/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/requests/init.py:104: RequestsDependencyWarning: urllib3 (1.26.19) or chardet (5.0.0)/charset_normalizer (2.0.12) doesn't match a supported version!
RequestsDependencyWarning)
Using TensorFlow backend.
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
2024-08-05 10:38:15,483 [INFO] Note: detected 96 virtual cores but NumExpr set to maximum of 64, check "NUMEXPR_MAX_THREADS" environment variable.
2024-08-05 10:38:15,483 [INFO] Note: NumExpr detected 96 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
2024-08-05 10:38:15,483 [INFO] NumExpr defaulting to 8 threads.
Error. nthreads cannot be larger than environment variable "NUMEXPR_MAX_THREADS" (64)/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/plot/heatmaps.py:6: MatplotlibDeprecationWarning:
The mpl_toolkits.axes_grid1.colorbar module was deprecated in Matplotlib 3.2 and will be removed two minor releases later. Use matplotlib.colorbar instead.
from mpl_toolkits.axes_grid1.colorbar import colorbar
2024-08-05 10:38:20.197334: I tensorflow/core/platform/cpu_feature_guard.cc:140] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
INFO [08-05 10:38:20] Load model
INFO [08-05 10:38:30] --regions not provided. Using regions from dataspec.yml
INFO [08-05 10:38:31] Resizing regions (fix=center) to model's input width of: 1000
INFO [08-05 10:38:32] Sort the bed file
INFO [08-05 10:38:33] Get model predictions and contribution scores
DeepExplain: running "deeplift" explanation method (5)
Model with multiple inputs: True
DeepExplain: running "deeplift" explanation method (5)
Model with multiple inputs: True
DeepExplain: running "deeplift" explanation method (5)
Model with multiple inputs: True
DeepExplain: running "deeplift" explanation method (5)
Model with multiple inputs: True
DeepExplain: running "deeplift" explanation method (5)
Model with multiple inputs: True
DeepExplain: running "deeplift" explanation method (5)
Model with multiple inputs: True
DeepExplain: running "deeplift" explanation method (5)
Model with multiple inputs: True
DeepExplain: running "deeplift" explanation method (5)
Model with multiple inputs: True
DeepExplain: running "deeplift" explanation method (5)
Model with multiple inputs: True
DeepExplain: running "deeplift" explanation method (5)
Model with multiple inputs: True
INFO [08-05 18:22:39] Setup bigWigs for writing
INFO [08-05 18:22:40] Writing to bigWigs
100%|██████████| 101834/101834 [01:44<00:00, 979.15it/s]INFO [08-05 18:24:24] Done writing. Closing bigWigs
INFO [08-05 18:27:47] Done! Output files stored as: output4/train/H3K4me3_Pituitary/bigwigs/*
/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/requests/init.py:104: RequestsDependencyWarning: urllib3 (1.26.19) or chardet (5.0.0)/charset_normalizer (2.0.12) doesn't match a supported version!
RequestsDependencyWarning)
Using TensorFlow backend.
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
2024-08-05 18:27:58,753 [INFO] Note: detected 96 virtual cores but NumExpr set to maximum of 64, check "NUMEXPR_MAX_THREADS" environment variable.
2024-08-05 18:27:58,753 [INFO] Note: NumExpr detected 96 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
2024-08-05 18:27:58,753 [INFO] NumExpr defaulting to 8 threads.
Error. nthreads cannot be larger than environment variable "NUMEXPR_MAX_THREADS" (64)/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/plot/heatmaps.py:6: MatplotlibDeprecationWarning:
The mpl_toolkits.axes_grid1.colorbar module was deprecated in Matplotlib 3.2 and will be removed two minor releases later. Use matplotlib.colorbar instead.
