Bug with Bacteria and Phage track in Functional Annotation

[mlmoore9]

I ran the functional annotation on my phage genome and there is an issue with the Bacteria and Phage track. Here is a screenshot of the error. It should be a pretty average size genome. Please let me know if you need any more information and thank you for your help.

[nathandunn]

Do you get the same error if you load the track directly from JBrowse?

[cmdcolin]

Can probably increase chunkSizeLimit in your config file. That would be editing the trackList.json to have something like "chunkSizeLimit": "5000000" (that would be ~5mb, which you can even increase that). This says its downloading more than a megabyte of gene annotation data, which is probably totally fine. Probably jbrowse should increase it's default for this....

[cmdcolin]

Sometimes there are also cases where you can optimize gff3tabix loading so that it loads less data but I'd try increasing chunkSizeLimit first

[cmdcolin]

Note: increased the default in jbrowse dev branch...

[nathandunn]

@cmdcolin is that a recommendation for me in all cases or @mlmoore9 in this case?

[cmdcolin]

Well, if you would like to fix this issue, you can

(a) Increase chunkSizeLimit in your gff3tabix track's config file (b) Update to jbrowse dev branch which has increased the default chunkSizeLimit

[nathandunn]

I see.

The current version of Apollo is 1.6.10 (I usually just update automatically)

If that isn’t sufficient, then the user could fix this by either setting this explicitly in the track file or setting the branch to dev in the apollo config:

https://genomearchitect.readthedocs.io/en/latest/Configure.html#jbrowse-plugins-and-configuration

On Oct 5, 2020, at 10:37 AM, Colin Diesh notifications@github.com wrote:

Well, if you would like to fix this issue, you can

(a) Increase chunkSizeLimit in your gff3tabix track's config file (b) Update to jbrowse dev branch which has increased the default chunkSizeLimit

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/GMOD/Apollo/issues/2518#issuecomment-703780723, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFXNKXFSGK3VFFBL4CDQHLSJH74HANCNFSM4SCJCZGQ.

[mlmoore9]

Hi Colin and Nathan,

Could either of you you explain how I would update to the jbrowse dev branch with the increased chunksize limit? I have been accessing Apollo by clicking the icon on the Galaxy main page.

I also tried modifying the track's config file but couldn't find any lines referencing chunksize, so I wasn't sure what to add.

Thank you for your help! Best, Madeline

On Mon, Oct 5, 2020 at 10:43 AM Nathan Dunn notifications@github.com wrote:

I see.

The current version of Apollo is 1.6.10 (I usually just update automatically)

If that isn’t sufficient, then the user could fix this by either setting this explicitly in the track file or setting the branch to dev in the apollo config:

https://genomearchitect.readthedocs.io/en/latest/Configure.html#jbrowse-plugins-and-configuration

On Oct 5, 2020, at 10:37 AM, Colin Diesh notifications@github.com wrote:

Well, if you would like to fix this issue, you can

(a) Increase chunkSizeLimit in your gff3tabix track's config file (b) Update to jbrowse dev branch which has increased the default chunkSizeLimit

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/GMOD/Apollo/issues/2518#issuecomment-703780723>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAFXNKXFSGK3VFFBL4CDQHLSJH74HANCNFSM4SCJCZGQ .

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/GMOD/Apollo/issues/2518#issuecomment-703784410, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARHP3Y7QULL5X4LP5Z4OZUTSJIAVVANCNFSM4SCJCZGQ .

[nathandunn]

You should be able to temporarily edit the chunkSizeLimit in JBrowse / Apollo by clicking on the track and “Edit Config”.

You may need to add it explicitly if not already there (I haven’t tried it).

@cmdcolin

That being said, it would be worth contacting your admin and referring them to this thread so that they can change it explicitly for everyone.

What site are you accessing it from?

On Oct 5, 2020, at 1:03 PM, mlmoore9 notifications@github.com wrote:

Hi Colin and Nathan,

Could either of you you explain how I would update to the jbrowse dev branch with the increased chunksize limit? I have been accessing Apollo by clicking the icon on the Galaxy main page.

