使用BioPython读取FASTA校准时出现内存错误
我正在使用BioPython在我的工作场所的计算集群上以120个序列(每个约20kb)的顺序进行读取。我的代码在我自己的计算机上运行得很好(Mac OSX Mavericks,运行的文件大小是多少?您的RAM在本地计算机上是什么样子的?另外,您使用的是哪个版本的python?32位还是64位?文件是2.4 MB。本地计算机RAM是4GB。如何检查python是32位还是64位?谢谢!它将显示在python解释器的顶部。您可以打开IDLE或只输入python也就是说,2.4MB是相对较小的。如果你能用4GB内存运行它,那么计算量就不会那么大了。使用BioPython读取FASTA校准时出现内存错误,python,cluster-computing,biopython,Python,Cluster Computing,Biopython,我正在使用BioPython在我的工作场所的计算集群上以120个序列(每个约20kb)的顺序进行读取。我的代码在我自己的计算机上运行得很好(Mac OSX Mavericks,运行的文件大小是多少?您的RAM在本地计算机上是什么样子的?另外,您使用的是哪个版本的python?32位还是64位?文件是2.4 MB。本地计算机RAM是4GB。如何检查python是32位还是64位?谢谢!它将显示在python解释器的顶部。您可以打开IDLE或只输入python也就是说,2.4MB是相对较小的。如果你
from Bio import AlignIO
alignment = AlignIO.read("my_aligment.fasta","fasta")
Traceback (most recent call last):
File "./my_program.py", line 42, in <module>
alignment = AlignIO.read(align, "fasta")
File "/workplace/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/site-packages/Bio/AlignIO/__init__.py", line 423, in read
first = next(iterator)
File "/workplace/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/site-packages/Bio/AlignIO/__init__.py", line 370, in parse
for a in i:
File "/workplace/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/site-packages/Bio/AlignIO/__init__.py", line 270, in _SeqIO_to_alignment_iterator
records = list(SeqIO.parse(handle, format, alphabet))
File "/workplace/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/site-packages/Bio/SeqIO/__init__.py", line 586, in parse
for r in i:
File "/workplace/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/site-packages/Bio/SeqIO/FastaIO.py", line 121, in FastaIterator
for title, sequence in SimpleFastaParser(handle):
File "/workplace/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/site-packages/Bio/SeqIO/FastaIO.py", line 55, in SimpleFastaParser
line = handle.readline()
MemoryError