from mpl_toolkits.axes_grid1.colorbar import colorbar
INFO [08-05 18:28:03] Using the following premade configuration: modisco-50k
Used config: ----------------------------------------
import bpnet
import bpnet.configurables as bpnet2
INFO [08-05 18:28:03] Loading the contribution file: output4/train/H3K4me3_Pituitary/contrib.deeplift.h5
INFO [08-05 18:28:03] Loading ranges
INFO [08-05 18:28:06] Subsetting ranges according to interval_from_task
INFO [08-05 18:28:06] Using 61095 / 101834 regions after --only-task-regions subset
INFO [08-05 18:28:06] Saving the included samples from ContribFile to /path/to/bpnet/BovineFAANG/23_deep_learning/bpnet/output4/train/H3K4me3_Pituitary/modisco/H3K4me3_Pituitary_M08/modisco-run.subset-contrib-file.npy
INFO [08-05 18:28:33] Using null-contrib-file: output4/train/H3K4me3_Pituitary/contrib.deeplift.null.h5
MEMORY 3.65750272
On task H3K4me3_Pituitary_M08/profile/wn
Computing windowed sums on original
Generating null dist
Computing threshold
Thresholds from null dist were -0.17064952850341797 and 0.15632754564285278
Passing windows frac was 0.6703333717479135 , which is above 0.2 ; adjusting
Final raw thresholds are -0.23661255836486816 and 0.23661255836486816
Final transformed thresholds are -0.7999999164900431 and 0.7999999164900431
saving plot to figures/scoredist_0.png
Got 792553 coords
After resolving overlaps, got 792553 seqlets
Across all tasks, the weakest transformed threshold used was: 0.7999998164900431
MEMORY 8.43118592
792553 identified in total
min_metacluster_size_frac len(seqlets) = 15851 is more than min_metacluster_size=1000.
Using it as a new min_metacluster_size
Reducing weak_threshold_for_counting_sign to match weakest_transformed_thresh, from 0.8 to 0.7999998164900431
[0.79999978]
[0]
TF-MoDISco is using the TensorFlow backend.
/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/train.py:195: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
gin_macro_dict = yaml.load("\n".join(macros).replace("@", "").replace(" = %", ": ").replace(" = ", ": "))
/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/train.py:208: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
.replace(" = ", ": "))
Traceback (most recent call last):
File "/path/to/bpnet/bin/.conda/bpnet/bin/bpnet", line 8, in
sys.exit(main())
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/main.py", line 38, in main
argh.dispatch(parser)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/argh/dispatching.py", line 174, in dispatch
for line in lines:
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/argh/dispatching.py", line 277, in _execute_command
for line in result:
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/argh/dispatching.py", line 260, in _call
result = function(positional, *keywords)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/modisco.py", line 342, in bpnet_modisco_run
null_per_pos_scores=null_per_pos_scores)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/gin/config.py", line 1605, in gin_wrapper
utils.augment_exception_message_and_reraise(e, err_str)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/gin/utils.py", line 41, in augment_exception_message_and_reraise
raise proxy.with_traceback(exception.traceback) from None
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/gin/config.py", line 1582, in gin_wrapper
return fn(new_args, **new_kwargs)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/modisco.py", line 109, in modisco_run
null_per_pos_scores=null_per_pos_scores)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/tfmodisco_workflow/workflow.py", line 303, in call
metaclustering_results = metaclusterer.fit_transform(seqlets)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 100, in fit_transform
self.fit(seqlets)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 107, in fit
self._fit(attribute_vectors)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 296, in _fit
vector_activity_pattern = self.vector_to_pattern(vector)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 149, in vector_to_pattern
assert False
AssertionError:
In call to configurable 'modisco_run' (<function modisco_run at 0x8e6a9655a60>)
/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/requests/init.py:104: RequestsDependencyWarning: urllib3 (1.26.19) or chardet (5.0.0)/charset_normalizer (2.0.12) doesn't match a supported version!
RequestsDependencyWarning)
Using TensorFlow backend.
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
2024-08-05 18:43:51,180 [INFO] Note: detected 96 virtual cores but NumExpr set to maximum of 64, check "NUMEXPR_MAX_THREADS" environment variable.
2024-08-05 18:43:51,180 [INFO] Note: NumExpr detected 96 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
2024-08-05 18:43:51,180 [INFO] NumExpr defaulting to 8 threads.
