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WGLab / DeepMod

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications
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Run the software and report an error #6

Closed zifeng8824 closed 5 years ago

zifeng8824 commented 5 years ago

When I use this command： python ~/biosoft/DeepMod/bin/DeepMod.py detect --wrkBase fast5_files/ --Ref reference/reference.fasta --outFolder out_folder --Base C --modfile ~/biosoft/DeepMod/train_mod/rnn_f7_wd21_chr1to10_4/mod_train_f7_wd21_chr1to10 --threads 4 Several errors were made,like: File "/biosoft/DeepMod/bin/DeepMod.py", line 372, in args.func(args); File "/biosoft/DeepMod/bin/DeepMod.py", line 170, in mDetect from scripts import myDetect File "/biosoft/DeepMod/bin/scripts/myDetect.py", line 24, in import tensorflow as tf Module Not Found Error: No module named 'tensorflow' How can I fix these mistakes, thanks a lot!!

liuqianhn commented 5 years ago

@zifeng8824 May I know whether you install tensorflow successfully? To test it, in the command line, type python, and then import tensorflow as tf to see what you get.

zifeng8824 commented 5 years ago

Hello, the picture shows the input result, however tensorflow soft were displayed by command line, type conda list.thanks!

------------------ 原始邮件 ------------------ 发件人: "liuqianhn"notifications@github.com; 发送时间: 2019年5月22日(星期三) 晚上8:34 收件人: "WGLab/DeepMod"DeepMod@noreply.github.com; 抄送: "zifeng8824"zsk8920@gmail.com;"Mention"mention@noreply.github.com; 主题: Re: [WGLab/DeepMod] Run the software and report an error (#6)

@zifeng8824 May I know whether you install tensorflow successfully? To test it, in the command line, type python, and then import tensorflow as tf to see what you get.

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liuqianhn commented 5 years ago

Hi @zifeng8824 , I do not understand. could you please show what you get when you run import tensorflow as tf, since the error message indicates that tensorflow is not installed or not int the python path?

zifeng8824 commented 5 years ago

Hi, Currently, China will stop Anaconda mirror service indefinitely. How can I install this series of software? when I run import tensorflow as tf,there is nothing displayed.As is shown in the figure.

------------------ 原始邮件 ------------------ 发件人: "liuqianhn"notifications@github.com; 发送时间: 2019年6月5日(星期三) 晚上9:23 收件人: "WGLab/DeepMod"DeepMod@noreply.github.com; 抄送: "zifeng8824"zsk8920@gmail.com;"Mention"mention@noreply.github.com; 主题: Re: [WGLab/DeepMod] Run the software and report an error (#6)

Hi @zifeng8824 , I do not understand. could you please show what you get when you run import tensorflow as tf, since the error message indicates that tensorflow is not installed or not int the python path?

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liuqianhn commented 5 years ago

Hi @zifeng8824 , you might try to use pip install. I do not see any figure. BTW, which python do you used, python2.7 or python 3+?

zifeng8824 commented 5 years ago

Hi,when I run import tensorflow as tf,there is nothing displayed. like this.I used python 3.6.8 (mdeepmod) [zhangshengkui@mu01 envs]$ python Python 3.6.8 |Anaconda, Inc.| (default, Dec 30 2018, 01:22:34) [GCC 7.3.0] on linux Type "help", "copyright", "credits" or "license" for more information.

import tensorflow as tf

------------------ 原始邮件 ------------------ 发件人: "liuqianhn"notifications@github.com; 发送时间: 2019年6月10日(星期一) 晚上10:23 收件人: "WGLab/DeepMod"DeepMod@noreply.github.com; 抄送: "zifeng8824"zsk8920@gmail.com;"Mention"mention@noreply.github.com; 主题: Re: [WGLab/DeepMod] Run the software and report an error (#6)

Hi @zifeng8824 , you might try to use pip install. I do not see any figure. BTW, which python do you used, python2.7 or python 3+

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liuqianhn commented 5 years ago

