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weir12 / DENA

Deep learning model used to detect RNA m6a with read level based on the Nanopore direct RNA data.
MIT License
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Abnormal result: The prediction output file is empty #8

Closed Derryxu closed 2 years ago

Derryxu commented 2 years ago

Hi, I tried to use DENA pre-train model to predict m6A of my data, I followed the step 4 (prediction) on my data.However, the output file both result.tsv and result_details.tsv are empty. It seems data problem, so I check extracted features file:

  1. the candidate_predict_pos.txt 
    cc6m_2244_T7_ecorv  57  62  +   AAACC
cc6m_2244_T7_ecorv  64  69  +   GGACC
cc6m_2244_T7_ecorv  100 105 +   GGACT
cc6m_2244_T7_ecorv  121 126 +   GGACC
cc6m_2244_T7_ecorv  173 178 +   AGACT
  2. the features tmp file 
    >cc6m_2595_T7_ecorv_724_GAACC
adec290a-fa23-4951-9863-51c26c65ab5e    15.0,5.0,2.0,3.0,4.0,116.0,12.0,29.0,19.0,6.0,2.05947621375705,0.05645722345324113,-0.6669842273497038,-1.1006984040938008,-0.04247432038586929,1.896162953567763,0.0775064880998608,-0.7244704949363322,-1.1033572585754785,-0.061418658567826176,nan,nan,nan,nan,nan
fb801573-cb5c-4303-bc93-2a03078640d3    37.0,36.0,43.0,39.0,27.0,54.0,47.0,15.0,19.0,139.0,2.1592956780773624,0.21144323911696417,-0.5459008501149659,-1.3049430979691616,-0.14210523308214737,2.103417210260246,0.19766736049756647,-0.5841787317127636,-1.3049430979691616,-0.1443903048444529,nan,nan,nan,nan,nan
0c957530-bdeb-4fe8-831b-7af44316226b    24.0,26.0,26.0,26.0,19.0,53.0,29.0,23.0,16.0,6.0,1.6108504242449508,0.3408191542598859,-0.5112268966474004,-1.0857024459872902,0.07775649380342814,1.389964503297866,0.19353955346470164,-0.47542923568932577,-1.073641710605908,0.019864963972790688,nan,nan,nan,nan,nan
  3. I also print the intermediate variable predict_label, all nan 
    predict_label
tensor([[nan, nan],
    [nan, nan],
    [nan, nan],
    ...,
    [nan, nan],
    [nan, nan],
    [nan, nan]])
......

    How could I resolve it? Thanks in advance.

weir12 commented 2 years ago

Hi， I noticed that the last five columns of the feature table are missing values, which should have been the current standard deviation. My guess is that you maybe forgot to add--include-event-stdev to thetombo re-sguiggle command option. I suggest you re-runtombo re-sguiggle command and add this option.I will add this note to the DENA readme For an explanation of this parameter, please refer to https://nanoporetech.github.io/tombo/resquiggle.html best wishes weir

Derryxu commented 2 years ago

Hi, Thank you very much for your reply. I'll re-run tombo re-sguiggle command with the option --include-event-stdev and close the issue after finishing all my data if there have no further errors. Best wishes. xu