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nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
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from numpy.core._multiarray_umath import ( KeyboardInterrupt #371

Closed qianxin-kxy closed 1 year ago

qianxin-kxy commented 1 year ago

Hello, I ran Gubbins through the following code and encountered the following error. I don't know where the problem occurred?

$ run_gubbins.py -p gubbins clean.full.aln --threads 100

Running joint ancestral reconstruction with pyjar OpenBLAS blas_thread_init: pthread_create failed for thread 21 of 128: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 4096 current, 4124035 max OpenBLAS blas_thread_init: pthread_create failed for thread 22 of 128: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 4096 current, 4124035 max ………………There are many similar codes……………… OpenBLAS blas_thread_init: pthread_create failed for thread 125 of 128: Resource temporarily unavailable OpenBLAS blas_thread_init: pthread_create failed for thread 126 of 128: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 4096 current, 4124035 max OpenBLAS blas_thread_init: RLIMIT_NPROC 4096 current, 4124035 max OpenBLAS blas_thread_init: pthread_create failed for thread 126 of 128: Resource temporarily unavailable OpenBLAS blas_thread_init: pthread_create failed for thread 127 of 128: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 4096 current, 4124035 max OpenBLAS blas_thread_init: RLIMIT_NPROC 4096 current, 4124035 max OpenBLAS blas_thread_init: pthread_create failed for thread 127 of 128: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 4096 current, 4124035 max Process SpawnPoolWorker-17: Process SpawnPoolWorker-12: Traceback (most recent call last): File "/data/users/kxy/miniconda3/envs/gubbins/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/data/users/kxy/miniconda3/envs/gubbins/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/data/users/kxy/miniconda3/envs/gubbins/lib/python3.10/multiprocessing/pool.py", line 114, in worker task = get() File "/data/users/kxy/miniconda3/envs/gubbins/lib/python3.10/multiprocessing/queues.py", line 367, in get return _ForkingPickler.loads(res) File "/data/users/kxy/miniconda3/envs/gubbins/lib/python3.10/site-packages/gubbins/init.py", line 16, in from gubbins import common File "/data/users/kxy/miniconda3/envs/gubbins/lib/python3.10/site-packages/gubbins/common.py", line 32, in from Bio import AlignIO File "/data/users/kxy/miniconda3/envs/gubbins/lib/python3.10/site-packages/Bio/AlignIO/init.py", line 140, in from Bio.Align import MultipleSeqAlignment File "/data/users/kxy/miniconda3/envs/gubbins/lib/python3.10/site-packages/Bio/Align/init.py", line 25, in import numpy File "/data/users/kxy/miniconda3/envs/gubbins/lib/python3.10/site-packages/numpy/init.py", line 140, in from . import core File "/data/users/kxy/miniconda3/envs/gubbins/lib/python3.10/site-packages/numpy/core/init.py", line 23, in from . import multiarray File "/data/users/kxy/miniconda3/envs/gubbins/lib/python3.10/site-packages/numpy/core/multiarray.py", line 10, in from . import overrides File "/data/users/kxy/miniconda3/envs/gubbins/lib/python3.10/site-packages/numpy/core/overrides.py", line 6, in from numpy.core._multiarray_umath import ( KeyboardInterrupt

The screen shows a lot of duplicates like the codes above.

In addition, the output folder contains the following files:

clean.full.aln RAxML_log.clean.full.iteration_1 clean.full.iteration_1.tre.rooted RAxML_log.clean.full.iteration_1_reconstruction RAxML_bestTree.clean.full.iteration_1 RAxML_parsimonyTree.clean.full.iteration_1 RAxML_binaryModelParameters.clean.full.iteration_1_reconstruction RAxML_result.clean.full.iteration_1 RAxML_info.clean.full.iteration_1 RAxML_result.clean.full.iteration_1_reconstruction RAxML_info.clean.full.iteration_1_reconstruction

nickjcroucher commented 1 year ago

This is not a Gubbins issue, this relates to the machine you are using: https://stackoverflow.com/questions/52026652/openblas-blas-thread-init-pthread-create-resource-temporarily-unavailable. You probably need to use fewer threads.