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wdecoster / NanoPlot

Plotting scripts for long read sequencing data
http://nanoplot.bioinf.be
MIT License
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NanoPlot crashed with the following et #206

Closed AMTZ-ssi closed 3 years ago

AMTZ-ssi commented 4 years ago

If you read this then NanoPlot 1.30.1 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 "/srv/data/tools/public_envs/amtz_test_ont/lib/python3.8/concurrent/futures/process.py", line 239, in _process_worker r = call_item.fn(*call_item.args, *call_item.kwargs) File "/srv/data/tools/public_envs/amtz_test_ont/lib/python3.8/concurrent/futures/process.py", line 198, in _process_chunk return [fn(args) for args in chunk] File "/srv/data/tools/public_envs/amtz_test_ont/lib/python3.8/concurrent/futures/process.py", line 198, in return [fn(*args) for args in chunk] File "/srv/data/tools/public_envs/amtz_test_ont/lib/python3.8/site-packages/nanoget/extraction_functions.py", line 383, in process_fastq_rich for record in SeqIO.parse(inputfastq, "fastq"): File "/srv/data/tools/public_envs/amtz_test_ont/lib/python3.8/site-packages/Bio/SeqIO/Interfaces.py", line 68, in next return next(self.records) File "/srv/data/tools/public_envs/amtz_test_ont/lib/python3.8/site-packages/Bio/SeqIO/QualityIO.py", line 1081, in iterate for title_line, seq_string, quality_string in FastqGeneralIterator(handle): File "/srv/data/tools/public_envs/amtz_test_ont/lib/python3.8/site-packages/Bio/SeqIO/QualityIO.py", line 977, in FastqGeneralIterator raise ValueError( ValueError: Lengths of sequence and quality values differs for 7045e61d-e2e6-4efc-9285-e9f908fbf8d6 runid=ed8ecd5ace06dcfdeb5f2318ba216a62f9b3bc24 read=6904 ch=121 start_time=2020-09-10T14:14:20Z flow_cell_id=FAN60354 protocol_group_id=BAAN_Ligation sample_id=BAAN_Ligation_1_200910 (2629 and 2529). """

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

Traceback (most recent call last): File "/srv/data/tools/public_envs/amtz_test_ont/bin/NanoPlot", line 8, in sys.exit(main()) File "/srv/data/tools/public_envs/amtz_test_ont/lib/python3.8/site-packages/nanoplot/NanoPlot.py", line 55, in main datadf = get_input( File "/srv/data/tools/public_envs/amtz_test_ont/lib/python3.8/site-packages/nanoget/nanoget.py", line 92, in get_input dfs=[out for out in executor.map(extraction_function, files)], File "/srv/data/tools/public_envs/amtz_test_ont/lib/python3.8/site-packages/nanoget/nanoget.py", line 92, in dfs=[out for out in executor.map(extraction_function, files)], File "/srv/data/tools/public_envs/amtz_test_ont/lib/python3.8/concurrent/futures/process.py", line 484, in _chain_from_iterable_of_lists for element in iterable: File "/srv/data/tools/public_envs/amtz_test_ont/lib/python3.8/concurrent/futures/_base.py", line 611, in result_iterator yield fs.pop().result() File "/srv/data/tools/public_envs/amtz_test_ont/lib/python3.8/concurrent/futures/_base.py", line 432, in result return self.__get_result() File "/srv/data/tools/public_envs/amtz_test_ont/lib/python3.8/concurrent/futures/_base.py", line 388, in __get_result raise self._exception ValueError: Lengths of sequence and quality values differs for 7045e61d-e2e6-4efc-9285-e9f908fbf8d6 runid=ed8ecd5ace06dcfdeb5f2318ba216a62f9b3bc24 read=6904 ch=121 start_time=2020-09-10T14:14:20Z flow_cell_id=FAN60354 protocol_group_id=BAAN_Ligation sample_id=BAAN_Ligation_1_200910 (2629 and 2529).

wdecoster commented 4 years ago

More information would have been useful, but it looks like you are using fastq as input, and BioPython (a module which I use to parse fastq files) complains that the FASTQ record with ID 7045e61d-e2e6-4efc-9285-e9f908fbf8d6 is corrupted.