Open pdoris opened 9 months ago
christopher-vollmers
commented
9 months ago Hi,
That error suggests that you are running out of RAM running minimap2. Can I ask how much RAM you have on the machine you are using? RAM usage of minimap2 (as I understand it) depends on the genome reference size so it's pretty much fixed and most often >30GB.
pdoris
commented
9 months ago Thanks, increased memory, problem solved....until I reach the P module.
Looks like a spawn error....Mac OS 14.2 py 3.9.18, also tried with pyenv 3.8.18, some result
Module P - .sam to .clean.sorted.psl conversion converting sam output to psl formatTraceback (most recent call last):0000
File "
File "
File "
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/context.py", line 284, in _Popen
self._popen = self._Popen(self)
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/context.py", line 284, in _Popen
return Popen(process_obj)
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in init
return Popen(process_obj)
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in init
self._popen = self._Popen(self)
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/context.py", line 284, in _Popen
return Popen(process_obj)
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in init
super().init(process_obj)00000
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/popen_fork.py", line 19, in init
super().init(process_obj)
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/popen_fork.py", line 19, in init
super().init(process_obj)
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/popen_fork.py", line 19, in init
self._launch(process_obj)
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
self._launch(process_obj)
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
_check_not_importing_main()
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
self._launch(process_obj)
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
raise RuntimeError('''
RuntimeError:
_check_not_importing_main()
File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
An attempt has been made to start a new process before the
current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
raise RuntimeError('''RuntimeError: An attempt has been made to start a new process before the current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.
prep_data = spawn.get_preparation_data(process_obj._name)File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data _check_not_importing_main() File "/Users/pdoris/.pyenv/versions/3.8.18/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main raise RuntimeError(''' RuntimeError: An attempt has been made to start a new process before the current process has finished its bootstrapping phase.
This probably means that you are not using fork to start your
child processes and you have forgotten to use the proper idiom
in the main module:
if __name__ == '__main__':
freeze_support()
...
The "freeze_support()" line can be omitted if the program
is not going to be frozen to produce an executable.Traceback (most recent call last):
File "
christopher-vollmers
commented
9 months ago That's an error I haven't seen before... What operating system are you using to run this?
It's definitely a multiprocessing error in emtrey.py and I'm researching the error now.
I'm asking because a lot of pages mention this error to be a Windows thing which I have much less experience with...
I'll see whether I can reproduce and fix this somehow. I have some ideas.
pdoris
commented
9 months ago Mac OSX 14.2
This might be helpful to you:
https://stackoverflow.com/questions/60691363/runtimeerrorfreeze-support-on-mac
Thanks,
I have finished some smaller analysis on a Linux server, but that is currently down and my big job was in the queue for three days! So this is a mac problem…and maybe windows too.
Peter
From: christopher-vollmers @.> Date: Friday, February 9, 2024 at 1:38 PM To: christopher-vollmers/Mandalorion @.> Cc: Doris, Peter A @.>, Author @.> Subject: Re: [christopher-vollmers/Mandalorion] segfault in alignment module (Issue #1) External: Increase caution when handling links and attachments.
That's an error I haven't seen before... What operating system are you using to run this?
It's definitely a multiprocessing error in emtrey.py and I'm researching the error now.
I'm asking because a lot of pages mention this error to be a Windows thing which I have much less experience with...
I'll see whether I can reproduce and fix this somehow. I have some ideas.
— Reply to this email directly, view it on GitHubhttps://github.com/christopher-vollmers/Mandalorion/issues/1#issuecomment-1936497616, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUEQOHF67MVBLQBJLP47RVLYSZ3KFAVCNFSM6AAAAABC26XI6CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZWGQ4TONRRGY. You are receiving this because you authored the thread.Message ID: @.***>
christopher-vollmers
commented
9 months ago It's a spawn vs fork issue for sure. We aren't testing this on MacOS so there might be other spots this will break as well... My guess is this will run fine on a Linux machine.