Hi @zifeng8824 , your output indicates tensorflow is installed successfully. May I know when you run deepmod, did you conda activate mdeepmod? It seems that when you run deepmod, python cannot find tensorflow.

zifeng8824 commented 5 years ago

Hi, I conda activate mdeepmod.When I type the following command, the error on the screen reads as follows. Thanks. (mdeepmod) [zhangshengkui@cu02 methylation_example]$ python ~/biosoft/DeepMod/bin/DeepMod.py detect --wrkBase sdfag_20161030_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_40170_ch270_read15_strand.fast5 --Ref reference/reference.fasta --outFolder out_folder --Base C --modfile ~/biosoft/DeepMod/train_mod/rnn_f7_wd21_chr1to10_4/mod_train_f7_wd21_chr1to10 --threads 4

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: /lustre/zhangshengkui/07.zhangshengkui/03.methylation_test/methylation_example
                  outLevel: 2
                   wrkBase: sdfag_20161030_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_40170_ch270_read15_strand.fast5
                    FileID: mod
                 outFolder: out_folder/
                 recursive: 1
          files_per_thread: 1000
                   threads: 4
                windowsize: 21
                  alignStr: minimap2
               basecall_1d: Basecall_1D_000
          basecall_2strand: BaseCalled_template
                    ConUnk: True
               outputlayer: 
                      Base: C
               mod_cluster: 0
                   predDet: 1
                       Ref: reference/reference.fasta
                      fnum: 7
                    hidden: 100
                   modfile: /lustre/zhangshengkui/biosoft/DeepMod/train_mod/rnn_f7_wd21_chr1to10_4/mod_train_f7_wd21_chr1to10
                    region: [[None, None, None]]