Error. nthreads cannot be larger than environment variable "NUMEXPR_MAX_THREADS" (64)/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/plot/heatmaps.py:6: MatplotlibDeprecationWarning:
The mpl_toolkits.axes_grid1.colorbar module was deprecated in Matplotlib 3.2 and will be removed two minor releases later. Use matplotlib.colorbar instead.
from mpl_toolkits.axes_grid1.colorbar import colorbar
INFO [08-05 18:43:54] Using the following premade configuration: modisco-50k
Used config: ----------------------------------------
import bpnet
import bpnet.configurables as bpnet2
INFO [08-05 18:43:54] Loading the contribution file: output4/train/H3K4me3_Pituitary/contrib.deeplift.h5
INFO [08-05 18:43:55] Loading ranges
INFO [08-05 18:43:55] Subsetting ranges according to interval_from_task
INFO [08-05 18:43:55] Using 40739 / 101834 regions after --only-task-regions subset
INFO [08-05 18:43:55] Saving the included samples from ContribFile to /path/to/bpnet/BovineFAANG/23_deep_learning/bpnet/output4/train/H3K4me3_Pituitary/modisco/H3K4me3_Pituitary_M22/modisco-run.subset-contrib-file.npy
INFO [08-05 18:44:11] Using null-contrib-file: output4/train/H3K4me3_Pituitary/contrib.deeplift.null.h5
MEMORY 2.681278464
On task H3K4me3_Pituitary_M22/profile/wn
Computing windowed sums on original
Generating null dist
Computing threshold
Thresholds from null dist were -0.1577587127685547 and 0.14074981212615967
Passing windows frac was 0.6907501511613752 , which is above 0.2 ; adjusting
Final raw thresholds are -0.20982933044433594 and 0.20982933044433594
Final transformed thresholds are -0.7999991984815232 and 0.7999991984815232
saving plot to figures/scoredist_0.png
Got 557402 coords
After resolving overlaps, got 557402 seqlets
Across all tasks, the weakest transformed threshold used was: 0.7999990984815233
MEMORY 6.52306432
557402 identified in total
min_metacluster_size_frac len(seqlets) = 11148 is more than min_metacluster_size=1000.
Using it as a new min_metacluster_size
Reducing weak_threshold_for_counting_sign to match weakest_transformed_thresh, from 0.8 to 0.7999990984815233
[0.79999692]
[0]
TF-MoDISco is using the TensorFlow backend.
/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/train.py:195: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
gin_macro_dict = yaml.load("\n".join(macros).replace("@", "").replace(" = %", ": ").replace(" = ", ": "))
/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/train.py:208: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
.replace(" = ", ": "))
Traceback (most recent call last):
File "/path/to/bpnet/bin/.conda/bpnet/bin/bpnet", line 8, in
sys.exit(main())
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/main.py", line 38, in main
argh.dispatch(parser)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/argh/dispatching.py", line 174, in dispatch
for line in lines:
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/argh/dispatching.py", line 277, in _execute_command
for line in result:
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/argh/dispatching.py", line 260, in _call
result = function(positional, *keywords)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/modisco.py", line 342, in bpnet_modisco_run
null_per_pos_scores=null_per_pos_scores)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/gin/config.py", line 1605, in gin_wrapper
utils.augment_exception_message_and_reraise(e, err_str)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/gin/utils.py", line 41, in augment_exception_message_and_reraise
raise proxy.with_traceback(exception.traceback) from None
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/gin/config.py", line 1582, in gin_wrapper
return fn(new_args, **new_kwargs)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/modisco.py", line 109, in modisco_run
null_per_pos_scores=null_per_pos_scores)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/tfmodisco_workflow/workflow.py", line 303, in call
metaclustering_results = metaclusterer.fit_transform(seqlets)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 100, in fit_transform
self.fit(seqlets)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 107, in fit
self._fit(attribute_vectors)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 296, in _fit
vector_activity_pattern = self.vector_to_pattern(vector)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 149, in vector_to_pattern
assert False
AssertionError:
In call to configurable 'modisco_run' (<function modisco_run at 0xc6a36f55a60>)