I'll need a few days to figure out how to force fork over spawn in macOS and then find a Mac to test this on.
But there is a lot more multiprocessing happening later in Mandalorion and all of that will break probably as well.
A quick thing to try is to make python3.7 your default python3 and try to run Mandalorion that way for now.
pdoris
commented
9 months ago Doing this now and will let you know
A quick thing to try is to make python3.7 your default python3 and try to run Mandalorion that way for now.
From: christopher-vollmers @.> Date: Friday, February 9, 2024 at 1:56 PM To: christopher-vollmers/Mandalorion @.> Cc: Doris, Peter A @.>, Author @.> Subject: Re: [christopher-vollmers/Mandalorion] segfault in alignment module (Issue #1) External: Increase caution when handling links and attachments.
It's a spawn vs fork issue for sure. We aren't testing this on MacOS so there might be other spots this will break as well... My guess is this will run fine on a Linux machine.
I'll need a few days to figure out how to force fork over spawn in macOS and then find a Mac to test this on.
But there is a lot more multiprocessing happening later in Mandalorion and all of that will break probably as well.
A quick thing to try is to make python3.7 your default python3 and try to run Mandalorion that way for now.
— Reply to this email directly, view it on GitHubhttps://github.com/christopher-vollmers/Mandalorion/issues/1#issuecomment-1936521715, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUEQOHBEX5QVXSO2DGZH57DYSZ5QDAVCNFSM6AAAAABC26XI6CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZWGUZDCNZRGU. You are receiving this because you authored the thread.Message ID: @.***>
pdoris
commented
9 months ago It is running OK under py 3.7.17
@.*** Mandalorion % python3 Mando.py -p results -g UCSC2GRCr8.sorted.gtf -G GRCr8.fasta -f Consensus_reads.fofn -M P
Mandalorion - Isoform identification and quantification
Version - v4.3.0 - That's no moon. It's an isoform
Module P - .sam to .clean.sorted.psl conversion converting sam output to psl format
processing read 300000From: christopher-vollmers @.> Date: Friday, February 9, 2024 at 1:56 PM To: christopher-vollmers/Mandalorion @.> Cc: Doris, Peter A @.>, Author @.> Subject: Re: [christopher-vollmers/Mandalorion] segfault in alignment module (Issue #1) External: Increase caution when handling links and attachments.
It's a spawn vs fork issue for sure. We aren't testing this on MacOS so there might be other spots this will break as well... My guess is this will run fine on a Linux machine.
I'll need a few days to figure out how to force fork over spawn in macOS and then find a Mac to test this on.
But there is a lot more multiprocessing happening later in Mandalorion and all of that will break probably as well.
A quick thing to try is to make python3.7 your default python3 and try to run Mandalorion that way for now.
— Reply to this email directly, view it on GitHubhttps://github.com/christopher-vollmers/Mandalorion/issues/1#issuecomment-1936521715, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUEQOHBEX5QVXSO2DGZH57DYSZ5QDAVCNFSM6AAAAABC26XI6CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZWGUZDCNZRGU. You are receiving this because you authored the thread.Message ID: @.***>
My command is
python3 Mando.py -p /work2/06127/pdoris/frontera/Mandalorion/Mandalorion/ -g UCSC2GRCr8.sorted.gtf -G GRCr8.fasta -f Consensus_reads.fofn -M A
Mandalorion - Isoform identification and quantification
Version - v4.3.0 - That's no moon. It's an isoform
this produces a very big combined fasta file. 35541118333 Feb 5 16:39 Combined.fasta
sh: line 1: 36889 Segmentation fault /work2/06127/pdoris/frontera/Mandalorion/Mandalorion/minimap2/minimap2 -G 400k --secondary=no -ax splice:hq --cs=long -uf -t 8 GRCr8.fasta /work2/06127/pdoris/frontera/Mandalorion/Mandalorion///tmp//Combined.fasta > /work2/06127/pdoris/frontera/Mandalorion/Mandalorion///tmp//mm2Alignments.sam