Error!!! No Raw_reads/Signal data /Raw/Reads

[bakeronit]

Hi all,

I am using DeepMod to detect 5mC. I had converted multi-fast5 files into single fast5 files. and each file looks like:

/                        Group
/Analyses                Group
/Analyses/Basecall_1D_000 Group
/Analyses/Basecall_1D_000/BaseCalled_template Group
/Analyses/Basecall_1D_000/BaseCalled_template/Fastq Dataset {SCALAR}
/Analyses/Basecall_1D_000/Summary Group
/Analyses/Basecall_1D_000/Summary/basecall_1d_template Group
/Analyses/Segmentation_000 Group
/Analyses/Segmentation_000/Summary Group
/Analyses/Segmentation_000/Summary/segmentation Group
/Raw                     Group
/Raw/Reads               Group
/Raw/Reads/Read_548      Group
/Raw/Reads/Read_548/Signal Dataset {5819/Inf}
/UniqueGlobalKey         Group
/UniqueGlobalKey/channel_id Group
/UniqueGlobalKey/context_tags Group
/UniqueGlobalKey/tracking_id Group

It seems there are Signal data in the file ,however, I got errors:
Error!!! No Raw_reads/Signal data /Raw/Reads xxxx

Can you help me with the error? Thank you.

Attached is the whole output.
stdout.txt

[liuqianhn]

@bakeronit It seems that there is an error in

      for raw_data in sp_param['f5reader'][fast5_rawReads].values(): pass;
      sp_param['raw_attributes'] = dict(raw_data.attrs.items())

      sp_param['raw_signals'] = raw_data['Signal'][()]

You can either use DeepMod2 or share the fast5 file for testing. Thanks.

[bakeronit]

Thanks for the reply. I found the reason might be the compress format of my fast5 is vbz instead of gzip. Install ont-vbz-hdf-plugin solves the problem.

Although, I got new error of no events data after ... it might be some basecalling issue

[liuqianhn]

@bakeronit Thank you for sharing the solution. Feel free to share other errors if you want.