "downloading the index file..." then gave the following error:

events.js:72
        throw er; // Unhandled 'error' event
              ^
Error: spawn ENOENT
    at errnoException (child_process.js:1011:11)
    at Process.ChildProcess._handle.onexit (child_process.js:802:34)

What could this be?

Thanks!

Ke


On Wed, May 10, 2017 at 9:55 AM, Colin <[hidden email]> wrote:
The ldserver assumes that it can fetch the tabix VCF similar to how the browser does, so it receives as an argument the URL to the file e.g. the "http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz" part of the request.


For example, in this case, the url (after urldecoding) says http://jbrowse.xxxxx.com/data/json/Gohir_v11//../../raw/Gohir_v11/WGS/ACH1718_d20.vcf.gz, does this file exist if you visit it manually?

-Colin

On Wed, May 10, 2017 at 9:38 AM, Ke Jiang <[hidden email]> wrote:
Hi,

I gave a try with this and got this error:

Unable to load http://localhost:4730?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz status 0

I noticed some output from the linkage_server prompt sating

[khttp_connect_file] fail to open file (HTTP code: 404).
[main] fail to open the data file.

Is this because the server couldn't find the calculated LD data? So where are these data calculated and stored so I could go and take a look?

Thanks!

Ke

On Thu, May 4, 2017 at 1:03 PM, Ke Jiang <[hidden email]> wrote:
Thanks, Colin! When I read this in the docs, I thought it meant linkage server was an option...

"Optionally, LD can be calculated from the VCF files on the server side using plink and rendered as a classic block view."

This is gonna be hard for me, as I'm not the administrator of the server, but I'll give it a try.

Thanks!

Ke

On Thu, May 4, 2017 at 12:23 PM, Colin <[hidden email]> wrote:
Currently, LDTrack requires the "linkage_server" part of the code to be running. To setup, go into the linkage_server folder, run `npm install`, and then `node index.js`, then set the ldviewer config in trackList.json to point to that node.js microservice (default runs on port 4730) 

-Colin

On Thu, May 4, 2017 at 10:39 AM, Ke Jiang <[hidden email]> wrote:
Hi,

Trying to use the MultiVariantViewer plugin, I've got the "Grid" type working but when I try switching to the "LDTrack" type it throws the following error:

Unable to load undefined?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz status 404

If the Grid is working, the location of the vcf.gz should be fine. But looks like the url constructed is not pointing to the right place.

Any thoughts?

Thanks!

Ke

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Re: MultiVariantViewer plugin problem

Ke Jiang
Not quite there yet. I frequently run into complete blank rendering, even in a small interval as big as 10kb. And both "Matrix" and "LDTrack" gave blank rendering. Can't see any error messages on the linkage server side, as well as in the JS console. Any thoughts?

On Wed, May 10, 2017 at 11:35 AM, Colin <[hidden email]> wrote:
cc list resolved


-Colin

On Wed, May 10, 2017 at 10:56 AM, Ke Jiang <[hidden email]> wrote:
Hi, Colin,

You were absolutely right. The plink in the system is not called plink2 but simply plink. Now I put the full path to plink in the index.js and seems it's working now.

Thank you very much for the help!

Ke

On Wed, May 10, 2017 at 10:42 AM, Colin <[hidden email]> wrote:
Hehe I always say, a new error message is better than the same one over and over again (I am sure that type of thinking is crazy though)


ENOENT is a "No such file or directory"

Is plink2 installed? I think it would give that if it tried to run plink2 and it failed. You can customize the path to the plink exe in the ldserver/index.js too if needed (e.g. it might not be called plink2 on your system) 


-Colin

On Wed, May 10, 2017 at 10:37 AM, Ke Jiang <[hidden email]> wrote:
OK. I moved the vcf.gz and tbi to jbrowse_folder/data/json/Gohir_v11, so I can download the vcf at this url directly:


And changed the configuration accordingly. I'm still getting the "unable to load" error:

Unable to load http://localhost:4730?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2FACH1718_d20.vcf.gz status 0

The linkage server prompt said "downloading the index file..." then gave the following error:

events.js:72
        throw er; // Unhandled 'error' event
              ^
Error: spawn ENOENT
    at errnoException (child_process.js:1011:11)
    at Process.ChildProcess._handle.onexit (child_process.js:802:34)

What could this be?

Thanks!

Ke


On Wed, May 10, 2017 at 9:55 AM, Colin <[hidden email]> wrote:
The ldserver assumes that it can fetch the tabix VCF similar to how the browser does, so it receives as an argument the URL to the file e.g. the "http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz" part of the request.


For example, in this case, the url (after urldecoding) says http://jbrowse.xxxxx.com/data/json/Gohir_v11//../../raw/Gohir_v11/WGS/ACH1718_d20.vcf.gz, does this file exist if you visit it manually?

-Colin

On Wed, May 10, 2017 at 9:38 AM, Ke Jiang <[hidden email]> wrote:
Hi,

I gave a try with this and got this error:

Unable to load http://localhost:4730?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz status 0

I noticed some output from the linkage_server prompt sating

[khttp_connect_file] fail to open file (HTTP code: 404).
[main] fail to open the data file.

Is this because the server couldn't find the calculated LD data? So where are these data calculated and stored so I could go and take a look?

Thanks!

Ke

On Thu, May 4, 2017 at 1:03 PM, Ke Jiang <[hidden email]> wrote:
Thanks, Colin! When I read this in the docs, I thought it meant linkage server was an option...

