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borenstein-lab / burrito

A visualization tool for exploratory data analysis of metagenomic data
https://elbo-spice.gs.washington.edu/shiny/burrito/
GNU General Public License v3.0
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Can not upload sampling grouping #10

Closed Jessie-HOU closed 3 years ago

Jessie-HOU commented 3 years ago

Hi there!

Is BURRITO can be used normally now? I uploaded my files but the it can not generate plots. Another issue is I can not upload sample grouping file successfully. After I press 'Assemble the BURRITO', the page will be the following: 微信图片_20201103172605

Thanks in advance for any suggstions!

Best Regards, Jessie

engal commented 3 years ago

Hi,

I think I need a bit more information to help you, hopefully you can give me a few more details:

  1. Which upload options are you using? Are you just uploading a Greengenes OTU table, or are you also uploading your own genomic content or function attribution table?

  2. How long have you left BURRITO open after uploading your files? If you are uploading a genomic content or function attribution table, those files tend to be very large, and BURRITO needs to wait for those to finish uploading to the server before it can begin processing your data. The picture you sent is what you would see if BURRITO is still waiting on files to finish uploading.

  3. Could you provide examples of your input files? The first 5-10 lines of each file you are uploading should be sufficient for me to check on potential formatting issues.

Thanks!

Jessie-HOU commented 3 years ago

Hello Borenstein-Lab/Burrito,

Thank you for your reply.

  1. My uploading options are: Taxonomy abundance table with custom taxonomy; a function attribution table with no hierarchy; a sample metadata file. Please see my attached upload page screenshot for details.

  2. You are right, my files are quite large (maximum > 1G). I have waited for more than 20 minutes for my large data. Then I have subset my data into very small test files and try again, but still failed. Please see attached file for my test file.

  3. For test files, full OTU_table is OTU s19030002 s19030004 s19030006 s19030007 s19030011 36500f9a8052d9f8c6b8680a0bbc9477 0 40585 0 0 8 7dc7ab0760a5f336e64713ebbedc3208 601 0 13412 342 0 c54979568a2e94e7ca090bce9a9afb7c 487 10696 0 170 0 ddcf0a6602972dd683d08036fc370e4b 1785 0 0 0 0 4ce8e13338c6646de43039d364b9ddb7 1257 271 3987 82 0 Full sample metadata is: Sample Group s19030002 pre s19030004 post s19030006 pre s19030007 pre s19030011 post You can see from the screenshot that I cannot upload my sample metadata file even if I have tried. Full taxonomy table is: OTU Kingdom Phylum Class Order Family Genus Species 36500f9a8052d9f8c6b8680a0bbc9477 kBacteria pBacteroidetes cBacteroidia oBacteroidales fBacteroidaceae gBacteroides 7dc7ab0760a5f336e64713ebbedc3208 kBacteria pBacteroidetes cBacteroidia oBacteroidales fBacteroidaceae gBacteroides sBacteroides vulgatus c54979568a2e94e7ca090bce9a9afb7c kBacteria pFirmicutes cClostridia oClostridiales fRuminococcaceae gFaecalibacterium ddcf0a6602972dd683d08036fc370e4b kBacteria pFirmicutes cClostridia oClostridiales fRuminococcaceae gRuminococcus 2 4ce8e13338c6646de43039d364b9ddb7 kBacteria pActinobacteria cActinobacteria oBifidobacteriales fBifidobacteriaceae g__Bifidobacterium First 10 lines of function contribution table is: Gene Sample OTU GeneCountPerGenome OTUAbundanceInSample CountContributedByOTU K00001 s19030002 4ce8e13338c6646de43039d364b9ddb7 2 1.953024858 3.906049716 K00001 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00003 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00003 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00003 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00008 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00012 s19030002 7dc7ab0760a5f336e64713ebbedc3208 2 2.801355465 5.602710929 K00012 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00013 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00013 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 See the attached input test files for detail. In brief, I run qiime2-data2 pipeline to obtain the OTU table based on silva 132 database, and run picrust2 based on KO (i.e. KEGG Orthology) database to obtain function contribution table. By the way, is it necessary for me to upload Function hierarchy file? If yes, how to prepare the 'function hierarchy' file for my case? Many thanks for your help!