Total files=0 WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version. Instructions for updating: Colocations handled automatically by placer. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version. Instructions for updating: Colocations handled automatically by placer. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version. Instructions for updating: Colocations handled automatically by placer. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version. Instructions for updating: Colocations handled automatically by placer. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: BasicLSTMCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.LSTMCell, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: MultiRNNCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.StackedRNNCells, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:47: static_bidirectional_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.Bidirectional(keras.layers.RNN(cell, unroll=True)), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/rnn.py:1565: static_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.RNN(cell, unroll=True), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: BasicLSTMCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.LSTMCell, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: MultiRNNCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.StackedRNNCells, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: BasicLSTMCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.LSTMCell, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: BasicLSTMCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.LSTMCell, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:47: static_bidirectional_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.Bidirectional(keras.layers.RNN(cell, unroll=True)), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: MultiRNNCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.StackedRNNCells, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/rnn.py:1565: static_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.RNN(cell, unroll=True), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: MultiRNNCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.StackedRNNCells, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:47: static_bidirectional_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.Bidirectional(keras.layers.RNN(cell, unroll=True)), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/rnn.py:1565: static_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.RNN(cell, unroll=True), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:47: static_bidirectional_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.Bidirectional(keras.layers.RNN(cell, unroll=True)), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/rnn.py:1565: static_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.RNN(cell, unroll=True), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:526: to_float (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Use tf.cast instead. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:788: div (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Deprecated in favor of operator or tf.math.divide. 2019-06-11 13:17:03.093664: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA 2019-06-11 13:17:03.102813: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2399815000 Hz 2019-06-11 13:17:03.104122: I tensorflow/compiler/xla/service/service.cc:150] XLA service 0x2b3753c67eb0 executing computations on platform Host. Devices: 2019-06-11 13:17:03.104175: I tensorflow/compiler/xla/service/service.cc:158] StreamExecutor device (0): , WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:526: to_float (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Use tf.cast instead. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:788: div (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Deprecated in favor of operator or tf.math.divide. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:526: to_float (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Use tf.cast instead. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:526: to_float (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Use tf.cast instead. 2019-06-11 13:17:03.353193: W tensorflow/core/graph/graph_constructor.cc:1272] Importing a graph with a lower producer version 26 into an existing graph with producer version 27. Shape inference will have run different parts of the graph with different producer versions. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:788: div (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Deprecated in favor of operator or tf.math.divide. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:788: div (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Deprecated in favor of operator or tf.math.divide. 2019-06-11 13:17:03.456784: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA 2019-06-11 13:17:03.465213: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2399815000 Hz 2019-06-11 13:17:03.466852: I tensorflow/compiler/xla/service/service.cc:150] XLA service 0x2b3753e68840 executing computations on platform Host. Devices: 2019-06-11 13:17:03.466912: I tensorflow/compiler/xla/service/service.cc:158] StreamExecutor device (0): , 2019-06-11 13:17:03.487622: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA 2019-06-11 13:17:03.496318: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2399815000 Hz 2019-06-11 13:17:03.497889: I tensorflow/compiler/xla/service/service.cc:150] XLA service 0x2b3753e69130 executing computations on platform Host. Devices: 2019-06-11 13:17:03.497933: I tensorflow/compiler/xla/service/service.cc:158] StreamExecutor device (0): , 2019-06-11 13:17:03.508583: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA 2019-06-11 13:17:03.518531: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2399815000 Hz 2019-06-11 13:17:03.520060: I tensorflow/compiler/xla/service/service.cc:150] XLA service 0x2b3753e68bc0 executing computations on platform Host. Devices: 2019-06-11 13:17:03.520111: I tensorflow/compiler/xla/service/service.cc:158] StreamExecutor device (0): , 2019-06-11 13:17:03.736622: W tensorflow/core/graph/graph_constructor.cc:1272] Importing a graph with a lower producer version 26 into an existing graph with producer version 27. Shape inference will have run different parts of the graph with different producer versions. 2019-06-11 13:17:03.766287: W tensorflow/core/graph/graph_constructor.cc:1272] Importing a graph with a lower producer version 26 into an existing graph with producer version 27. Shape inference will have run different parts of the graph with different producer versions. 2019-06-11 13:17:03.787947: W tensorflow/core/graph/graph_constructor.cc:1272] Importing a graph with a lower producer version 26 into an existing graph with producer version 27. Shape inference will have run different parts of the graph with different producer versions. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/training/saver.py:1266: checkpoint_exists (from tensorflow.python.training.checkpoint_management) is deprecated and will be removed in a future version. Instructions for updating: Use standard file APIs to check for files with this prefix. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/training/saver.py:1266: checkpoint_exists (from tensorflow.python.training.checkpoint_management) is deprecated and will be removed in a future version. Instructions for updating: Use standard file APIs to check for files with this prefix. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/training/saver.py:1266: checkpoint_exists (from tensorflow.python.training.checkpoint_management) is deprecated and will be removed in a future version. Instructions for updating: Use standard file APIs to check for files with this prefix. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/training/saver.py:1266: checkpoint_exists (from tensorflow.python.training.checkpoint_management) is deprecated and will be removed in a future version. Instructions for updating: Use standard file APIs to check for files with this prefix. Per-read Prediction consuming time 8 Find: out_folder//mod 0 rnn.pred.ind [] Genomic-position Detection consuming time 0 (mdeepmod) [zhangshengkui@cu02 methylation_example]$

------------------ 原始邮件 ------------------ 发件人: "liuqianhn"notifications@github.com; 发送时间: 2019年6月11日(星期二) 中午11:35 收件人: "WGLab/DeepMod"DeepMod@noreply.github.com; 抄送: "zifeng8824"zsk8920@gmail.com;"Mention"mention@noreply.github.com; 主题: Re: [WGLab/DeepMod] Run the software and report an error (#6)

Hi @zifeng8824 , your output indicates tensorflow is installed successfully. May I know when you run deepmod, did you conda activate mdeepmod? It seems that when you run deepmod, python cannot find tensorflow.

