Burrito : Unable to update file

[sandipansamaddar]

Hi, I have a couple of confusion and questions.If I get some help it will be really appreciated.

1. When I am uploading my files it doesn't seem to upload and return to No file selected. Is there a problem in the server?

2. What are the inputs required for the analysis?

• Abundance table : I have used dada2 pipeline for my analysis which gave me a ASV table. Will it work?
• Taxonomy file: I have assigned taxonomy using silva. Will it work? -Functional Data: The metagenomic contribution table from Picrust2. Will it work? -Metadata: Metadata file

So are all the four files required for the analysis? If yes what is the preferred format? CSV, TSV or TXT?

Thanks,

Sandipan

[engal]

Hi Sandipan,

Glad you're interested in using BURRITO! Hopefully I can help.

For your first question, this is a visual bug, the file is likely being successfully uploaded but the input form displays "No file selected". We think this bug will be fixed once we finish the server migration we're currently undergoing.

For you second question, a dada2 ASV table will only work if you also provide both a taxonomy file and one of either a genomic content table or a metagenomic contribution table. It sounds like you already have a taxonomy file and an associated metagenomic contribution table, so this should all work.

The abundance table, taxonomy file, and metagenomic contribution table will all be required given that you are using non-Greengenes taxonomic IDs. The metadata file is only used for grouping samples visually by whatever metadata variable you choose (and for some automatic statistical tests BURRITO runs to compare between the different values of that variable).

You can use either comma-separated or tab-separated formats, both will work. The only requirement is that the row/column formatting matches the formats described in the documentation or shown in the input examples.

Hope that helps!

[sandipansamaddar]

Thanks ! I uploaded the files and it is running. I hope I can get the results.  Thanks for your help. Sandipan

Sent from Yahoo Mail for iPhone

On Wednesday, January 15, 2020, 4:47 PM, engal notifications@github.com wrote:

Hi Sandipan,

Glad you're interested in using BURRITO! Hopefully I can help.

For your first question, this is a visual bug, the file is likely being successfully uploaded but the input form displays "No file selected". We think this bug will be fixed once we finish the server migration we're currently undergoing.

For you second question, a dada2 ASV table will only work if you also provide both a taxonomy file and one of either a genomic content table or a metagenomic contribution table. It sounds like you already have a taxonomy file and an associated metagenomic contribution table, so this should all work.

The abundance table, taxonomy file, and metagenomic contribution table will all be required given that you are using non-Greengenes taxonomic IDs. The metadata file is only used for grouping samples visually by whatever metadata variable you choose (and for some automatic statistical tests BURRITO runs to compare between the different values of that variable).

You can use either comma-separated or tab-separated formats, both will work. The only requirement is that the row/column formatting matches the formats described in the documentation or shown in the input examples.

Hope that helps!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[sandipansamaddar]

Hi,It is running for around 24 hours but still in the first step. Is that normal? Thanks, Sandipan

--------Sandipan Samaddar, PhDPostdoctoral Fellow, Scow Lab University of California, DavisDept. of Land Air & Water Resources+1-(530)-220-3895ssamaddar@ucdavis.edu

On Wednesday, 15 January, 2020, 4:47:29 pm GMT-8, engal <notifications@github.com> wrote:  

Hi Sandipan,

Glad you're interested in using BURRITO! Hopefully I can help.

For your first question, this is a visual bug, the file is likely being successfully uploaded but the input form displays "No file selected". We think this bug will be fixed once we finish the server migration we're currently undergoing.

For you second question, a dada2 ASV table will only work if you also provide both a taxonomy file and one of either a genomic content table or a metagenomic contribution table. It sounds like you already have a taxonomy file and an associated metagenomic contribution table, so this should all work.

The abundance table, taxonomy file, and metagenomic contribution table will all be required given that you are using non-Greengenes taxonomic IDs. The metadata file is only used for grouping samples visually by whatever metadata variable you choose (and for some automatic statistical tests BURRITO runs to compare between the different values of that variable).

You can use either comma-separated or tab-separated formats, both will work. The only requirement is that the row/column formatting matches the formats described in the documentation or shown in the input examples.

