Closed AyanoClarke closed 1 year ago
After re-basecalling by guppy
, the problem is solved. The command is here:
guppy_basecaller -i fast5 -c dna_r9.4.1_450bps_hac_prom.cfg -s basecalling --fast5_out
and use fast5 files in basecalling/workspace
for the next analysis. it works.
the structure of the new fast5 file is
> h5ls -r basecalling/workspace/b82c9dc6-29df-4807-8c88-9911a29f503c.fast5
#/ 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/BaseCalled_template/Move Dataset {956}
#/Analyses/Basecall_1D_000/Summary Group
#/Analyses/Basecall_1D_000/Summary/basecall_1d_template Group
#/Analyses/RawGenomeCorrected_000 Group
#/Analyses/RawGenomeCorrected_000/BaseCalled_template Group
#/Analyses/RawGenomeCorrected_000/BaseCalled_template/Alignment Group
#/Analyses/RawGenomeCorrected_000/BaseCalled_template/Events Dataset {402}
#/Analyses/Segmentation_000 Group
#/Analyses/Segmentation_000/Summary Group
#/Analyses/Segmentation_000/Summary/segmentation Group
#/Raw Group
#/Raw/Reads Group
#/Raw/Reads/Read_8 Group
#/Raw/Reads/Read_8/Signal Dataset {4963/Inf}
#/UniqueGlobalKey Group
#/UniqueGlobalKey/channel_id Group
#/UniqueGlobalKey/context_tags Group
#/UniqueGlobalKey/tracking_id Group
Is there any chance for tombo not to use the Analyses group?
Another solution is to use the summary file in tombo preprocess annotate_raw_with_fastqs
I meet the same problem, the fast5s can't be added any annotation. I use dorado basecall, and it's inputs are pod5 file of multi reads. maybe this reason?
Hi, everyone
when I run
tombo preprocess annotate_raw_with_fastqs
get no results. the full command of a small example isAnd I check the fast5 file by
h5ls -r
and get noAnalyses
group.This problem occurred after software and file format have been updated on the ONT sequencer. How to solve it? Thank you for your time and we look forward to your reply.