Getting an empty .fastq file as output when ran poretools command on multiple .fast5 files

Question

[SV]

Hello everyone,
I am trying to do assembly and annotation for oxford nanopore data, bacterial genome (have multiple .fast5 and fastq files with me). For this, I am referring to this link: https://angus.readthedocs.io/en/2017/analyzing_nanopore_data.html
So, according to steps given I am trying to convert multiple .fast5 files into a .fastq file. I tried,
1. poretools fastq $directory > data.fastq
2. poretools fastq ./*.fast5 > data.fastq (from usage examples for poretools: https://poretools.readthedocs.io/en/latest/content/examples.html)
but, this gives me an empty .fastq file. So I tried test data given on the link that I am referring to as input to poretools, it works well. I am not getting that, why any command for poretools is not working for my data, also it doesn't give any error. I also have multiple .fastq files with me, but not sure how to proceed for assembly and annotation.
Can anyone please help?
Thank you!

[GenoMax]

I also have multiple .fastq files with me, but not sure how to proceed for assembly and annotation.

Do you know if these files are from guppy caller (if the data is recent that is likely true)? If so you could proceed with assembly.

Answer 1

[WouterDeCoster]

Poretools was one of the first tools to be developed for working with fast5 data, but can nowadays be considered deprecated. It has no use anymore, since the basecaller (guppy) outputs fastq directly.

It is possible that your fast5 doesn't contain basecalls, and as such cannot write a fastq file.

Just use guppy to basecall fast5 files to fastq output, you won't need other tools.

[SV]

Ok, thanks @WouterDeCoster. I installed guppy using pip install guppy, it installed successfully, but when tried guppy_basecaller --help it says guppy_basecaller: command not found. Is guppy a working tool?

https://pypi.org/project/guppy/

[WouterDeCoster]

Wrong guppy. Do you have access to the nanopore community?

[SV]

I am a guest member of the nanopore community. I tried to create an account but they ask to select kits for a paid account. I need only access to the tool but did not find that option in the account creation process. Can you please help?

[WouterDeCoster]

Do you have access to https://community.nanoporetech.com/protocols/Guppy-protocol/v/GPB_2003_v1_revM_14Dec2018 after logging in with your guest account?

[SV]

No, I don't have access. When selected guppy for linux, it directs me to the Software Downloads page, which I don't have access to

[WouterDeCoster]

I've asked ONT about this and will get back to you if I hear anything.

[SV]

Ok, thanks! So basically for linux I would need Installing from the tar.gz archive file or Installing from an .rpm file options, where I don't have access to. Could you suggest any other option till then?