liyu95
commented
4 years ago Hi, thank you very much for your interest! Could you please have a try to see if the given examples could be run or not? It would be easier for us to do the trouble-shooting.
Open solomonchak opened 4 years ago
liyu95
commented
4 years ago Hi, thank you very much for your interest! Could you please have a try to see if the given examples could be run or not? It would be easier for us to do the trouble-shooting.
solomonchak
commented
4 years ago Here's what I got when I used phage_lambda.fasta in the example folder. Thanks for helping!
(base) node219-45 DeepSimulator >: deep_simulator.sh -i ./example/phage_lambda.fasta -c 1 -B 2 -D 1 -K 30 -M 0
Pre-process input genome...
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
Pre-process input genome done!
Executing the preprocessing step...
('The average length is: ', 8258.0441988950279)
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
Finished the preprocessing step!
Key parameters for simulation are shown below
event_std : 1.0
filter_freq : 950
signal_std : 1.0
Running the context-dependent pore model...
Traceback (most recent call last):
File "/home/t/tchak/DeepSimulator/pore_model/src/context_simulator.py", line 2, in
Failed to load the native TensorFlow runtime.
See https://www.tensorflow.org/install/install_sources#common_installation_problems
for some common reasons and solutions. Include the entire stack trace above this error message when asking for help. DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'. Finished generate the simulated signals and fast5 files! Running Basecalling... Basecalling with Guppy_CPU... ONT Guppy basecalling software version 3.1.5+781ed57 config file: /home/t/tchak/DeepSimulator/base_caller/guppy_3.1.5/ont-guppy-cpu/data/dna_r9.4.1_450bps_hac.cfg model file: /home/t/tchak/DeepSimulator/base_caller/guppy_3.1.5/ont-guppy-cpu/data/template_r9.4.1_450bps_hac.jsn input path: /home/t/tchak/DeepSimulator/phage_lambda_DeepSimu/fast5 save path: /home/t/tchak/DeepSimulator/phage_lambda_DeepSimu/fastq chunk size: 1000 chunks per runner: 1000 records per file: 4000 num basecallers: 1 cpu mode: ON threads per caller: 1
Found 0 fast5 files to process. Init time: 3568 ms
0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----|
Caller time: 100 ms, Samples called: 0, samples/s: 0 Finishing up any open output files. Basecalling completed successfully. Basecalling finished! Checking the read accuracy... awk: fatal: division by zero attempted Here is the mapping identity: of 0 (pass 0 + fail 0) reads passed base-calling.
Hi,
Thanks for the great program. I installed it without error but got an error related to TenserFlow when I test it. Can you please help us?
Pre-process input genome... DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'. Pre-process input genome done! Executing the preprocessing step... ('The average length is: ', 8032.0172451638146) DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'. Finished the preprocessing step! Key parameters for simulation are shown below event_std : 1.0 filter_freq : 950 signal_std : 1.0 Running the context-dependent pore model... Traceback (most recent call last): File "/home/t/tchak/DeepSimulator/pore_model/src/context_simulator.py", line 2, in
from con_reg_seq import
File "/home/t/tchak/DeepSimulator/pore_model/src/con_reg_seq.py", line 3, in
import tensorflow as tf
File "/home/t/tchak/miniconda2/envs/tensorflow_cdpm/lib/python2.7/site-packages/tensorflow/init.py", line 24, in
from tensorflow.python import
File "/home/t/tchak/miniconda2/envs/tensorflow_cdpm/lib/python2.7/site-packages/tensorflow/python/init.py", line 49, in
from tensorflow.python import pywrap_tensorflow
File "/home/t/tchak/miniconda2/envs/tensorflow_cdpm/lib/python2.7/site-packages/tensorflow/python/pywrap_tensorflow.py", line 52, in
raise ImportError(msg)
ImportError: Traceback (most recent call last):
File "/home/t/tchak/miniconda2/envs/tensorflow_cdpm/lib/python2.7/site-packages/tensorflow/python/pywrap_tensorflow.py", line 41, in
from tensorflow.python.pywrap_tensorflow_internal import *
File "/home/t/tchak/miniconda2/envs/tensorflow_cdpm/lib/python2.7/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in
_pywrap_tensorflow_internal = swig_import_helper()
File "/home/t/tchak/miniconda2/envs/tensorflow_cdpm/lib/python2.7/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
_mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/t/tchak/miniconda2/envs/tensorflow_cdpm/lib/python2.7/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so)
Failed to load the native TensorFlow runtime. ...