/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/requests/init.py:104: RequestsDependencyWarning: urllib3 (1.26.19) or chardet (5.0.0)/charset_normalizer (2.0.12) doesn't match a supported version! RequestsDependencyWarning) Using TensorFlow backend. /path/to/bpnet/bin/.conda/bpnet/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)]) /path/to/bpnet/bin/.conda/bpnet/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)]) /path/to/bpnet/bin/.conda/bpnet/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)]) /path/to/bpnet/bin/.conda/bpnet/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)]) /path/to/bpnet/bin/.conda/bpnet/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)]) /path/to/bpnet/bin/.conda/bpnet/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)]) 2024-08-05 10:38:15,483 [INFO] Note: detected 96 virtual cores but NumExpr set to maximum of 64, check "NUMEXPR_MAX_THREADS" environment variable. 2024-08-05 10:38:15,483 [INFO] Note: NumExpr detected 96 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8. 2024-08-05 10:38:15,483 [INFO] NumExpr defaulting to 8 threads. Error. nthreads cannot be larger than environment variable "NUMEXPR_MAX_THREADS" (64)/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/plot/heatmaps.py:6: MatplotlibDeprecationWarning: The mpl_toolkits.axes_grid1.colorbar module was deprecated in Matplotlib 3.2 and will be removed two minor releases later. Use matplotlib.colorbar instead. from mpl_toolkits.axes_grid1.colorbar import colorbar 2024-08-05 10:38:20.197334: I tensorflow/core/platform/cpu_feature_guard.cc:140] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA INFO [08-05 10:38:20] Load model INFO [08-05 10:38:30] --regions not provided. Using regions from dataspec.yml INFO [08-05 10:38:31] Resizing regions (fix=center) to model's input width of: 1000 INFO [08-05 10:38:32] Sort the bed file INFO [08-05 10:38:33] Get model predictions and contribution scores DeepExplain: running "deeplift" explanation method (5) Model with multiple inputs: True DeepExplain: running "deeplift" explanation method (5) Model with multiple inputs: True DeepExplain: running "deeplift" explanation method (5) Model with multiple inputs: True DeepExplain: running "deeplift" explanation method (5) Model with multiple inputs: True DeepExplain: running "deeplift" explanation method (5) Model with multiple inputs: True DeepExplain: running "deeplift" explanation method (5) Model with multiple inputs: True DeepExplain: running "deeplift" explanation method (5) Model with multiple inputs: True DeepExplain: running "deeplift" explanation method (5) Model with multiple inputs: True DeepExplain: running "deeplift" explanation method (5) Model with multiple inputs: True DeepExplain: running "deeplift" explanation method (5) Model with multiple inputs: True INFO [08-05 18:22:39] Setup bigWigs for writing INFO [08-05 18:22:40] Writing to bigWigs 100%|██████████| 101834/101834 [01:44<00:00, 979.15it/s]INFO [08-05 18:24:24] Done writing. Closing bigWigs INFO [08-05 18:27:47] Done! Output files stored as: output4/train/H3K4me3_Pituitary/bigwigs/*
/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/requests/init.py:104: RequestsDependencyWarning: urllib3 (1.26.19) or chardet (5.0.0)/charset_normalizer (2.0.12) doesn't match a supported version! RequestsDependencyWarning) Using TensorFlow backend. /path/to/bpnet/bin/.conda/bpnet/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)]) /path/to/bpnet/bin/.conda/bpnet/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)]) /path/to/bpnet/bin/.conda/bpnet/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)]) /path/to/bpnet/bin/.conda/bpnet/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)]) /path/to/bpnet/bin/.conda/bpnet/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)]) /path/to/bpnet/bin/.conda/bpnet/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)]) 2024-08-05 18:27:58,753 [INFO] Note: detected 96 virtual cores but NumExpr set to maximum of 64, check "NUMEXPR_MAX_THREADS" environment variable. 2024-08-05 18:27:58,753 [INFO] Note: NumExpr detected 96 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8. 2024-08-05 18:27:58,753 [INFO] NumExpr defaulting to 8 threads. Error. nthreads cannot be larger than environment variable "NUMEXPR_MAX_THREADS" (64)/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/plot/heatmaps.py:6: MatplotlibDeprecationWarning: The mpl_toolkits.axes_grid1.colorbar module was deprecated in Matplotlib 3.2 and will be removed two minor releases later. Use matplotlib.colorbar instead. from mpl_toolkits.axes_grid1.colorbar import colorbar INFO [08-05 18:28:03] Using the following premade configuration: modisco-50k Used config: ---------------------------------------- import bpnet import bpnet.configurables as bpnet2
Parameters for PeakPredictionProfileMetric:
==============================================================================
None.
