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bioinfomaticsCSU / deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads
GNU General Public License v3.0
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model_path #11

Closed Hannah1746 closed 5 years ago

Hannah1746 commented 5 years ago

So when I try to run: deepsignal call_mods --input_path fast5s.al.CpG.signal_features.17bases.rawsignals_360.tsv --model_path model.CpG.R9.4_1D.human_hx1.bn17.sn360/bn_17.sn_360.epoch_7.ckpt --result_file fast5s.al.CpG.call_mods.tsv --nproc 10 --is_gpu no the model path is wrong. From the trainer I downloaded form: http://bioinformatics.csu.edu.cn/resources/softs/nipeng/DeepSignal/index.html I get a file named: model.CpG.R9.4_1D.human_hx1.bn17.sn360 but when I go into the file there is no file named: bn_17.sn_360.epoch_7.ckpt witch of the files should I be using for the second half of the model_path? Screenshot from 2019-05-30 11-49-58

PengNi commented 5 years ago

Hi @Hannah1746 ,

We've updated a new and more stable model, which can be downloaded from google drive or clemson. We will also update the model in http://bioinformatics.csu.edu.cn/resources/softs/nipeng/DeepSignal/index.html soon. Sorry for making you confused.

Best, Peng

yaeba commented 5 years ago

Hi @PengNi ,

I have downloaded the latest trained model from google drive and bioinformatics but there is still no sign of a .ckpt file usable for calling methylation. Screen Shot 2019-07-11 at 3 59 07 pm

PengNi commented 5 years ago

Hi @yaeba ,

Sorry for making you confused. *.ckpt actually is prefix of those file names. It is a tensorflow feature. The prefix is used to indicate those files in the folder, all together as a model (a bunch of parameters). So you can use /path/to/model/bn_17.sn_360.epoch_7.ckpt as the value of --model_path .

Best, Peng

yaeba commented 5 years ago

Thanks for clearing that up for me @PengNi