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WGLab / DeepMod2

DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads
MIT License
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Please refer to DeepMod2 for the updated tool. #4

Closed fire-activate closed 9 months ago

fire-activate commented 2 years ago

My instructions are /home/qiulimei/softwore/DeepMod/bin/DeepMod.py detect --Ref /home/qiulimei/nanopolish/reference.fasta --modfile /home/qiulimei/softwore/DeepMod/train_deepmod/rnn_conmodA_P100wd21_f7ne1u0_4/mod_train_conmodA_P100wd21_f3ne1u0 --Base A --wrkBase /home/qiulimei/nanopolish/output/workspace/pass --outFolder /home/qiulimei/nanopolish/result But there is： Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/2d938cbc-7e74-43fb-98c4-db98ebd4b1fc.fast5 Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/71a14234-8cf3-425c-8195-75c90cd156f6.fast5 Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/3bddd188-3d9a-4e58-ac9f-473769f4ee90.fast5 Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/50fbbdbc-6bbe-4c7d-ab2a-d9dcc96daf0d.fast5 Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/d7134f4a-063c-4f58-b30c-194c5100fc51.fast5 Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/27a978e1-ef10-4ab2-87d7-a525b220b749.fast5 Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/29b03e41-2a10-4cb4-a094-1f9f0db37a81.fast5 Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/7c9338db-5059-4b23-a32b-e3b7aef93154.fast5 Error!!! No events data in /home/qiulimei/nanopolish/output/workspace/pass/0/b0b3ecd8-0e41-46b1-87e9-e98487a0e17a.fast5

I checked one of the fast5 files and found that there was an event / Group /Analyses Group /Analyses/Basecall_1D_000 Group /Analyses/Basecall_1D_000/BaseCalled_template Group /Analyses/Basecall_1D_000/BaseCalled_template/Events Dataset {17342} /Analyses/Basecall_1D_000/BaseCalled_template/Fastq Dataset {SCALAR} /Analyses/Basecall_1D_000/Configuration Group /Analyses/Basecall_1D_000/Configuration/basecall_1d Group /Analyses/Basecall_1D_000/Summary Group I can see that I am using Events data in fast5, but deepmod still reports an error The Deepmod author sent me to deepmod2 to get the updated tools

What I don't know is what the updated tools is ? https://github.com/WGLab/DeepMod/issues/56

Looking forward to your reply,Thank you

umahsn commented 2 years ago

Hi,

The updated version DeepMod2 works with FAST5 files basecalled with Guppy or resquiggled with Tombo. Please check this example page to see how to prepare your fast5 files for DeepMod2.