working with KBase

[DanaU]

I am currently studying Biotechnology, and my Bachelor’s thesis is leading me into the field of Bioinformatics. Specifically, I am working with the MinION 1bB and the MinKNOW software to generate sequencing data. My goal is to process the obtained FASTQ sequence data using the KBase platform. However, I have encountered some challenges because I have single-end reads, while KBase only accepts FASTQ Reads Non-Interleaved as the upload format, which is not directly produced by MinKNOW (since it only generates single-end reads).

Additionally, I have tried to assemble the sequences using the Flye assembler on KBase but am running into problems. The error message reads:

Server error: 'Error running /kb/module/Flye-2.9.4/bin/flye --nano-corr /kb/module/work/tmp/renamed_0e2f3d6d-56f7-4dc3-a372-97c30cbe45eb.single.fastq --out-dir /kb/module/work/tmp/flye_24fdabe8-18d4-49a9-83dd-46e82bb3ac8d; see logs under "Job Status" for details.'

I am currently trying to understand whether it is even possible to use KBase effectively under these conditions and how to resolve the issues with Flye, as the tool does not work as expected with my data.

Best regards, Dana

[fchatonnet]

Dear Dana,

from what I've seen (I'm not a user of KBase) you need to select the correct format for your files when you upload them. There is no default format for fastq files, so you must choose "single end reads" in the dropdown menu, see https://docs.kbase.us/data/upload-do...importing-data.
For your other error when running Flye, I guess you have to read the logs generated during your attempt to have an idea of what went wrong. It's usually a good idea to read the manuals of FAQ of the tools you want to use, and to carefully read the error codes or logfiles to get an idea of what happened. Then, you can also search internet for similar errors (stackoverflow or biostars websites are great for bioinformatic questions) and find how others have solved them.
Good luck for your training!