Hope that helps!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[engal]

Hi Sandipan,

Other users have experienced similar issues, and it is likely due to our server not being able to handle the size of your data. We're currently in the process of migrating to a new server that should provide better support for ASV-based data sets. Until we are finished with this process, you can still explore subsets of your data using BURRITO if you filter out some ASVs and/or functions.

I'll update this issue once we've finished our server migration.

Sorry for the inconvenience.

[sandipansamaddar]

Hello,I tried today with a much smaller dataset but it is getting disconnected from server while calculating hierarchies. May I get some help for that? Thanks, Sandipan--------Sandipan Samaddar, PhDPostdoctoral Fellow, Scow Lab University of California, DavisDept. of Land Air & Water Resources+1-(530)-220-3895ssamaddar@ucdavis.edu

On Tuesday, 21 January, 2020, 12:09:54 pm GMT-8, engal <notifications@github.com> wrote:  

Hi Sandipan,

Other users have experienced similar issues, and it is likely due to our server not being able to handle the size of your data. We're currently in the process of migrating to a new server that should provide better support for ASV-based data sets. Until we are finished with this process, you can still explore subsets of your data using BURRITO if you filter out some ASVs and/or functions.

I'll update this issue once we've finished our server migration.

Sorry for the inconvenience.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[engal]

Are you able to provide example files for the data you are submitting? This would help me confirm that the problems are with the server and not with the input data.

[sandipansamaddar]

These are the three files, and apart from these there is the legacy file which is around 208 MB. One snapshot for that file below:

It is running upto step 2 then suddenly showing

and exiting. Any help will be appreciated. Thanks, Sandipan --------Sandipan Samaddar, PhDPostdoctoral Fellow, Scow Lab University of California, DavisDept. of Land Air & Water Resources+1-(530)-220-3895ssamaddar@ucdavis.edu

On Tuesday, 21 January, 2020, 12:42:03 pm GMT-8, engal <notifications@github.com> wrote:  

Are you able to provide example files for the data you are submitting? This would help me confirm that the problems are with the server and not with the input data.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[engal]

I don't see any attachments, which I suspect is because you replied via email. If you want to attach files, I think you'll need to add them in a comment.

[sandipansamaddar]

Sorry for replying late.

There are total four files (three attached), and apart from the three attached there is the legacy file which is around 208 MB. One snapshot for that file is below:

After I input the files its running up to step 2 and then showing,

and exiting.

Any help will be appreciated.

Thanks,

Sandipan

ASVs_count.txt ASVs_taxonomy.txt metadata.txt

[engal]

Hi Sandipan,

The default functional hierarchy for BURRITO maps KO IDs to higher-level functional categorizations, not EC numbers. We don't currently have a default alternative hierarchy for EC numbers, so you have a few options:

1. Use PICRUSt2 to generate a contribution table for KO IDs, rather than EC numbers. Once you have created this file, you can upload it in place of your current contribution table and leave all of your other settings the same.
2. Create your own custom function hierarchy table mapping EC numbers to higher-level functional classifications. Once you have created this file, you would need to select the "Custom function hierarchy" option in the "Function hierarchy" section of the upload page and upload the associated custom file.
3. Run BURRITO without a hierarchy for functions. For this option, you do not need to generate/regenerate any new files, you would just select the "Custom function IDs with no hierarchy" option in the "Function hierarchy" section of the upload page.

I'm not sure which option would work best for you. Please let me know if you have any questions about any of them.

Best, Alex

[sandipansamaddar]

Hi, So this time I used the table with KO IDs and uploaded it. It didn't show the error which it was showing earlier but I waited for 72 hours and still it showed it was in the second step.

Any approximate date when will the server migration be finished? Can I perform the analysis locally?

Thanks,

Sandipan

[engal]

Hi Sandipan,

Sorry for the delayed response, we're currently finalizing the server migration. Could you try using the version of BURRITO at http://elbo-spice.cs.tau.ac.il/burrito/?

