laguda-1996
commented
4 years ago Display at terminal：
Nanopore sequencing data analysis is resourece-intensive and time consuming. Some potential strong recommendations are below: If your reference genome is large as human genome and your Nanopore data is huge, It would be faster to run this program parallelly to speed up. You might run different input folders of your fast5 files and give different output names (--FileID) or folders (--outFolder) A good way for this is to run different chromosome individually.
Current directory: /home/dsy/software/DeepMod
outLevel: 2
wrkBase: /home/dsy/2T_WD/深度学习_识别m6a/数据/m6a/RNAAB090763.fast5.tar.gz/fast5/1204665-1.fast5
FileID: m6a
outFolder: 123/
recursive: 1
files_per_thread: 1000
threads: 6
windowsize: 21
alignStr: minimap2
SignalGroup: simple
move: False
basecall_1d: Basecall_1D_000
basecall_2strand: BaseCalled_template
ConUnk: True
outputlayer:
Base: A
mod_cluster: 0
predDet: 1
Ref: /home/dsy/2T_WD/深度学习_识别m6a/数据/reference_fasta/jiaomu.fna
fnum: 7
hidden: 100
modfile: train_mod/rnn_conmodA_P100wd21_f7ne1u0_4/mod_train_conmodA_P100wd21_f3ne1u0
region: [[None, None, None]]/home/dsy/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint8 = np.dtype([("qint8", np.int8, 1)]) /home/dsy/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint8 = np.dtype([("quint8", np.uint8, 1)]) /home/dsy/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint16 = np.dtype([("qint16", np.int16, 1)]) /home/dsy/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint16 = np.dtype([("quint16", np.uint16, 1)]) /home/dsy/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:521: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint32 = np.dtype([("qint32", np.int32, 1)]) /home/dsy/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:526: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. np_resource = np.dtype([("resource", np.ubyte, 1)]) WARNING:tensorflow:From /home/dsy/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/contrib/learn/python/learn/datasets/base.py:198: retry (from tensorflow.contrib.learn.python.learn.datasets.base) is deprecated and will be removed in a future version. Instructions for updating: Use the retry module or similar alternatives. Total files=7999 2020-04-21 22:26:13.699284: I tensorflow/core/platform/cpu_feature_guard.cc:140] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA 2020-04-21 22:26:13.924880: I tensorflow/core/platform/cpu_feature_guard.cc:140] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA 2020-04-21 22:26:14.099183: I tensorflow/core/platform/cpu_feature_guard.cc:140] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA 2020-04-21 22:26:14.369383: I tensorflow/core/platform/cpu_feature_guard.cc:140] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA 2020-04-21 22:26:14.648059: I tensorflow/core/platform/cpu_feature_guard.cc:140] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA 2020-04-21 22:26:15.275578: I tensorflow/core/platform/cpu_feature_guard.cc:140] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA Error!!! No Fastq data in /home/dsy/2T_WD/深度学习_识别m6a/数据/m6a/RNAAB090763.fast5.tar.gz/fast5/1204665-1.fast5/GXB01170_20180726_FAH84534_GA20000_sequencing_run_RNAAB090763_92733_read_396_ch_503_strand.fast5 /home/dsy/software/DeepMod/bin/scripts/myDetect.py:157: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. events_data = sp_param['f5reader'][event_path].value Error!!! No Fastq data in /home/dsy/2T_WD/深度学习_识别m6a/数据/m6a/RNAAB090763.fast5.tar.gz/fast5/1204665-1.fast5/GXB01170_20180726_FAH84534_GA20000_mux_scan_RNAAB090763_45082_read_10_ch_76_strand.fast5 /home/dsy/software/DeepMod/bin/scripts/myDetect.py:157: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. events_data = sp_param['f5reader'][event_path].value Error!!! No Fastq data in /home/dsy/2T_WD/深度学习_识别m6a/数据/m6a/RNAAB090763.fast5.tar.gz/fast5/1204665-1.fast5/GXB01170_20180726_FAH84534_GA20000_mux_scan_RNAAB090763_45082_read_12_ch_331_strand.fast5 /home/dsy/software/DeepMod/bin/scripts/myDetect.py:157: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. events_data = sp_param['f5reader'][event_path].value /home/dsy/software/DeepMod/bin/scripts/myDetect.py:157: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead. events_data = sp_param['f5reader'][event_path].value Error!!! No Fastq data in /home/dsy/2T_WD/深度学习_识别m6a/数据/m6a/RNAAB090763.fast5.tar.
liuqianhn
chenchen-eng
Hello, I have the same problem when I use it. This is my fast5 file, the result of viewing with h5ls - r / Group /Analyses Group /Analyses/Basecall_1D_000 Group /Analyses/Basecall_1D_000/BaseCalled_template Group /Analyses/Basecall_1D_000/BaseCalled_template/Events Dataset {1561} /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 /Analyses/Basecall_1D_000/Summary/basecall_1d_template Group /Analyses/Calibration_Strand_Detection_000 Group /Analyses/Calibration_Strand_Detection_000/Configuration Group /Analyses/Calibration_Strand_Detection_000/Configuration/calib_detector Group /Analyses/Calibration_Strand_Detection_000/Summary Group /Analyses/Calibration_Strand_Detection_000/Summary/calibration_strand_template Group /Analyses/Segmentation_000 Group /Analyses/Segmentation_000/Configuration Group /Analyses/Segmentation_000/Configuration/stall_removal Group /Analyses/Segmentation_000/Summary Group /Analyses/Segmentation_000/Summary/segmentation Group /PreviousReadInfo Group /Raw Group /Raw/Reads Group /Raw/Reads/Read_6 Group /Raw/Reads/Read_6/Signal Dataset {23415/Inf} /UniqueGlobalKey Group /UniqueGlobalKey/channel_id Group /UniqueGlobalKey/context_tags Group /UniqueGlobalKey/tracking_id Group
What should I do? I look forward to your reply