Hi,
Thanks for information.
How many micrographs and particles do you have in the entire
dataset? Possibly a memory leak. I will investigate.
Best regards,
Takanori Nakane
On 2019/04/30 18:32, Tomas KOUBA wrote:
> Having the same issue, on 6 mics of the dataset it worked fine on the
> entire dataset failed with this error.
>
> The _autopick.star files are written in the output directory thought.
>
> A temporary solutions is to take the _autopick.star files, copy them
> next to your mics and import them as coordinates.
>
> HTH
>
> T.
>
>
>
> On 2019-04-30 16:04, Takanori Nakane wrote:
>> Hi,
>>
>> Does this happen all the time, or only for a particular dataset and/or
>> condition (e.g. no picked particles at all)?
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>>> I'm seeing an error thrown at the conclusion of running AutoPick in
>>> RELION
>>> 3.0.4:
>>>
>>> terminate called after throwing an instance of 'std::bad_alloc'
>>> what(): std::bad_alloc
>>> [cn3672:mpi_rank_0][error_sighandler] Caught error: Aborted (signal 6)
>>> srun: error: cn3672: task 0: Aborted
>>>
>>> I believe the actual job was ok, and the error is thrown at the end
>>> of the
>>> job. Is there any trick to prevent this?
>>>
>>> David Hoover
>>> HPC @ NIH
>>>
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