I also tried modifying the track's config file but couldn't find any lines referencing chunksize, so I wasn't sure what to add.

Thank you for your help! Best, Madeline

On Mon, Oct 5, 2020 at 10:43 AM Nathan Dunn notifications@github.com wrote:

I see.

The current version of Apollo is 1.6.10 (I usually just update automatically)

If that isn’t sufficient, then the user could fix this by either setting this explicitly in the track file or setting the branch to dev in the apollo config:

https://genomearchitect.readthedocs.io/en/latest/Configure.html#jbrowse-plugins-and-configuration

On Oct 5, 2020, at 10:37 AM, Colin Diesh notifications@github.com wrote:

Well, if you would like to fix this issue, you can

(a) Increase chunkSizeLimit in your gff3tabix track's config file (b) Update to jbrowse dev branch which has increased the default chunkSizeLimit

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/GMOD/Apollo/issues/2518#issuecomment-703780723>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAFXNKXFSGK3VFFBL4CDQHLSJH74HANCNFSM4SCJCZGQ .

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/GMOD/Apollo/issues/2518#issuecomment-703784410, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARHP3Y7QULL5X4LP5Z4OZUTSJIAVVANCNFSM4SCJCZGQ .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/GMOD/Apollo/issues/2518#issuecomment-703857820, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFXNKWXAKE3BGSOBX24NQDSJIQ7PANCNFSM4SCJCZGQ.

[cmdcolin]

@nathandunn Unfortunately it is not possible to edit chunkSizeLimit through the GUI edit config

I also tried modifying the track's config file but couldn't find any lines

There is likely not an entry for chunkSizeLimit there by default, but if you added a line that increases it I think that would work

So if you can see a track config such as

{
"label": "trackid",
"urlTemplate": "file.gff.gz",
"type": "CanvasFeatures",
/* etc */
}

Might not look exactly like that but just find your track, and then make it say

{
"label": "trackid",
"urlTemplate": "file.gff.gz",
"type": "CanvasFeatures",
"chunkSizeLimit": 50000000
/* etc */
}

That would make the limit 50mb and would likely never be hit. If you have the gff3 file you are using I could also test to see if there is anything that is making it request such a large amount by default too, even fetching 1MB is sort of abnormal which is what you are seeing.

[MoffMade]

Howdy! I think this may for our CPT Apollo instance? Are you experiencing the issue on https://cpt.tamu.edu/apollo ?

[mlmoore9]

Hi Cory!

Yes, I receive this error when using Apollo through the CPT site (at the link you included).

On Tue, Oct 6, 2020 at 2:47 PM Cory Maughmer notifications@github.com wrote:

Howdy! I think this may for our CPT Apollo instance? Are you experiencing the issue on https://cpt.tamu.edu/apollo ?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/GMOD/Apollo/issues/2518#issuecomment-704570672, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARHP3Y2YICQN764CHW5KVCLSJOF6LANCNFSM4SCJCZGQ .

[MoffMade]

I checked your organism, it looks like it was created before we implemented the increase in chunkSize as the others mentioned above. Unfortunately we don't have a way to retroactively apply the fix to your track but if you re-run the functional workflow again it should re-create it with the proper settings to load.

Thanks for your understanding, and if you need further help on this please email me at cory.maughmer@tamu.edu or you can open issues at our forked repository (https://github.com/TAMU-CPT/Apollo)

[mlmoore9]

Thanks Cory. Sounds good, I'll run the annotation again.

On Wed, Oct 7, 2020 at 12:55 PM Cory Maughmer notifications@github.com wrote:

I checked your organism, it looks like it was created before we implemented the increase in chunkSize as the others mentioned above. Unfortunately we don't have a way to retroactively apply the fix to your track but if you re-run the functional workflow again it should re-create it with the proper settings to load.

Thanks for your understanding, and if you need further help on this please email me at cory.maughmer@tamu.edu or you can open issues at our forked repository (https://github.com/TAMU-CPT/Apollo)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/GMOD/Apollo/issues/2518#issuecomment-705159716, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARHP3Y4E33GKWUN6FWRQVZLSJTBTZANCNFSM4SCJCZGQ .