Best regards, Jessie

On Wed, Nov 4, 2020 at 3:11 AM engal notifications@github.com wrote:

Hi,

I think I need a bit more information to help you, hopefully you can give me a few more details:

1.

Which upload options are you using? Are you just uploading a Greengenes OTU table, or are you also uploading your own genomic content or function attribution table? 2.

How long have you left BURRITO open after uploading your files? If you are uploading a genomic content or function attribution table, those files tend to be very large, and BURRITO needs to wait for those to finish uploading to the server before it can begin processing your data. The picture you sent is what you would see if BURRITO is still waiting on files to finish uploading. 3.

Could you provide examples of your input files? The first 5-10 lines of each file you are uploading should be sufficient for me to check on potential formatting issues.

Thanks!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/borenstein-lab/burrito/issues/10#issuecomment-721322248, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHE7VRFNIECSGUZQ2DF3TPLSOBIUTANCNFSM4TIP5BAQ .

OTU s19030002 s19030004 s19030006 s19030007 s19030011 36500f9a8052d9f8c6b8680a0bbc9477 0 40585 0 0 8 7dc7ab0760a5f336e64713ebbedc3208 601 0 13412 342 0 c54979568a2e94e7ca090bce9a9afb7c 487 10696 0 170 0 ddcf0a6602972dd683d08036fc370e4b 1785 0 0 0 0 4ce8e13338c6646de43039d364b9ddb7 1257 271 3987 82 0

Sample Group s19030002 pre s19030004 post s19030006 pre s19030007 pre s19030011 post

OTU Kingdom Phylum Class Order Family Genus Species 36500f9a8052d9f8c6b8680a0bbc9477 kBacteria pBacteroidetes cBacteroidia oBacteroidales fBacteroidaceae gBacteroides
7dc7ab0760a5f336e64713ebbedc3208 kBacteria pBacteroidetes cBacteroidia oBacteroidales fBacteroidaceae gBacteroides sBacteroides vulgatus c54979568a2e94e7ca090bce9a9afb7c kBacteria pFirmicutes cClostridia oClostridiales fRuminococcaceae gFaecalibacterium ddcf0a6602972dd683d08036fc370e4b kBacteria pFirmicutes cClostridia oClostridiales fRuminococcaceae gRuminococcus 2
4ce8e13338c6646de43039d364b9ddb7 kBacteria pActinobacteria cActinobacteria oBifidobacteriales fBifidobacteriaceae g__Bifidobacterium

Gene Sample OTU GeneCountPerGenome OTUAbundanceInSample CountContributedByOTU K00001 s19030002 4ce8e13338c6646de43039d364b9ddb7 2 1.953024858 3.906049716 K00001 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00003 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00003 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00003 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00008 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00012 s19030002 7dc7ab0760a5f336e64713ebbedc3208 2 2.801355465 5.602710929 K00012 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00013 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00013 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00013 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00013 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00014 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00014 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00014 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00014 s19030002 ddcf0a6602972dd683d08036fc370e4b 2 8.320165564 16.64033113 K00016 s19030002 4ce8e13338c6646de43039d364b9ddb7 2 1.953024858 3.906049716 K00016 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00018 s19030002 7dc7ab0760a5f336e64713ebbedc3208 2 2.801355465 5.602710929 K00018 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00018 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00024 s19030002 7dc7ab0760a5f336e64713ebbedc3208 2 2.801355465 5.602710929 K00027 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00027 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00029 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00031 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00031 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00031 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00031 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00033 s19030002 4ce8e13338c6646de43039d364b9ddb7 2 1.953024858 3.906049716 K00033 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00036 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00036 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00041 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00046 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00048 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00048 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00052 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00052 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00052 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00052 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00053 s19030002 4ce8e13338c6646de43039d364b9ddb7 2 1.953024858 3.906049716 K00053 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00053 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00053 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00057 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00057 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00057 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00057 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00058 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00058 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00058 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00058 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00059 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00059 s19030002 7dc7ab0760a5f336e64713ebbedc3208 2 2.801355465 5.602710929 K00059 s19030002 c54979568a2e94e7ca090bce9a9afb7c 3 1.134991773 3.404975319 K00059 s19030002 ddcf0a6602972dd683d08036fc370e4b 3 8.320165564 24.96049669 K00067 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00067 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00067 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00074 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00075 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00075 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00075 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00075 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00077 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00077 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00077 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00088 s19030002 4ce8e13338c6646de43039d364b9ddb7 2 1.953024858 3.906049716 K00088 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00088 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00088 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00097 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00099 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00099 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00099 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00099 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00100 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00100 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00100 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00133 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00133 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00133 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00133 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00134 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00134 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00134 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00134 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00145 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00145 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00145 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00145 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00147 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00147 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00147 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00147 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00169 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00170 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00171 s19030002 ddcf0a6602972dd683d08036fc370e4b 1 8.320165564 8.320165564 K00172 s19030002 ddcf0a6602972dd683d08036fc370e4b 2 8.320165564 16.64033113 K00174 s19030002 7dc7ab0760a5f336e64713ebbedc3208 2 2.801355465 5.602710929 K00174 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00175 s19030002 7dc7ab0760a5f336e64713ebbedc3208 2 2.801355465 5.602710929 K00175 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00176 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00177 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00179 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00179 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00180 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00180 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00198 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00208 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00210 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00215 s19030002 4ce8e13338c6646de43039d364b9ddb7 1 1.953024858 1.953024858 K00215 s19030002 7dc7ab0760a5f336e64713ebbedc3208 1 2.801355465 2.801355465 K00215 s19030002 c54979568a2e94e7ca090bce9a9afb7c 1 1.134991773 1.134991773 K00215 s19030002 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engal commented 3 years ago

Hi Jessie,

One thing I can answer quickly, if you're looking at KOs, then you do not need to upload a function hierarchy table, the default hierarchy table will work.

Regarding your files:

Your sample metadata file looks fine.

In your taxonomic hierarchy file, each row should have an entry for each column. If you don't have a species assignment for an OTU, you could put something like "s__Unknown" or similar.

Given that you are using the function contribution table option, it's likely that it will take quite some time to upload your data. It sounds like you've already tried testing with a subset of your data, which should help identifying any formatting issues (like in your taxonomic hierarchy table). If you are not already doing so, I would also strongly recommend that you compress the function contribution table using gzip before upload. This should decrease the upload the time as well.

If BURRITO is waiting on the page that you sent a picture of and no error messages have appeared and the screen has not gone grey, that means that the data is still uploading and you should wait. Depending on your connection, the size of your data, and your distance from the server, the upload can take quite some time.

Let me know if fixing that problem in the taxonomic hierarchy file helps.

Jessie-HOU commented 3 years ago

Dear Borenstein-Lab/Burrito,

Thank you for your suggestion. For the test files, I followed your advice by adding 's__unknown' in the empty 'species' column in the taxonomic hierarchy file. And compress my function contribution (39KB in size after compression) table. After that, I once again uploaded these test files (ps: this time I chose the default BRITE function hierarchy), but still failed to upload the metadata files. Then I press 'Assembly the BURRITO' button, it turn out to be the grey page as follows: [image: image.png]

Finally, I waited on this page for 20 minutes, is there anything wrong at all? Why can the metadata file not be uploaded? If the test data still needs such a long time for uploading, it is not possible for me to use BURRITO for my real data. Many thanks again!

Best regards, Jessie

On Thu, Nov 5, 2020 at 8:32 AM engal notifications@github.com wrote:

Hi Jessie,

One thing I can answer quickly, if you're looking at KOs, then you do not need to upload a function hierarchy table, the default hierarchy table will work.

Regarding your files:

Your sample metadata file looks fine.

In your taxonomic hierarchy file, each row should have an entry for each column. If you don't have a species assignment for an OTU, you could put something like "s__Unknown" or similar.

Given that you are using the function contribution table option, it's likely that it will take quite some time to upload your data. It sounds like you've already tried testing with a subset of your data, which should help identifying any formatting issues (like in your taxonomic hierarchy table). If you are not already doing so, I would also strongly recommend that you compress the function contribution table using gzip before upload. This should decrease the upload the time as well.

If BURRITO is waiting on the page that you sent a picture of and no error messages have appeared and the screen has not gone grey, that means that the data is still uploading and you should wait. Depending on your connection, the size of your data, and your distance from the server, the upload can take quite some time.

Let me know if fixing that problem in the taxonomic hierarchy file helps.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/borenstein-lab/burrito/issues/10#issuecomment-722050156, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHE7VREHORIZJOUEY4RWFNTSOHXABANCNFSM4TIP5BAQ .

engal commented 3 years ago

Hi Jessie,

Sorry, it doesn't look like the image made it through. I'm not sure, but maybe if you make the reply post on GitHub rather than via email, attaching files to the reply post might work better.

When you say you got to the grey page, did it give you a message saying you were disconnected from the server?

And when you say it failed to upload the metadata files, do you mean you get an error when you try to run BURRITO, or are you running into an issue when you are trying to select the metadata file? There's currently a visual bug where choosing a sample metadata file will not display the name on the upload page even if it has been successfully uploaded. You can check if it has finished uploading by using the dropdown menu below and seeing if the column names in your metadata file are available for you to select.

I think that compressed contribution table might be small enough that you could attach it in a reply post, which would let me try it out along with the test files you sent earlier.

Jessie-HOU commented 3 years ago

Hi Engel,

Sorry, it doesn't look like the image made it through. I'm not sure, but maybe if you make the reply post on GitHub rather than via email, attaching files to the reply post might work better.

Sorry, here is the page after I clicked on the 'Assembly the BURRITO' button. image

When you say you got to the grey page, did it give you a message saying you were disconnected from the server?

No, the above occurred immediately after I clicked on the 'Assembly the BURRITO' button, without any warning or error message.

And when you say it failed to upload the metadata files, do you mean you get an error when you try to run BURRITO, or are you running into an issue when you are trying to select the metadata file? There's currently a visual bug where choosing a sample metadata file will not display the name on the upload page even if it has been successfully uploaded. You can check if it has finished uploading by using the dropdown menu below and seeing if the column names in your metadata file are available for you to select

I didn't get any error when I try to upload the metadata file. Though it allowed uploading the metadada file by popping up a file selection window for me to choose the metadata file, it has no any response after I chose the file. That is to say, unlike other files (e.g. taxonomy.txt, functional contribution file), the metadata was still not present in the BURRITO upload page after I chose the metadata file. Could you help me to debug the test files by having a try? The test files are as follows:

ASV_for_burrito.txt

metadata.txt

taxonomy.txt

KO_contrib.txt

Please note that I have to give you the uncompressed function contribution file (kindly you can compress it if you like), since github does not support .zip file. Thank you very much for your help.

Best regards, Jessie

engal commented 3 years ago

Hi Jessie,

Thanks for the additional information.

I just want to clarify a couple of things. First, the image you attached shows the "progress" page for BURRITO. When it reads "Data processing not yet started" at the top, that means that BURRITO is still waiting for the selected files to finish uploading to the server before it can start processing the data. Once the files have finished uploading, then the progress page will keep you updated on what BURRITO is doing in terms of processing steps. If you did not receive a disconnect message and the screen hasn't turned grey, then that means you are still connected to the server and things should be working as expected.

Second, there is a known visual bug on the upload page concerning the sample metadata file. When you select a sample metadata file, even if the file is successfully selected and uploaded, the name of the file will not be displayed (we have yet to track down exactly why the "No file selected" text is not being updated to the name of the file). However, after selecting your metadata file, you can confirm that the metadata file was successfully uploaded by going to the dropdown menu directly below and checking that the columns in your metadata file are selectable in the dropdown menu.

Unfortunately, the more general problem you are running into just got a lot more confusing. I used the files you attached, and when I ran BURRITO, it quickly (couple of seconds) and successfully generated the following visualization (note grouping by metadata):

burrito_screenshot

So all of your files appear to be correctly formatted and appropriate for BURRITO. The question now seems to be: why are your files not successfully, or at least not quickly, being uploaded to the server from your machine? At this point, by main concern is that there might be some issue with your connection to the server. Can you try running BURRITO with these test files one more time? I want to take a look at the server-side logs, but I can't currently identify which logs belong to your previous attempts to run BURRITO. If you run it again, I should be able to isolate the newest logs and check to see if anything is going wrong on the server.

Thanks for your patience.

Jessie-HOU commented 3 years ago

Dear Engal,

Thank you for your reply. Once again, I uploaded the files but failed by obtainng the same 'Data processing not yet started' page, even if I have waited for about 10 minutes. Then I changed my browser from Google chrome to Internet Explorer and trying uploading these files again, but I cannot even press 'Ensemble the BURRITO' button (when I clicked on it, nothing happens. That is, it didn't appear the 'Data processing not yet started' page but remained to be in the upload page).

In addition, I asked my colleague to upload these test files using his desktop computer, but that still failed with the same problem (i.e. It showed 'Data processing not yet started' page). Maybe this issue is related to our lab's connection to the server? I am using BURRITO in Hong Kong. Many thanks again for your patient reply!

Best regards, Jessie

engal commented 3 years ago

Hi Jessie,

Quick note: BURRITO is not currently supported on IE, but you could try Firefox, Safari, or Opera as alternative browsers just to check.

Based on everything so far, a connection issue seems possible. Have you tried the example dataset (the "Try Out BURRITO" button at the top of the page)? If that works, then it does seem like there is a specific problem with files from your location being transferred to the server.

If this is the case, I'm not entirely sure how to fix it, though you might try consulting your IT department if possible.

Best, engal

Jessie-HOU commented 3 years ago

Dear Engal,

I have tried BURRITO on Safari but still failed (with the same issue as using google chrome previously).

I have tried clicked on 'Try out BURRITO' button for 3 times, but it also showed me a page ''Data processing not yet started' even if I have waited for 5 minutes on this page. In other words, 'Try out BURRITO' and using my test data just got the same problem.

Best regards, Jessie

engal commented 3 years ago

Hi Jessie,

Thanks for the update, good to know it's not just a Chrome issue.

The fact that the example doesn't work is definitely odd. That option requires no data to be uploaded, it should only send things back to you. So this isn't just a file upload problem.

Is it possible for you to try running the BURRITO example ("Try out BURRITO") on a different machine, possibly outside your lab? For example, from a home computer, or anything outside the network that you've been trying from? If you are just running the example, you won't need your actual data.

Jessie-HOU commented 3 years ago

Hi Engal,

You are right! This problem is due to the web connection of my colleage. I have successfully run "Try out BURRITO" and the test data on my home computer and my friend's computer who is outside my University. But it still failed when I asked colleagues in other lab within the University to try BURRITO. I can just run the data at home! That's it! Thank you very much for your kind help.

Best regards, Jessie

engal commented 3 years ago

Hi Jessie,

Thanks for the update. I'll close this for now, but please let us know if you run into any other issues.