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liuqianhn commented 5 years ago

Hi @zifeng8824 , --wrkBase is expecting a folder which contain fast5 file. In the log file above, it seems that a fast5 file is used for --wrkBase and thus no fast5 file would be found.

zifeng8824 commented 5 years ago

Hi, the ex_fast5_files folder contain 10 fast5 files, the error on the screen reads as follows. the Nanopolish software provide the example folfers.

(mdeepmod) [zhangshengkui@cu02 methylation_example]$ python ~/biosoft/DeepMod/bin/DeepMod.py detect --wrkBase ex_fast5_files/ --Ref reference.fasta --outFolder out_folder --Base C --modfile ~/biosoft/DeepMod/train_mod/rnn_f7_wd21_chr1to10_4/mod_train_f7_wd21_chr1to10 --threads 4 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: /lustre/zhangshengkui/07.zhangshengkui/03.methylation_test/methylation_example
                  outLevel: 2
                   wrkBase: ex_fast5_files/
                    FileID: mod
                 outFolder: out_folder/
                 recursive: 1
          files_per_thread: 1000
                   threads: 4
                windowsize: 21
                  alignStr: minimap2
               basecall_1d: Basecall_1D_000
          basecall_2strand: BaseCalled_template
                    ConUnk: True
               outputlayer: 
                      Base: C
               mod_cluster: 0
                   predDet: 1
                       Ref: reference.fasta
                      fnum: 7
                    hidden: 100
                   modfile: /lustre/zhangshengkui/biosoft/DeepMod/train_mod/rnn_f7_wd21_chr1to10_4/mod_train_f7_wd21_chr1to10
                    region: [[None, None, None]]

