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xiaochuanle / hifimeth

High-fidelity 5mC DNA methylation detection model for PacBio HiFi reads
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Load 0 features including 0 samples #2

Open aewrwdw opened 1 year ago

aewrwdw commented 1 year ago

Hello Mr Xiao, I'm using hifimeth case1 to deal with human genome CCS data, but I couldn't get the proper result. I've looked up the log which back-feeded the information below:

model: /hifimeth/models/hifimeth-mol-k400.ckpt kmer size: 400 batch size: 512 dl_workers: 48 features directory: 5mc-call Total params: 368928 Total trainable params: 368928 number of chunks: 16 5mc-call/chunk_0.bin 5mc-call/chunk_0.samples [Wed Sep 6 21:45:49 2023] process 5mc-call/chunk_0.bin Load 0 features including 0 samples [Wed Sep 6 21:45:52 2023] probability path: 5mc-call/chunk_0.prob 5mc-call/chunk_1.bin 5mc-call/chunk_1.samples [Wed Sep 6 21:45:52 2023] process 5mc-call/chunk_1.bin Load 0 features including 0 samples

The input data is orginal CCS data in bam format, I'm not sure where is the error, could you please tell me how to deal with it or is there any parameter error? Thank you so much!

xiaochuanle commented 1 year ago

It seems that the kinetics information is missing in your BAM input. For each BAM record, the kinetics information includes four tags: fi:B:C, ri:B:C, fp:B:C and rp:B:C. No samples will be extracted if any one of this four tags is missing in a BAM record.