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gaoyubang / nanom6A

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Empty result file from extract raw and feature fast #16

Open Wardale24 opened 2 years ago

Wardale24 commented 2 years ago

Hi,

When running extract_raw_and_feature_fast.py the process finishes with no error messages, but both result files are empty. Any ideas why this could be?

python nanom6A_2021_10_22/extract_raw_and_feature_fast.py --cpu=20 --fl=datasets/data.txt -o result_data --clip=10

100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1813370/1813370 [00:58<00:00, 31101.48it/s]

ynren1020 commented 2 years ago

Hi @Wardale24 , I have the same issue when I run this step, have you solved this problem? Hi @gaoyubang , Do you know why we got empty output when we run "extract_raw_and_feature_fast"? Thanks a lot for your help!

Wardale24 commented 2 years ago

Hi @ynren1020 , no reply and no progress on my side. I will comment here if I do find the solution though!

ynren1020 commented 2 years ago

Thank you for your response, Alex. I will also let you know if I figure it out.

Yanan Ren

On Mon, Apr 11, 2022 at 2:46 AM Alex Wardale @.***> wrote:

Hi @ynren1020 https://github.com/ynren1020 , no reply and no progress on my side. I will comment here if I do find the solution though!

— Reply to this email directly, view it on GitHub https://github.com/gaoyubang/nanom6A/issues/16#issuecomment-1094662676, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGFIHCN3CDYOCXKMW3N3KOLVEPKDVANCNFSM5SH6GNXA . You are receiving this because you were mentioned.Message ID: @.***>

William-chen777 commented 1 year ago

Hello everybody! I had solved the problem. Just by installing the tombo=1.5

BernieeeX commented 1 year ago

Hello everybody! I had solved the problem. Just by installing the tombo=1.5

hiiiii William, what did you mean by installing tombo=1.5? Using tombo 1.5 to do the resquiggle?

atongmuuu commented 1 month ago

I've had the same problem. I found that it was due to missing "Signal" data in the fast5 file.

Toki-Haruka commented 1 month ago

Hello everybody, I just fixed my problem by generating the files.txt with the absolute path of fast5 files and now it works well. Just change the 'single' of find single -name "*.fast5" >files.txt to the absolute path of your fast5 files.