NanoPlot crash in reading a pacbio bam file

NanoPlot -t 1 --color yellow --bam /home/mariano/Documents/Wellinger/Telomerase/TEL06R/Sequel.RunS140_S2.004.BC1299_Forward.TEL06R.ccs.bam --downsample 10000 -o /home/mariano/Documents/Wellinger/Telomerase/TEL06R/Sequel.RunS140_S2.004.BC1299_Forward.TEL06R.ccs.bam.bamplots_downsampled

If you read this then NanoPlot 1.34.0 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/mariano/miniconda3/lib/python3.8/concurrent/futures/process.py", line 239, in _process_worker
    r = call_item.fn(*call_item.args, **call_item.kwargs)
  File "/home/mariano/miniconda3/lib/python3.8/concurrent/futures/process.py", line 198, in _process_chunk
    return [fn(*args) for args in chunk]
  File "/home/mariano/miniconda3/lib/python3.8/concurrent/futures/process.py", line 198, in <listcomp>
    return [fn(*args) for args in chunk]
  File "/home/mariano/miniconda3/lib/python3.8/site-packages/nanoget/extraction_functions.py", line 155, in process_bam
    samfile = check_bam(bam)
  File "/home/mariano/miniconda3/lib/python3.8/site-packages/nanoget/extraction_functions.py", line 102, in check_bam
    samfile = pysam.AlignmentFile(bam, "rb")
  File "pysam/libcalignmentfile.pyx", line 742, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 991, in pysam.libcalignmentfile.AlignmentFile._open
ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
"""

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

Traceback (most recent call last):
  File "/home/mariano/miniconda3/bin/NanoPlot", line 8, in <module>
    sys.exit(main())
  File "/home/mariano/miniconda3/lib/python3.8/site-packages/nanoplot/NanoPlot.py", line 59, in main
    datadf = get_input(
  File "/home/mariano/miniconda3/lib/python3.8/site-packages/nanoget/nanoget.py", line 92, in get_input
    dfs=[out for out in executor.map(extraction_function, files)],
  File "/home/mariano/miniconda3/lib/python3.8/site-packages/nanoget/nanoget.py", line 92, in <listcomp>
    dfs=[out for out in executor.map(extraction_function, files)],
  File "/home/mariano/miniconda3/lib/python3.8/concurrent/futures/process.py", line 484, in _chain_from_iterable_of_lists
    for element in iterable:
  File "/home/mariano/miniconda3/lib/python3.8/concurrent/futures/_base.py", line 611, in result_iterator
    yield fs.pop().result()
  File "/home/mariano/miniconda3/lib/python3.8/concurrent/futures/_base.py", line 439, in result
    return self.__get_result()
  File "/home/mariano/miniconda3/lib/python3.8/concurrent/futures/_base.py", line 388, in __get_result
    raise self._exception
ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False

[wdecoster]

Aha, that makes sense. Maybe blasr is still in use, not sure. I am going to reopen this issue as a reminder to look at blasr-bam files…

[mavino]

I am new to pacbio, I was just exploring smrt tools and I came across with blasr first…