INFO [08-05 18:28:03] Loading the contribution file: output4/train/H3K4me3_Pituitary/contrib.deeplift.h5 INFO [08-05 18:28:03] Loading ranges INFO [08-05 18:28:06] Subsetting ranges according to
sys.exit(main())
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/main.py", line 38, in main
argh.dispatch(parser)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/argh/dispatching.py", line 174, in dispatch
for line in lines:
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/argh/dispatching.py", line 277, in _execute_command
for line in result:
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/argh/dispatching.py", line 260, in _call
result = function( positional, *keywords)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/modisco.py", line 342, in bpnet_modisco_run
null_per_pos_scores=null_per_pos_scores)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/gin/config.py", line 1605, in gin_wrapper
utils.augment_exception_message_and_reraise(e, err_str)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/gin/utils.py", line 41, in augment_exception_message_and_reraise
raise proxy.with_traceback(exception.traceback) from None
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/gin/config.py", line 1582, in gin_wrapper
return fn(new_args, **new_kwargs)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/modisco.py", line 109, in modisco_run
null_per_pos_scores=null_per_pos_scores)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/tfmodisco_workflow/workflow.py", line 303, in call
metaclustering_results = metaclusterer.fit_transform(seqlets)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 100, in fit_transform
self.fit(seqlets)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 107, in fit
self._fit(attribute_vectors)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 296, in _fit
vector_activity_pattern = self.vector_to_pattern(vector)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 149, in vector_to_pattern
assert False
AssertionError:
In call to configurable 'modisco_run' (<function modisco_run at 0x8e6a9655a60>)
/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/requests/init.py:104: RequestsDependencyWarning: urllib3 (1.26.19) or chardet (5.0.0)/charset_normalizer (2.0.12) doesn't match a supported version!
RequestsDependencyWarning)
Using TensorFlow backend.
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
/path/to/bpnet/bin/.conda/bpnet/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)])
2024-08-05 18:43:51,180 [INFO] Note: detected 96 virtual cores but NumExpr set to maximum of 64, check "NUMEXPR_MAX_THREADS" environment variable.
2024-08-05 18:43:51,180 [INFO] Note: NumExpr detected 96 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
2024-08-05 18:43:51,180 [INFO] NumExpr defaulting to 8 threads.
Error. nthreads cannot be larger than environment variable "NUMEXPR_MAX_THREADS" (64)/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/plot/heatmaps.py:6: MatplotlibDeprecationWarning:
The mpl_toolkits.axes_grid1.colorbar module was deprecated in Matplotlib 3.2 and will be removed two minor releases later. Use matplotlib.colorbar instead.
from mpl_toolkits.axes_grid1.colorbar import colorbar
INFO [08-05 18:43:54] Using the following premade configuration: modisco-50k
Used config: ----------------------------------------
import bpnet
import bpnet.configurables as bpnet2
interval_from_taskINFO [08-05 18:28:06] Using 61095 / 101834 regions after --only-task-regions subset INFO [08-05 18:28:06] Saving the included samples from ContribFile to /path/to/bpnet/BovineFAANG/23_deep_learning/bpnet/output4/train/H3K4me3_Pituitary/modisco/H3K4me3_Pituitary_M08/modisco-run.subset-contrib-file.npy INFO [08-05 18:28:33] Using null-contrib-file: output4/train/H3K4me3_Pituitary/contrib.deeplift.null.h5 MEMORY 3.65750272 On task H3K4me3_Pituitary_M08/profile/wn Computing windowed sums on original Generating null dist Computing threshold Thresholds from null dist were -0.17064952850341797 and 0.15632754564285278 Passing windows frac was 0.6703333717479135 , which is above 0.2 ; adjusting Final raw thresholds are -0.23661255836486816 and 0.23661255836486816 Final transformed thresholds are -0.7999999164900431 and 0.7999999164900431 saving plot to figures/scoredist_0.png Got 792553 coords After resolving overlaps, got 792553 seqlets Across all tasks, the weakest transformed threshold used was: 0.7999998164900431 MEMORY 8.43118592 792553 identified in total min_metacluster_size_frac len(seqlets) = 15851 is more than min_metacluster_size=1000. Using it as a new min_metacluster_size Reducing weak_threshold_for_counting_sign to match weakest_transformed_thresh, from 0.8 to 0.7999998164900431 [0.79999978] [0] TF-MoDISco is using the TensorFlow backend. /path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/train.py:195: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. gin_macro_dict = yaml.load("\n".join(macros).replace("@", "").replace(" = %", ": ").replace(" = ", ": ")) /path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/train.py:208: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. .replace(" = ", ": ")) Traceback (most recent call last): File "/path/to/bpnet/bin/.conda/bpnet/bin/bpnet", line 8, inParameters for PeakPredictionProfileMetric:
==============================================================================
None.
