Installation fails in macOS #59
Description
Hello, I installed DeepSimulator inside a conda environment. It returned me a lot of errors, regarding the correct versions of numPy and tensorflow. When the following command is executed:
./deep_simulator.sh -i example/artificial_human_chr22.fastaI got that output:
% ./deep_simulator.sh -i example/artificial_human_chr22.fasta
Pre-process input genome...
./deep_simulator.sh: line 256: activate: No such file or directory
Traceback (most recent call last):
File "/Users/mikeph/Bioinformatics/DeepSimulator/./util/genome_preprocess.py", line 7, in <module>
from Bio import SeqIO
ImportError: No module named Bio
./deep_simulator.sh: line 262: deactivate: No such file or directory
Pre-process input genome done!
Executing the preprocessing step...
./deep_simulator.sh: line 275: activate: No such file or directory
ls: /Users/mikeph/Bioinformatics/DeepSimulator/artificial_human_chr22_DeepSimu/processed_genome*: No such file or directory
./deep_simulator.sh: line 289: deactivate: No such file or directory
cat: /Users/mikeph/Bioinformatics/DeepSimulator/artificial_human_chr22_DeepSimu/sampled_read_*: No such file or directory
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-independent pore model...
./deep_simulator.sh: line 372: activate: No such file or directory
Traceback (most recent call last):
File "/Users/mikeph/Bioinformatics/DeepSimulator/./pore_model/src/kmer_simulator.py", line 1, in <module>
from poremodel_util import *
File "/Users/mikeph/Bioinformatics/DeepSimulator/pore_model/src/poremodel_util.py", line 8, in <module>
import h5py
ImportError: No module named h5py
./deep_simulator.sh: line 384: deactivate: No such file or directory
Finished generate the simulated signals and fast5 files!
Running Basecalling...
Basecalling with Guppy_GPU...
./deep_simulator.sh: line 401: /Users/mikeph/Bioinformatics/DeepSimulator/./base_caller/guppy_3.1.5/ont-guppy/bin/guppy_basecaller: cannot execute binary file
Basecalling finished!
Checking the read accuracy...
awk: division by zero
source line number 1
Here is the mapping identity: of 0 (pass 0 + fail 0) reads passed base-calling.I don't know if that's a problem with non-updated version dependencies. I sure hope it's not an abandonware, it's the only ONT assembly simulation.
How to reproduce the problem
- git clone the repo
- create a conda env for DeepSimulator
- ./install.sh
- ./deep_simulator.sh -i example/artificial_human_chr22.fasta
My system specs
- Intel i7 4th Gen
- 16GB RAM
- macOS Big Sur 11.7.11