NanoPlot crashed #415
Description
If you read this then NanoPlot 1.44.1 has crashed :-(
Please try updating NanoPlot and see if that helps...
If not, please report this issue at https://github.com/wdecoster/NanoPlot/issues
If you could include the log file that would be really helpful.
Thanks!
concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/sboto/anaconda3/lib/python3.8/concurrent/futures/process.py", line 239, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/home/sboto/anaconda3/lib/python3.8/concurrent/futures/process.py", line 198, in _process_chunk
return [fn(*args) for args in chunk]
File "/home/sboto/anaconda3/lib/python3.8/concurrent/futures/process.py", line 198, in
return [fn(*args) for args in chunk]
File "/home/sboto/anaconda3/lib/python3.8/site-packages/nanoget/extraction_functions.py", line 396, in process_fastq_plain
data=[res for res in extract_from_fastq(inputfastq) if res],
File "/home/sboto/anaconda3/lib/python3.8/site-packages/nanoget/extraction_functions.py", line 396, in
data=[res for res in extract_from_fastq(inputfastq) if res],
File "/home/sboto/anaconda3/lib/python3.8/site-packages/nanoget/extraction_functions.py", line 407, in extract_from_fastq
for rec in SeqIO.parse(fq, "fastq"):
File "/home/sboto/anaconda3/lib/python3.8/site-packages/Bio/SeqIO/Interfaces.py", line 73, in next
return next(self.records)
File "/home/sboto/anaconda3/lib/python3.8/site-packages/Bio/SeqIO/QualityIO.py", line 1080, in iterate
for title_line, seq_string, quality_string in FastqGeneralIterator(handle):
File "/home/sboto/anaconda3/lib/python3.8/site-packages/Bio/SeqIO/QualityIO.py", line 939, in FastqGeneralIterator
raise ValueError("End of file without quality information.")
ValueError: End of file without quality information.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/sboto/anaconda3/bin/NanoPlot", line 8, in
sys.exit(main())
File "/home/sboto/anaconda3/lib/python3.8/site-packages/nanoplot/NanoPlot.py", line 62, in main
datadf = get_input(
File "/home/sboto/anaconda3/lib/python3.8/site-packages/nanoget/nanoget.py", line 110, in get_input
dfs=[out for out in executor.map(extraction_function, files)],
File "/home/sboto/anaconda3/lib/python3.8/site-packages/nanoget/nanoget.py", line 110, in
dfs=[out for out in executor.map(extraction_function, files)],
File "/home/sboto/anaconda3/lib/python3.8/concurrent/futures/process.py", line 484, in _chain_from_iterable_of_lists
for element in iterable:
File "/home/sboto/anaconda3/lib/python3.8/concurrent/futures/_base.py", line 611, in result_iterator
yield fs.pop().result()
File "/home/sboto/anaconda3/lib/python3.8/concurrent/futures/_base.py", line 439, in result
return self.__get_result()
File "/home/sboto/anaconda3/lib/python3.8/concurrent/futures/_base.py", line 388, in __get_result
raise self._exception
(base) sboto@A2021:/media/sboto/TOSHIBA EXT/GW-CH2_Lib2_250627/CH2-Lib2-Sm9-16/20250627_1323_MN45336_AXN357_9c5528f5/fastq_pass/barcode08$