Comments (9)
A fresh install following the instructions (except that I had to remove python=3.8
from the install command but I was installing into python 3.8) on a AWS linux machine leads to the following:
root INFO @ 03/25/23 04:09:39:
# ARGUMENT LIST:
# Cool URI at 5kb = SKNAS-MboI-allReps-filtered.mcool::/resolutions/5000
# Cool URI at 10kb = SKNAS-MboI-allReps-filtered.mcool::/resolutions/10000
# Cool URI at 50kb = SKNAS-MboI-allReps-filtered.mcool::/resolutions/50000
# Balance Type = CNV
# Reference Genome = hg38
# Included Chromosomes = ['#', 'X']
# Probability Cutoff for 5kb SVs = 0.8
# Probability Cutoff for 10kb SVs = 0.8
# Probability Cutoff for 50kb SVs = 0.99999
# Output File Prefix = SK-N-AS
# Output Format = full
# Log file name = SK-N-AS.log
root INFO @ 03/25/23 04:09:39: Predict SVs at 5kb resolution ...
Traceback (most recent call last):
File "/home/ec2-user/miniconda3/envs/EagleC/bin/predictSV-single-resolution", line 276, in <module>
run()
File "/home/ec2-user/miniconda3/envs/EagleC/bin/predictSV-single-resolution", line 110, in run
from eaglec.scoreUtils import intraPredict, interPredict
File "eaglec/scoreUtils.pyx", line 11, in init eaglec.scoreUtils
File "/home/ec2-user/miniconda3/envs/EagleC/lib/python3.8/site-packages/eaglec/utilities.py", line 9, in <module>
from cooler import ice
File "/home/ec2-user/miniconda3/envs/EagleC/lib/python3.8/site-packages/cooler/__init__.py", line 12, in <module>
from . import balance, create, fileops, parallel, tools
File "/home/ec2-user/miniconda3/envs/EagleC/lib/python3.8/site-packages/cooler/balance.py", line 8, in <module>
from .parallel import partition, split
File "/home/ec2-user/miniconda3/envs/EagleC/lib/python3.8/site-packages/cooler/parallel.py", line 10, in <module>
from .core import get
File "/home/ec2-user/miniconda3/envs/EagleC/lib/python3.8/site-packages/cooler/core/__init__.py", line 9, in <module>
from ._tableops import delete, get, put
File "/home/ec2-user/miniconda3/envs/EagleC/lib/python3.8/site-packages/cooler/core/_tableops.py", line 1, in <module>
import h5py
File "/home/ec2-user/miniconda3/envs/EagleC/lib/python3.8/site-packages/h5py/__init__.py", line 46, in <module>
from ._conv import register_converters as _register_converters
File "h5py/_conv.pyx", line 1, in init h5py._conv
File "h5py/h5t.pyx", line 293, in init h5py.h5t
File "/home/ec2-user/miniconda3/envs/EagleC/lib/python3.8/site-packages/numpy/__init__.py", line 320, in __getattr__
raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'typeDict'
Traceback (most recent call last):
File "/home/ec2-user/miniconda3/envs/EagleC/bin/predictSV", line 176, in <module>
run()
File "/home/ec2-user/miniconda3/envs/EagleC/bin/predictSV", line 112, in run
subprocess.check_call(' '.join(command), shell=True)
File "/home/ec2-user/miniconda3/envs/EagleC/lib/python3.8/subprocess.py", line 364, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'predictSV-single-resolution -H SKNAS-MboI-allReps-filtered.mcool::/resolutions/5000 --balance-type CNV -O SK-N-AS.CNN_SVs.5K.txt --genome hg38 --output-format full -C "#" "X" --prob-cutoff 0.8 --logFile SK-N-AS.log' returned non-zero exit status 1.
I resolved it by updating numpy:
pip install numpy==1.21
from eaglec.
I was able to resolve the issue after switching to the 3.8 version.
Thanks a lot.
from eaglec.
Could you upgrade your python version to 3.8 and try again?
from eaglec.
I'm having the exact same issue (on mac):
$ python
Python 3.8.16 | packaged by conda-forge | (default, Feb 1 2023, 16:05:36)
[Clang 14.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import eaglec
>>> import eaglec.utilities
>>> import eaglec.scoreUtils
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'eaglec.scoreUtils'
>>>
from eaglec.
Thanks for the quick responses @XiaoTaoWang! Note that the error above was on linux. The error on mac is still not resolved....any ideas what's going on there?
from eaglec.
Hi, thanks so much for the feedback! I guess that the error occurred due to a discrepancy between the compiler I used and the one on your Mac. Did you install EagleC on the M1/M2 chip? My Mac is still based on the old intel chip, which may be the reason for the difference.
from eaglec.
