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We are new to Nanopore sequencing.... We tried using DeepNano2 tool for basecalling, but while running we are facing date-time format error. Can anyone suggest what can be done to rectify the error. Following is the terminal,
(base) admin1@admin1-ThinkStation-P340:$ conda activate deepnanoblitz
(deepnanoblitz) admin1@admin1-ThinkStation-P340:$ cd deepnano-blitz
(deepnanoblitz) admin1@admin1-ThinkStation-P340:~/deepnano-blitz$ deepnano2_caller.py --output /home/admin1/SY6_ND_rawreads/fast5/all.fastq --reads /home/admin1/SY6_ND_rawreads/fast5/*.fast5 --network-type 96 --beam-size 5 --threads 13 --output-format fastq --gzip-output
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/site-packages/deepnano2-0.1-py3.9-linux-x86_64.egg/EGG-INFO/scripts/deepnano2_caller.py", line 47, in call_file
start_time = add_time_seconds(exp_start_time, start_time / sampling_rate)
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/site-packages/deepnano2-0.1-py3.9-linux-x86_64.egg/EGG-INFO/scripts/deepnano2_caller.py", line 29, in add_time_seconds
base_time = datetime.datetime.strptime(base_time_str, '%Y-%m-%dT%H:%M:%SZ')
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/_strptime.py", line 568, in _strptime_datetime
tt, fraction, gmtoff_fraction = _strptime(data_string, format)
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/_strptime.py", line 349, in _strptime
raise ValueError("time data %r does not match format %r" %
ValueError: time data '2021-11-23T16:56:40.904360+05:30' does not match format '%Y-%m-%dT%H:%M:%SZ'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/admin1/miniconda3/envs/deepnanoblitz/bin/deepnano2_caller.py", line 4, in import('pkg_resources').run_script('deepnano2==0.1', 'deepnano2_caller.py')
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/site-packages/pkg_resources/init.py", line 656, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/site-packages/pkg_resources/init.py", line 1453, in run_script
exec(code, namespace, namespace)
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/site-packages/deepnano2-0.1-py3.9-linux-x86_64.egg/EGG-INFO/scripts/deepnano2_caller.py", line 135, in
for out in pool.imap_unordered(call_file, files):
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/multiprocessing/pool.py", line 870, in next
raise value
ValueError: time data '2021-11-23T16:56:40.904360+05:30' does not match format '%Y-%m-%dT%H:%M:%SZ'
(deepnanoblitz) admin1@admin1-ThinkStation-P340:~/deepnano-blitz$
Thank you in advance
The text was updated successfully, but these errors were encountered:
We are new to Nanopore sequencing.... We tried using DeepNano2 tool for basecalling, but while running we are facing date-time format error. Can anyone suggest what can be done to rectify the error. Following is the terminal,
(base) admin1@admin1-ThinkStation-P340:
$ conda activate deepnanoblitz$ cd deepnano-blitz(deepnanoblitz) admin1@admin1-ThinkStation-P340:
(deepnanoblitz) admin1@admin1-ThinkStation-P340:~/deepnano-blitz$ deepnano2_caller.py --output /home/admin1/SY6_ND_rawreads/fast5/all.fastq --reads /home/admin1/SY6_ND_rawreads/fast5/*.fast5 --network-type 96 --beam-size 5 --threads 13 --output-format fastq --gzip-output
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/site-packages/deepnano2-0.1-py3.9-linux-x86_64.egg/EGG-INFO/scripts/deepnano2_caller.py", line 47, in call_file
start_time = add_time_seconds(exp_start_time, start_time / sampling_rate)
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/site-packages/deepnano2-0.1-py3.9-linux-x86_64.egg/EGG-INFO/scripts/deepnano2_caller.py", line 29, in add_time_seconds
base_time = datetime.datetime.strptime(base_time_str, '%Y-%m-%dT%H:%M:%SZ')
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/_strptime.py", line 568, in _strptime_datetime
tt, fraction, gmtoff_fraction = _strptime(data_string, format)
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/_strptime.py", line 349, in _strptime
raise ValueError("time data %r does not match format %r" %
ValueError: time data '2021-11-23T16:56:40.904360+05:30' does not match format '%Y-%m-%dT%H:%M:%SZ'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/admin1/miniconda3/envs/deepnanoblitz/bin/deepnano2_caller.py", line 4, in
import('pkg_resources').run_script('deepnano2==0.1', 'deepnano2_caller.py')
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/site-packages/pkg_resources/init.py", line 656, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/site-packages/pkg_resources/init.py", line 1453, in run_script
exec(code, namespace, namespace)
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/site-packages/deepnano2-0.1-py3.9-linux-x86_64.egg/EGG-INFO/scripts/deepnano2_caller.py", line 135, in
for out in pool.imap_unordered(call_file, files):
File "/home/admin1/miniconda3/envs/deepnanoblitz/lib/python3.9/multiprocessing/pool.py", line 870, in next
raise value
ValueError: time data '2021-11-23T16:56:40.904360+05:30' does not match format '%Y-%m-%dT%H:%M:%SZ'
(deepnanoblitz) admin1@admin1-ThinkStation-P340:~/deepnano-blitz$
Thank you in advance
The text was updated successfully, but these errors were encountered: