Problems uploading fastq files

[Former user]

I am new to Enterobase, so I am still getting my bearings, but yesterday I was able to upload 29 strains with no issue. I tried to add another batch today and it would go completely through the processing stage and I would get a notification that they had been uploaded (see screenshots), but then they would not show up in the curated strain list nor in the jobs list. They are staying in Uploaded Reads tab saying “awaiting upload”. I added the files multiple times from multiple computers and browsers, but I am not having any success. Any thoughts?

Thanks for your help.

[khaled mohamed]

Could you please send me your enterobase username, which database you are working with e.g. E.coli? please in the future do not create an issue as Anonymous and provide the basic information such as your enterobase user name so we could help.

[Joy Waite-Cusic]

Sorry about that. Username: waitecuj Database: Salmonella

[Joy Waite-Cusic]

I was able to upload other fastq files for new samples today, but when I tried these ones again, I still had the same problem. They go clear through the upload process, but the Progress bar stays stuck on "Processing" and never changes to "Success".

[khaled mohamed]

There are 42 strains in the Salmonella database for the user waitecuj, creation date varying from 10/10/2018 to 15/10/2018.

Please note that when you upload your reads, they are being sent to a server to assembly them, there is a queue for the users reads so it takes some time to process the assembly.

To get the stains, explore to the database home from the main Enterobase web page, then select "Search Strains" and press "My Strains" button. You can find more details about that in the following link https://enterobase.readthedocs.io/en/latest//features/main-search-page.html

You can find more details about upload reads using the following link: https://enterobase.readthedocs.io/en/latest//features/add-upload-reads.html

[Joy Waite-Cusic]

Thank you for following up. Yes, I have 42 strains that I have been able to upload and I have no problem accessing them. I have attempted to upload about a dozen more strains via the same route and on different computers; however, they seem to get stuck at the end of the uploading process and never switch from "Processing" to "Success" and they never appear in the database or in the job queue.

[Joy Waite-Cusic]

Hi Thanks so much for your help. Currently the ones having problems are still stuck and it has been over a week. We are able to upload new individual files without issue showing the queue is going through. The ones that are stuck we are un able to upload those files again without them getting stuck and we wonder if it is your jobs that are currently going stopping new ones with the same file or if there are file problems.

thanks, JWC

[khaled mohamed]

I am wondering if it is possible to send me a list of the files which are stuck? did you eneter the reads manullay or you uploaded a file which conatins the meta data then drag and drop the files?

[Joy Waite-Cusic]

I figured out the problem - the run file names that wouldn't upload had a space in the name. However, there are a number of samples that remain stuck ("awaiting upload") in the "uploading summary". I don't seem to be able to remove these from my end. Would it be possible for you to remove those ones? I think I may have the same problem within the E. coli database.

[khaled mohamed]

You have 78 files which status are "Awaiting Upload", dated from 10/10/2018 to 24/10/2018 some of them are for "E.coli" and other are "Salmonella".

Did you try to delete them from upload_reads from database home page, then select "Uploaded Reads" tabs then select the files and mouse right click then select "Remove Select Rows" from the pull down menu?