Indeed I have the ARM chip, however, I did install everything using the i386 emulator and so it "should" work...I'm also happy to install from source. Where is the source-code hosted?
from eaglec.
I am using python3.8 and numpy==1.21, but no sure what was going wrong...
predictSV --hic-5k SKNAS-MboI-allReps-filtered.mcool::/resolutions/5000
--hic-10k SKNAS-MboI-allReps-filtered.mcool::/resolutions/10000
--hic-50k SKNAS-MboI-allReps-filtered.mcool::/resolutions/50000
-O SK-N-AS -g hg38 --balance-type ICE --output-format full
--prob-cutoff-5k 0.8 --prob-cutoff-10k 0.8 --prob-cutoff-50k 0.99999
root INFO @ 05/18/23 15:05:31:
ARGUMENT LIST:
Cool URI at 5kb = SKNAS-MboI-allReps-filtered.mcool::/resolutions/5000
Cool URI at 10kb = SKNAS-MboI-allReps-filtered.mcool::/resolutions/10000
Cool URI at 50kb = SKNAS-MboI-allReps-filtered.mcool::/resolutions/50000
Balance Type = ICE
Reference Genome = hg38
Included Chromosomes = ['#', 'X']
Probability Cutoff for 5kb SVs = 0.8
Probability Cutoff for 10kb SVs = 0.8
Probability Cutoff for 50kb SVs = 0.99999
Output File Prefix = SK-N-AS
Output Format = full
Log file name = SK-N-AS.log
root INFO @ 05/18/23 15:05:31: Predict SVs at 5kb resolution ...
root INFO @ 05/18/23 15:05:32: matched sequencing depth in human at 10Kb: 80181600.06574439
root INFO @ 05/18/23 15:05:32: Load CNN models from /disk3/users/dittman/.conda/envs/py38/lib/python3.8/site-packages/eaglec/data/bulk/50M-100M ...
2023-05-18 15:05:32.863496: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-05-18 15:05:32.869113: I tensorflow/core/common_runtime/process_util.cc:146] Creating new thread pool with default inter op setting: 2. Tune using inter_op_parallelism_threads for best performance.
Traceback (most recent call last):
File "/disk3/users/dittman/.conda/envs/py38/bin/predictSV-single-resolution", line 276, in
run()
File "/disk3/users/dittman/.conda/envs/py38/bin/predictSV-single-resolution", line 150, in run
cnn_models.append(create_cnn(cnn_weights))
File "eaglec/CNN.pyx", line 83, in eaglec.CNN.create_cnn
File "/disk3/users/dittman/.conda/envs/py38/lib/python3.8/site-packages/tensorflow/python/keras/engine/training.py", line 2319, in load_weights
with h5py.File(filepath, 'r') as f:
File "/disk3/users/dittman/.conda/envs/py38/lib/python3.8/site-packages/h5py/_hl/files.py", line 424, in init
fid = make_fid(name, mode, userblock_size,
File "/disk3/users/dittman/.conda/envs/py38/lib/python3.8/site-packages/h5py/_hl/files.py", line 190, in make_fid
fid = h5f.open(name, flags, fapl=fapl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5f.pyx", line 96, in h5py.h5f.open
OSError: Unable to open file (unable to open file: name = '/disk3/users/dittman/.conda/envs/py38/lib/python3.8/site-packages/eaglec/data/bulk/50M-100M/CNN-weights.0.1.0.4.0.6.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Traceback (most recent call last):
File "/disk3/users/dittman/.conda/envs/py38/bin/predictSV", line 176, in
run()
File "/disk3/users/dittman/.conda/envs/py38/bin/predictSV", line 112, in run
subprocess.check_call(' '.join(command), shell=True)
File "/disk3/users/dittman/.conda/envs/py38/lib/python3.8/subprocess.py", line 364, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'predictSV-single-resolution -H SKNAS-MboI-allReps-filtered.mcool::/resolutions/5000 --balance-type ICE -O SK-N-AS.CNN_SVs.5K.txt --genome hg38 --output-format full -C "#" "X" --prob-cutoff 0.8 --logFile SK-N-AS.log' returned non-zero exit status 1.