Total files=10 WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version. Instructions for updating: Colocations handled automatically by placer. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version. Instructions for updating: Colocations handled automatically by placer. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version. Instructions for updating: Colocations handled automatically by placer. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: BasicLSTMCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.LSTMCell, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: MultiRNNCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.StackedRNNCells, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version. Instructions for updating: Colocations handled automatically by placer. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:47: static_bidirectional_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.Bidirectional(keras.layers.RNN(cell, unroll=True)), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: BasicLSTMCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.LSTMCell, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/rnn.py:1565: static_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.RNN(cell, unroll=True), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: MultiRNNCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.StackedRNNCells, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: BasicLSTMCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.LSTMCell, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: MultiRNNCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.StackedRNNCells, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:47: static_bidirectional_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.Bidirectional(keras.layers.RNN(cell, unroll=True)), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/rnn.py:1565: static_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.RNN(cell, unroll=True), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:47: static_bidirectional_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.Bidirectional(keras.layers.RNN(cell, unroll=True)), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/rnn.py:1565: static_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.RNN(cell, unroll=True), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: BasicLSTMCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.LSTMCell, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:42: MultiRNNCell.init (from tensorflow.python.ops.rnn_cell_impl) is deprecated and will be removed in a future version. Instructions for updating: This class is equivalent as tf.keras.layers.StackedRNNCells, and will be replaced by that in Tensorflow 2.0. WARNING:tensorflow:From /lustre/zhangshengkui/biosoft/DeepMod/bin/scripts/myMultiBiRNN.py:47: static_bidirectional_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.Bidirectional(keras.layers.RNN(cell, unroll=True)), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/rnn.py:1565: static_rnn (from tensorflow.python.ops.rnn) is deprecated and will be removed in a future version. Instructions for updating: Please use keras.layers.RNN(cell, unroll=True), which is equivalent to this API WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:526: to_float (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Use tf.cast instead. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:788: div (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Deprecated in favor of operator or tf.math.divide. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:526: to_float (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Use tf.cast instead. 2019-06-12 07:47:40.368336: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA 2019-06-12 07:47:40.376681: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2399815000 Hz WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:788: div (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Deprecated in favor of operator or tf.math.divide. 2019-06-12 07:47:40.378212: I tensorflow/compiler/xla/service/service.cc:150] XLA service 0x2b5477f61130 executing computations on platform Host. Devices: 2019-06-12 07:47:40.378252: I tensorflow/compiler/xla/service/service.cc:158] StreamExecutor device (0): , 2019-06-12 07:47:40.501633: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA 2019-06-12 07:47:40.509853: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2399815000 Hz 2019-06-12 07:47:40.511361: I tensorflow/compiler/xla/service/service.cc:150] XLA service 0x2b5477f611a0 executing computations on platform Host. Devices: 2019-06-12 07:47:40.511402: I tensorflow/compiler/xla/service/service.cc:158] StreamExecutor device (0): , WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:526: to_float (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Use tf.cast instead. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:788: div (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Deprecated in favor of operator or tf.math.divide. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:526: to_float (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Use tf.cast instead. 2019-06-12 07:47:40.635995: W tensorflow/core/graph/graph_constructor.cc:1272] Importing a graph with a lower producer version 26 into an existing graph with producer version 27. Shape inference will have run different parts of the graph with different producer versions. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/ops/metrics_impl.py:788: div (from tensorflow.python.ops.math_ops) is deprecated and will be removed in a future version. Instructions for updating: Deprecated in favor of operator or tf.math.divide. 2019-06-12 07:47:40.698375: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA 2019-06-12 07:47:40.707428: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2399815000 Hz 2019-06-12 07:47:40.709247: I tensorflow/compiler/xla/service/service.cc:150] XLA service 0x2b5477f60540 executing computations on platform Host. Devices: 2019-06-12 07:47:40.709288: I tensorflow/compiler/xla/service/service.cc:158] StreamExecutor device (0): , 2019-06-12 07:47:40.766383: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA 2019-06-12 07:47:40.775237: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2399815000 Hz 2019-06-12 07:47:40.776989: I tensorflow/compiler/xla/service/service.cc:150] XLA service 0x2b5477f60c20 executing computations on platform Host. Devices: 2019-06-12 07:47:40.777045: I tensorflow/compiler/xla/service/service.cc:158] StreamExecutor device (0): , 2019-06-12 07:47:40.777092: W tensorflow/core/graph/graph_constructor.cc:1272] Importing a graph with a lower producer version 26 into an existing graph with producer version 27. Shape inference will have run different parts of the graph with different producer versions. 2019-06-12 07:47:40.988920: W tensorflow/core/graph/graph_constructor.cc:1272] Importing a graph with a lower producer version 26 into an existing graph with producer version 27. Shape inference will have run different parts of the graph with different producer versions. 2019-06-12 07:47:41.058207: W tensorflow/core/graph/graph_constructor.cc:1272] Importing a graph with a lower producer version 26 into an existing graph with producer version 27. Shape inference will have run different parts of the graph with different producer versions. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/training/saver.py:1266: checkpoint_exists (from tensorflow.python.training.checkpoint_management) is deprecated and will be removed in a future version. Instructions for updating: Use standard file APIs to check for files with this prefix. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/training/saver.py:1266: checkpoint_exists (from tensorflow.python.training.checkpoint_management) is deprecated and will be removed in a future version. Instructions for updating: Use standard file APIs to check for files with this prefix. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/training/saver.py:1266: checkpoint_exists (from tensorflow.python.training.checkpoint_management) is deprecated and will be removed in a future version. Instructions for updating: Use standard file APIs to check for files with this prefix. WARNING:tensorflow:From /lustre/zhangshengkui/anaconda3/envs/mdeepmod/lib/python3.6/site-packages/tensorflow/python/training/saver.py:1266: checkpoint_exists (from tensorflow.python.training.checkpoint_management) is deprecated and will be removed in a future version. Instructions for updating: Use standard file APIs to check for files with this prefix. Cannot open fast5 or other errors: ex_fast5_files/sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch375_read474_strand.fast5 Cannot open fast5 or other errors: ex_fast5_files/sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch89_read160_strand.fast5 Cannot open fast5 or other errors: ex_fast5_files/sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch462_read282_strand.fast5 Cannot open fast5 or other errors: ex_fast5_files/sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch12_read137_strand.fast5 Cannot open fast5 or other errors: ex_fast5_files/sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch121_read329_strand.fast5 Cannot open fast5 or other errors: ex_fast5_files/sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch439_read116_strand.fast5 Cannot open fast5 or other errors: ex_fast5_files/sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch462_read284_strand.fast5 Cannot open fast5 or other errors: ex_fast5_files/sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch179_read409_strand.fast5 Cannot open fast5 or other errors: ex_fast5_files/sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch325_read134_strand.fast5 Cannot open fast5 or other errors: ex_fast5_files/sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch438_read308_strand.fast5 [M::mm_idx_gen::2.1801.01] collected minimizers [M::mm_idx_gen::2.5991.32] sorted minimizers [M::main::2.5991.32] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::2.8051.30] mid_occ = 163 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::2.926*1.29] distinct minimizers: 8512566 (87.32% are singletons); average occurrences: 1.413; average spacing: 5.357 [M::main] Version: 2.17-r941 [M::main] CMD: minimap2 -ax map-ont reference.fasta /tmp/tmpdi0c9bsc.fa [M::main] Real time: 2.962 sec; CPU: 3.805 sec; Peak RSS: 0.563 GB Cur Prediction consuming time 3 for 0 0 Per-read Prediction consuming time 11 Find: out_folder//mod 0 rnn.pred.ind [] Genomic-position Detection consuming time 0

