How to get my files to basecall

[Hannah1746]

I am trying to get my files in the right format to run deepsignal and I am having a lot of troubles. My fast5 files need to be basecalled from my fastq files. In the instructions it says "If the basecall results are saved as fastq, run the [tombo proprecess annotate_raw_with_fastqs]". I have done that but I am getting this error: Help?

[PengNi]

Hi @Hannah1746 ,

the arg value of --fastq-filenames seems not right. One possible solution is to cat all fastqs in directory to one fastq file using the following command:

cat Gill_pratice_fastq/* > Gill_pratice_fastq.all.fastq

then use _Gill_praticefastq.all.fastq as the value of --fastq-filenames .

[Hannah1746]

I was doing that originally and it gave me the same error.

[PengNi]

Hi @Hannah1746 ,

It is a little bit difficult for us to guess the problem without having the data. However, the picture you uploaded indicates that in your fast5 directory there are only 6 fast5 files. This is abnormal and could be a possible reson. May be either your fast5 directory is incorrect or the fast5 files in it are multi-fast5-format.

So could you check the fast5 directory and tell me what you see (how many fast5 files in it, the size of one fast5 file)?

Best, Peng

[Hannah1746]

This is my Fast5 and Fastq. There is only 6 of them because I am just doing a test run with a small amount of data to make it work before I used my 1.4 terabits of data. I also shared these files with you on google drive.

[PengNi]

Hi @Hannah1746 ,

We checked the fast5 files you shared, the fast5 files are indeed multi-fast5-format. According to tombo, we now should use _multi_to_singlefast5 in ont_fast5_api to convert them first.

Best, Peng