search

WGLab / DeepMod

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications
Other
97 stars 35 forks source link

Any help appreciated with very cryptic errors #60

Open Arkadiy-Garber opened 1 year ago

Arkadiy-Garber commented 1 year ago 
Command: python /data/MAB/bin/DeepMod2/deepmod2 detect-guppy --threads 24 --fast5 ../../../fast5_pass/single_barcode12 --ref assembly.fasta --bam assembly.bam

RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd
RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd
RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd
RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd
RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd
RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd
2023-04-07 18:34:06.018981: Number of files: 110340

2023-04-07 18:34:06.078891: Processing BAM File.
2023-04-07 18:44:13.873240: Finished Processing BAM File.
2023-04-07 18:44:13.873400: Starting Per Read Methylation Detection.
2023-04-07 18:44:17.356034: 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:  SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/data/MAB/miniconda3/envs/deepmod2/lib/python3.9/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/data/MAB/bin/DeepMod2/src/guppy.py", line 176, in detect
    base_level_data, seq_len, mean_qscore, sequence_length = get_read_signal(read, params['guppy_group'])
  File "/data/MAB/bin/DeepMod2/src/guppy.py", line 121, in get_read_signal
    segment=read.get_analysis_attributes(guppy_group)['segmentation']
TypeError: 'NoneType' object is not subscriptable
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/data/MAB/bin/DeepMod2/deepmod2", line 150, in <module>
    run(params)
  File "/data/MAB/bin/DeepMod2/deepmod2", line 11, in run
    read_pred_file=modDetect.per_read_predict(params)
  File "/data/MAB/bin/DeepMod2/src/modDetect.py", line 59, in per_read_predict
    file_list=[file_name for file_name in res]
  File "/data/MAB/bin/DeepMod2/src/modDetect.py", line 59, in <listcomp>
    file_list=[file_name for file_name in res]
  File "/data/MAB/miniconda3/envs/deepmod2/lib/python3.9/multiprocessing/pool.py", line 870, in next
    raise value
TypeError: 'NoneType' object is not subscriptable

Thanks, Arkadiy

kaichop commented 1 year ago

if you are using deepmod2 please post the issue to deepmod2's repository.

On Fri, Apr 7, 2023 at 6:53 PM Arkadiy-Garber @.***> wrote:

Command: python /data/MAB/bin/DeepMod2/deepmod2 detect-guppy --threads 24 --fast5 ../../../fast5_pass/single_barcode12 --ref assembly.fasta --bam assembly.bam

RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd 2023-04-07 18:34:06.018981: Number of files: 110340

2023-04-07 18:34:06.078891: Processing BAM File. 2023-04-07 18:44:13.873240: Finished Processing BAM File. 2023-04-07 18:44:13.873400: Starting Per Read Methylation Detection. 2023-04-07 18:44:17.356034: 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: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/data/MAB/miniconda3/envs/deepmod2/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/data/MAB/bin/DeepMod2/src/guppy.py", line 176, in detect base_level_data, seq_len, mean_qscore, sequence_length = get_read_signal(read, params['guppy_group']) File "/data/MAB/bin/DeepMod2/src/guppy.py", line 121, in get_read_signal segment=read.get_analysis_attributes(guppy_group)['segmentation'] TypeError: 'NoneType' object is not subscriptable """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/data/MAB/bin/DeepMod2/deepmod2", line 150, in run(params) File "/data/MAB/bin/DeepMod2/deepmod2", line 11, in run read_pred_file=modDetect.per_read_predict(params) File "/data/MAB/bin/DeepMod2/src/modDetect.py", line 59, in per_read_predict file_list=[file_name for file_name in res] File "/data/MAB/bin/DeepMod2/src/modDetect.py", line 59, in file_list=[file_name for file_name in res] File "/data/MAB/miniconda3/envs/deepmod2/lib/python3.9/multiprocessing/pool.py", line 870, in next raise value TypeError: 'NoneType' object is not subscriptable

Thanks, Arkadiy

— Reply to this email directly, view it on GitHub https://github.com/WGLab/DeepMod/issues/60, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OETB2VRHKE5SWNSAZLXACLGPANCNFSM6AAAAAAWW7ZK2I . You are receiving this because you are subscribed to this thread.Message ID: @.***>