(py38) dittman@wd1:/Data$ pip install numpy==1.21/Data$ predictSV --hic-5k SKNAS-MboI-allReps-filtered.mcool::/resolutions/5000 --hic-10k SKNAS-MboI-allReps-filtered.mcool::/resolutions/10000 --hic-50k SKNAS-MboI-allReps-filtered.mcool::/resolutions/50000 -O SK-N-AS -g hg38 --balance-type ICE --output-format full --prob-cutoff-5k 0.8 --prob-cutoff-10k 0.8 --prob-cutoff-50k 0.99999
Requirement already satisfied: numpy==1.21 in /disk3/users/dittman/.conda/envs/py38/lib/python3.8/site-packages (1.21.0)
(py38) dittman@wd1:
root INFO @ 05/18/23 15:07:22:
ARGUMENT LIST:
Cool URI at 5kb = SKNAS-MboI-allReps-filtered.mcool::/resolutions/5000
Cool URI at 10kb = SKNAS-MboI-allReps-filtered.mcool::/resolutions/10000
Cool URI at 50kb = SKNAS-MboI-allReps-filtered.mcool::/resolutions/50000
Balance Type = ICE
Reference Genome = hg38
Included Chromosomes = ['#', 'X']
Probability Cutoff for 5kb SVs = 0.8
Probability Cutoff for 10kb SVs = 0.8
Probability Cutoff for 50kb SVs = 0.99999
Output File Prefix = SK-N-AS
Output Format = full
Log file name = SK-N-AS.log
root INFO @ 05/18/23 15:07:22: Predict SVs at 5kb resolution ...
root INFO @ 05/18/23 15:07:23: matched sequencing depth in human at 10Kb: 80181600.06574439
root INFO @ 05/18/23 15:07:23: Load CNN models from /disk3/users/dittman/.conda/envs/py38/lib/python3.8/site-packages/eaglec/data/bulk/50M-100M ...
2023-05-18 15:07:23.751928: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-05-18 15:07:23.756636: I tensorflow/core/common_runtime/process_util.cc:146] Creating new thread pool with default inter op setting: 2. Tune using inter_op_parallelism_threads for best performance.
Traceback (most recent call last):
File "/disk3/users/dittman/.conda/envs/py38/bin/predictSV-single-resolution", line 276, in
run()
File "/disk3/users/dittman/.conda/envs/py38/bin/predictSV-single-resolution", line 150, in run
cnn_models.append(create_cnn(cnn_weights))
File "eaglec/CNN.pyx", line 83, in eaglec.CNN.create_cnn
File "/disk3/users/dittman/.conda/envs/py38/lib/python3.8/site-packages/tensorflow/python/keras/engine/training.py", line 2319, in load_weights
with h5py.File(filepath, 'r') as f:
File "/disk3/users/dittman/.conda/envs/py38/lib/python3.8/site-packages/h5py/_hl/files.py", line 424, in init
fid = make_fid(name, mode, userblock_size,
File "/disk3/users/dittman/.conda/envs/py38/lib/python3.8/site-packages/h5py/_hl/files.py", line 190, in make_fid
fid = h5f.open(name, flags, fapl=fapl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5f.pyx", line 96, in h5py.h5f.open
OSError: Unable to open file (unable to open file: name = '/disk3/users/dittman/.conda/envs/py38/lib/python3.8/site-packages/eaglec/data/bulk/50M-100M/CNN-weights.0.1.0.4.0.6.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Traceback (most recent call last):
File "/disk3/users/dittman/.conda/envs/py38/bin/predictSV", line 176, in
run()
File "/disk3/users/dittman/.conda/envs/py38/bin/predictSV", line 112, in run
subprocess.check_call(' '.join(command), shell=True)
File "/disk3/users/dittman/.conda/envs/py38/lib/python3.8/subprocess.py", line 364, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'predictSV-single-resolution -H SKNAS-MboI-allReps-filtered.mcool::/resolutions/5000 --balance-type ICE -O SK-N-AS.CNN_SVs.5K.txt --genome hg38 --output-format full -C "#" "X" --prob-cutoff 0.8 --logFile SK-N-AS.log' returned non-zero exit status 1.
from eaglec.
Sorry for the late response. Have you downloaded the pre-trained models using download-pretrained-models
?
from eaglec.
Related Issues (20)
- unable to run the example on linux server (redhat) HOT 2
- Capture HiC data HOT 3
- EagleC HiChIP with Neoloopfinder HOT 4
- EagleC detecting too few SVs HOT 2
- Non human genomes HOT 4
- FileNotFoundError: [Errno 2] No such file or directory: 'Sample.CNN_SVs.10K.txt' HOT 2
- specify gpu number to use HOT 1
- Optimization loop failed HOT 1
- Application to dm6 HOT 1
- UnboundLocalError: local variable 'cnn_models' referenced before assignment
- Inquiry for KeyError:'sweight' HOT 2
- [Issue] Error when constructing DIA matrix and running predictSV script
- No module named 'eaglec.scoreUtils' HOT 7
- "TypeError: sequence item 18: expected str instance, NoneType found", continue with merge-redundant-SVs? HOT 2
- Failed to run "download-pretrained-models" HOT 1
- Hi-C 3.0 with DdeI+DpnII HOT 5
- TypeError: sequence item 18: expected str instance, NoneType found
- On the problem of standard sets
- how to generate file for '--cnv-file' in plot-intraSVs fuction? HOT 1
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