Reference uploading Error

[muzzamil1234]

Hi, hope you are doing well. my locally installed Insaflu is working fine but when i upload Reference file in fasta format only it give me error "Error creating the genbank file" how to solve this issue.

[dsobral]

Hello,

At the moment, fasta files used for references cannot have 'N' or other characters other than ACGT. Nonetheless, you should receive a message in the interface saying that, and not the "Error creating the genbank file" message you mention.

Therefore, there must be another issue going on. Does it happen with any fasta file, or just with that one in particular? You can try with one that is already in the platform to test (just name it differently).

Let us know.

Best, Daniel

[muzzamil1234]

"No, my reference sequence does not contain any 'N,' and this issue is not specific to one reference. I have tried different FASTA files as references, but the problem persists."

[dsobral]

Hello,

OK, thank you for the report. It is likely an issue with the prokka.

As a quick fix: If you have the genbank for the reference, you should use it when uploading the reference so INSaFLU will skip this process. If you don't have the genbank file, you can run prokka (or the more recent bakta) externally (eg. in Galaxy) to generate the genbank file, and then upload it with the fasta file in INSaFLU.

To effectively solve the issue you will need to go in the docker container running INSaFLU to pinpoint the issue with prokka.

My suggestion is that the issue is with the tbl2asn file.

Please go inside the docker container:

docker exec -it insaflu-server bash

Now test if prokka is working:

/software/prokka/bin/prokka /insaflu_web/INSaFLU/static/tests/managing_files/TwoGenesJoined.fasta --kingdom Viruses --locustag locus --genus Influenzavirus --species Influenzavirus --strain ref_PREFIX_FILES_OUT --gcode 11 --outdir temp --prefix prefix_out --force

I would think this will fail, possible due to tbl2asn. If that is the case, we need to get one and replace the previous

Still inside the docker

wget https://github.com/INSaFLU/docker/raw/master/components/insaflu-server/software/prokka/tbl2asn
chmod +x tbl2asn
cp /software/prokka/binaries/linux/tbl2asn /software/prokka/binaries/linux/tbl2asn_old
cp tbl2asn /software/prokka/binaries/linux

Test again if prokka is working

/software/prokka/bin/prokka /insaflu_web/INSaFLU/static/tests/managing_files/TwoGenesJoined.fasta --kingdom Viruses --locustag locus --genus Influenzavirus --species Influenzavirus --strain ref_PREFIX_FILES_OUT --gcode 11 --outdir temp --prefix prefix_out --force

Hopefully now it runs. you can now 'exit' the container, and see if the web interface is working,

Let us know.

Daniel

[muzzamil1234]

yes tbl2asn is not working, when i checked but also try to replace using command you mentioned above i think its not replacing or may have other issues. and yes i am trying to convert my fasta using galxay proka annotation.

[muzzamil1234]

and how to reset insaflu docker settings to default

[dsobral]

From your screenshot, it seems you have not run the last command of the list:

cp tbl2asn /software/prokka/binaries/linux/

One way to reset settings to the default values is to copy the .env (or its content) that is in the docker repository to the .env file in your insaflu container (/insaflu_web/INSaFLU/.env), and run the 'restart-apache' command.

[muzzamil1234]

now, reference uploading problem is solved.but when i create new project and add samples it is not processing, even i try different sample with built in references. , thats why i am asking to how to reset all settings