INFO [08-05 18:43:54] Loading the contribution file: output4/train/H3K4me3_Pituitary/contrib.deeplift.h5 INFO [08-05 18:43:55] Loading ranges INFO [08-05 18:43:55] Subsetting ranges according to
sys.exit(main())
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/main.py", line 38, in main
argh.dispatch(parser)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/argh/dispatching.py", line 174, in dispatch
for line in lines:
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/argh/dispatching.py", line 277, in _execute_command
for line in result:
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/argh/dispatching.py", line 260, in _call
result = function( positional, *keywords)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/modisco.py", line 342, in bpnet_modisco_run
null_per_pos_scores=null_per_pos_scores)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/gin/config.py", line 1605, in gin_wrapper
utils.augment_exception_message_and_reraise(e, err_str)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/gin/utils.py", line 41, in augment_exception_message_and_reraise
raise proxy.with_traceback(exception.traceback) from None
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/gin/config.py", line 1582, in gin_wrapper
return fn(new_args, **new_kwargs)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/modisco.py", line 109, in modisco_run
null_per_pos_scores=null_per_pos_scores)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/tfmodisco_workflow/workflow.py", line 303, in call
metaclustering_results = metaclusterer.fit_transform(seqlets)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 100, in fit_transform
self.fit(seqlets)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 107, in fit
self._fit(attribute_vectors)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 296, in _fit
vector_activity_pattern = self.vector_to_pattern(vector)
File "/path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/modisco/metaclusterers.py", line 149, in vector_to_pattern
assert False
AssertionError:
In call to configurable 'modisco_run' (<function modisco_run at 0xc6a36f55a60>)
interval_from_taskINFO [08-05 18:43:55] Using 40739 / 101834 regions after --only-task-regions subset INFO [08-05 18:43:55] Saving the included samples from ContribFile to /path/to/bpnet/BovineFAANG/23_deep_learning/bpnet/output4/train/H3K4me3_Pituitary/modisco/H3K4me3_Pituitary_M22/modisco-run.subset-contrib-file.npy INFO [08-05 18:44:11] Using null-contrib-file: output4/train/H3K4me3_Pituitary/contrib.deeplift.null.h5 MEMORY 2.681278464 On task H3K4me3_Pituitary_M22/profile/wn Computing windowed sums on original Generating null dist Computing threshold Thresholds from null dist were -0.1577587127685547 and 0.14074981212615967 Passing windows frac was 0.6907501511613752 , which is above 0.2 ; adjusting Final raw thresholds are -0.20982933044433594 and 0.20982933044433594 Final transformed thresholds are -0.7999991984815232 and 0.7999991984815232 saving plot to figures/scoredist_0.png Got 557402 coords After resolving overlaps, got 557402 seqlets Across all tasks, the weakest transformed threshold used was: 0.7999990984815233 MEMORY 6.52306432 557402 identified in total min_metacluster_size_frac len(seqlets) = 11148 is more than min_metacluster_size=1000. Using it as a new min_metacluster_size Reducing weak_threshold_for_counting_sign to match weakest_transformed_thresh, from 0.8 to 0.7999990984815233 [0.79999692] [0] TF-MoDISco is using the TensorFlow backend. /path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/train.py:195: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. gin_macro_dict = yaml.load("\n".join(macros).replace("@", "").replace(" = %", ": ").replace(" = ", ": ")) /path/to/bpnet/bin/.conda/bpnet/lib/python3.6/site-packages/bpnet/cli/train.py:208: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. .replace(" = ", ": ")) Traceback (most recent call last): File "/path/to/bpnet/bin/.conda/bpnet/bin/bpnet", line 8, in