(mdeepmod) [zhangshengkui@cu02 methylation_example]$ cd ex_fast5_files/ (mdeepmod) [zhangshengkui@cu02 ex_fast5_files]$ ll total 920 -rw-r----- 1 zhangshengkui cassava 93764 Jun 12 2019 sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch121_read329_strand.fast5 -rw-r----- 1 zhangshengkui cassava 30839 Jun 12 2019 sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch12_read137_strand.fast5 -rw-r----- 1 zhangshengkui cassava 44007 Jun 12 2019 sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch179_read409_strand.fast5 -rw-r----- 1 zhangshengkui cassava 143909 Jun 12 2019 sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch325_read134_strand.fast5 -rw-r----- 1 zhangshengkui cassava 30697 Jun 12 2019 sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch375_read474_strand.fast5 -rw-r----- 1 zhangshengkui cassava 79464 Jun 12 2019 sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch438_read308_strand.fast5 -rw-r----- 1 zhangshengkui cassava 229487 Jun 12 2019 sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch439_read116_strand.fast5 -rw-r----- 1 zhangshengkui cassava 41765 Jun 12 2019 sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch462_read282_strand.fast5 -rw-r----- 1 zhangshengkui cassava 76322 Jun 12 2019 sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch462_read284_strand.fast5 -rw-r----- 1 zhangshengkui cassava 149808 Jun 12 2019 sdfag_20161029_FNFAB42704_MN16454_sequencing_run_Chip103_Genomic_R9_4_450bps_tune_52368_ch89_read160_strand.fast5

------------------ 原始邮件 ------------------ 发件人: "liuqianhn"notifications@github.com; 发送时间: 2019年6月11日(星期二) 晚上9:53 收件人: "WGLab/DeepMod"DeepMod@noreply.github.com; 抄送: "zifeng8824"zsk8920@gmail.com;"Mention"mention@noreply.github.com; 主题: Re: [WGLab/DeepMod] Run the software and report an error (#6)

Hi @zifeng8824 , --wrkBase is expecting a folder which contain fast5 file. In the log file above, it seems that a fast5 file is used for --wrkBase and thus no fast5 file would be found.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

liuqianhn commented 5 years ago

Hi @zifeng8824 , could please send me one fast5 file via liuqianhn@hotmail.com for checking? Thank you.

liuqianhn commented 5 years ago

Hi @zifeng8824, I checked your fast5 files, which are not basecalled. Please download albacore from nanopore community and conduct basecalling before using DeepMod.

liuqianhn commented 5 years ago

I closed this issue since there is no further update. Please re-open it if you have related issues.