"Optionally, LD can be calculated from the VCF files on the server side using plink and rendered as a classic block view."

This is gonna be hard for me, as I'm not the administrator of the server, but I'll give it a try.

Thanks!

Ke

On Thu, May 4, 2017 at 12:23 PM, Colin <[hidden email]> wrote:
Currently, LDTrack requires the "linkage_server" part of the code to be running. To setup, go into the linkage_server folder, run `npm install`, and then `node index.js`, then set the ldviewer config in trackList.json to point to that node.js microservice (default runs on port 4730) 

-Colin

On Thu, May 4, 2017 at 10:39 AM, Ke Jiang <[hidden email]> wrote:
Hi,

Trying to use the MultiVariantViewer plugin, I've got the "Grid" type working but when I try switching to the "LDTrack" type it throws the following error:

Unable to load undefined?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz status 404

If the Grid is working, the location of the vcf.gz should be fine. But looks like the url constructed is not pointing to the right place.

Any thoughts?

Thanks!

Ke

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Re: MultiVariantViewer plugin problem

Colin
Not sure if you already notice but the Matrix and LDTrack tracks are unique track types where you refresh the data in the current view manually using the track menu. Does that help?



Inline image 1




-Colin



On Wed, May 10, 2017 at 12:05 PM, Ke Jiang <[hidden email]> wrote:
Not quite there yet. I frequently run into complete blank rendering, even in a small interval as big as 10kb. And both "Matrix" and "LDTrack" gave blank rendering. Can't see any error messages on the linkage server side, as well as in the JS console. Any thoughts?

On Wed, May 10, 2017 at 11:35 AM, Colin <[hidden email]> wrote:
cc list resolved


-Colin

On Wed, May 10, 2017 at 10:56 AM, Ke Jiang <[hidden email]> wrote:
Hi, Colin,

You were absolutely right. The plink in the system is not called plink2 but simply plink. Now I put the full path to plink in the index.js and seems it's working now.

Thank you very much for the help!

Ke

On Wed, May 10, 2017 at 10:42 AM, Colin <[hidden email]> wrote:
Hehe I always say, a new error message is better than the same one over and over again (I am sure that type of thinking is crazy though)


ENOENT is a "No such file or directory"

Is plink2 installed? I think it would give that if it tried to run plink2 and it failed. You can customize the path to the plink exe in the ldserver/index.js too if needed (e.g. it might not be called plink2 on your system) 


-Colin

On Wed, May 10, 2017 at 10:37 AM, Ke Jiang <[hidden email]> wrote:
OK. I moved the vcf.gz and tbi to jbrowse_folder/data/json/Gohir_v11, so I can download the vcf at this url directly:


And changed the configuration accordingly. I'm still getting the "unable to load" error:

Unable to load http://localhost:4730?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2FACH1718_d20.vcf.gz status 0

The linkage server prompt said "downloading the index file..." then gave the following error:

events.js:72
        throw er; // Unhandled 'error' event
              ^
Error: spawn ENOENT
    at errnoException (child_process.js:1011:11)
    at Process.ChildProcess._handle.onexit (child_process.js:802:34)

What could this be?

Thanks!

Ke


On Wed, May 10, 2017 at 9:55 AM, Colin <[hidden email]> wrote:
The ldserver assumes that it can fetch the tabix VCF similar to how the browser does, so it receives as an argument the URL to the file e.g. the "http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz" part of the request.


For example, in this case, the url (after urldecoding) says http://jbrowse.xxxxx.com/data/json/Gohir_v11//../../raw/Gohir_v11/WGS/ACH1718_d20.vcf.gz, does this file exist if you visit it manually?

-Colin

On Wed, May 10, 2017 at 9:38 AM, Ke Jiang <[hidden email]> wrote:
Hi,

I gave a try with this and got this error:

Unable to load http://localhost:4730?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz status 0

I noticed some output from the linkage_server prompt sating

[khttp_connect_file] fail to open file (HTTP code: 404).
[main] fail to open the data file.

Is this because the server couldn't find the calculated LD data? So where are these data calculated and stored so I could go and take a look?

Thanks!

Ke

On Thu, May 4, 2017 at 1:03 PM, Ke Jiang <[hidden email]> wrote:
Thanks, Colin! When I read this in the docs, I thought it meant linkage server was an option...

"Optionally, LD can be calculated from the VCF files on the server side using plink and rendered as a classic block view."

This is gonna be hard for me, as I'm not the administrator of the server, but I'll give it a try.

Thanks!

Ke

On Thu, May 4, 2017 at 12:23 PM, Colin <[hidden email]> wrote:
Currently, LDTrack requires the "linkage_server" part of the code to be running. To setup, go into the linkage_server folder, run `npm install`, and then `node index.js`, then set the ldviewer config in trackList.json to point to that node.js microservice (default runs on port 4730) 

-Colin

On Thu, May 4, 2017 at 10:39 AM, Ke Jiang <[hidden email]> wrote:
Hi,

Trying to use the MultiVariantViewer plugin, I've got the "Grid" type working but when I try switching to the "LDTrack" type it throws the following error:

Unable to load undefined?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz status 404

If the Grid is working, the location of the vcf.gz should be fine. But looks like the url constructed is not pointing to the right place.

Any thoughts?

Thanks!

Ke

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