Best, Alex

[engal]

Hi Sandipan,

One more quick update, our server migration has been finalized, but in that process the new location of BURRITO has been slightly changed. You can now find it at http://elbo-spice.cs.tau.ac.il/shiny/burrito/. Please let me know if you are still running into the same issues on the new server.

Best, Alex

[sandipansamaddar]

Hi, Thanks for the update. I tried but this time it never started. It stays on the page Data Processing not yet started. I left it overnight hoping that it will start but still is the same.

I am not sure what the problem is.

Looking forward.

Thanks,

Sandipan

[engal]

Hi Sandipan,

Just to check, it doesn't even get to the "Step 1: Uploading files" message now?

One thing you can try that another user had success with is that when you select your file on the upload page, wait for the file name to disappear and become "No file selected" again. Once that happens for all of your files, then try running BURRITO.

If that doesn't work, then there are a couple of things you can do that might help me understand the current issue better. Try running BURRITO in the following ways and let me know what error messages you get:

First, upload just your taxonomic abundance file (and no other files) and try running BURRITO.

Next, upload your taxonomic abundance and taxonomic hierarchy file and try running BURRITO.

Let me know if either A) BURRITO doesn't seem to be responding or B) what error message you get. In both cases, you should get error messages.

Sorry that this is taking so long to work out the issues you're running into.

Best, Alex

[sandipansamaddar]

Yes, it doesn't even proceed to step 1.

So now I tried what you said. I uploaded the files and waited to see if it turns to no file uploaded but it remains same. Earlier it used to allow me to select lowest taxonomic resolution or select groups from metadata but now the drop down is not showing anything which might mean files are not being uploaded.

Trying option A and B it shows the same but it doesn't produce any error messages also.

I am not sure what is going on. This is what it looks like.

Thanks,

Sandipan

[sandipansamaddar]

Just noticed that even the Try out Burrito tab shows the same and doesn't proceed to step 1.

Thanks,

Sandipan

[engal]

The example not working is very strange. Can you send me the output from the browser console when you try to run BURRITO?

[sandipansamaddar]

Just to update, it proceed to Step 2 now. I will wait for it to finish.

But now again in a different tab I tried to run the example but it shows same.

Output from the console is :

I appreciate your help.

[engal]

Hi Sandipan,

Based on the issues you've been having, my guess would be that there's a problem with the connection to the server. I'll need to talk with our IT department to see if they can help figure out what's going wrong.

Hopefully I can have some answers for you soon.

Best, Alex

[sandipansamaddar]

Thanks. Will wait to hear from you.

[engal]

Hi Sandipan,

I apologize for the long delay. The issue isn't exactly clear, and the best idea we've been able to come up with is that your connection with the server is being lost at some point. We previously had the browser periodically ping the server to try and maintain the connection when uploading files and when processing data, but it's possible that your connection might be dropping before then (especially since you were having trouble with the example). I've tried to address this by starting the server pings as soon as the app starts up.

One other thing I'd caution against is refreshing and rerunning BURRITO multiple times in quick succession, I'm not sure but this might cause confounding issues that make the underlying problem harder to diagnose. Instead, if BURRITO does fail and you want to try again, maybe close the page and wait for a minute or so before retrying. Another suggestion might be to try other browsers (we've testing with Chrome, Firefox, Opera, and Safari).

Please try again when you get a chance and let me know what happens.

Best, Alex

[mbeckma2]

I believe the issue I am having is due to not using greengenes. Could you provide an example of a genomic content table?

Thank you in advance. Micaela

[engal]

Hi Micaela,

You can find an example genomic content table on the upload page if you go to Functional Data -> Taxonomy-function linking method -> Custom genomic content table and click the "example" button on the right.

The format for this file is a 3 column table with column headers. The names of the columns shouldn't matter, but the order does: the first column contains taxonomic IDs that match those found in your taxonomic abundance table, the second column contains the gene (or ortholog or function) IDs you are interested in using, and the third column contains copy numbers. Each row defines the copy number of a specific gene in a specific taxon. If there is no row corresponding to a taxon-gene pair, then it is assumed that taxon does not contain that gene in its genome.

Hope that helps!

Best, Alex