Closed shimbalama closed 3 years ago
Hi Liam,
I can try :-) Which organism are you working on? Do you have a log file of one of the erroneous runs?
Cheers, Wouter
Thanks Wouter!
Working on human (cancer so ~60x deep)
log
Process Process-1:
Traceback (most recent call last):
File "/software/python/Python-3.6.1/lib/python3.6/multiprocessing/process.py", line 249, in _bootstrap
self.run()
File "/software/python/Python-3.6.1/lib/python3.6/multiprocessing/process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "/software/python/Python-3.6.1/lib/python3.6/concurrent/futures/process.py", line 181, in _process_worker
result=r))
File "/software/python/Python-3.6.1/lib/python3.6/multiprocessing/queues.py", line 355, in put
self._writer.send_bytes(obj)
File "/software/python/Python-3.6.1/lib/python3.6/multiprocessing/connection.py", line 200, in send_bytes
self._send_bytes(m[offset:offset + size])
File "/software/python/Python-3.6.1/lib/python3.6/multiprocessing/connection.py", line 393, in _send_bytes
header = struct.pack("!i", n)
struct.error: 'i' format requires -2147483648 <= number <= 2147483647
Traceback (most recent call last):
File "/software/python/Python-3.6.1/bin/NanoPlot", line 10, in
ty
Thanks for your patience, I think I have solved this in nanoget v1.16, which is now available through PyPI, and probably soon on conda. Could you test again?
I am planning a more thorough overhaul of the parsing functions and migration to faster alternatives, but that will take longer.
Hi Wouter,
--huge doesn't solve this problem for me. I have used NanoPlot for 2 years now without issue (thanks!), all bams created the same way (NGMLR to map ONT reads). The bam in question is 222GB.
Is this something you coul dlook into?
Ty, Liam