I was wrong. You are right. I am testing using 14m sequences and Pygr only
uses 1g memory. I am monitoring memory usage and let you know if I found
something strange.
BTW, I tried to use ScreedSequenceDB, which was working a month ago. But,
this time, using the same script, I got following error message saying there
is no 'name' attribute. I didn't do anything except updating pygr (screed is
same).
Traceback (most recent call last):
File "step6_make_screed_build_pygr.py", line 85, in <module>
msa = cnestedlist.NLMSA(msaName, mode = 'w', seqDict = unionDict,
axtFiles = axtList)
File "cnestedlist.pyx", line 1511, in pygr.cnestedlist.NLMSA.__init__
File "cnestedlist.pyx", line 1862, in pygr.cnestedlist.NLMSA.readAxtNet
File
"/data1/deepreds/projects/Pygr_Project/pygr/build/lib.linux-x86_64-2.5/pygr/seqdb.py",
line 814, in __len__
n += len(db)
File
"/data1/deepreds/projects/Pygr_Project/pygr/build/lib.linux-x86_64-2.5/pygr/seqdb.py",
line 305, in __len__
return len(self.seqInfoDict)
File "/usr/lib64/python2.5/UserDict.py", line 175, in __len__
return len(self.keys())
File
"/data1/deepreds/projects/Pygr_Project/pygr/build/lib.linux-x86_64-2.5/pygr/screed_pygr_api.py",
line 98, in keys
return self.sdb.keys()
File "screed.pyx", line 220, in screed.dbread.keys
File "screed.pyx", line 91, in screed._dbread_name_iter.__next__
File "screed.pyx", line 56, in screed._dbread_record.__getattr__
AttributeError: name
Namshin Kim
> 16m sequence IDs != 16 gb of memory! Or at least it shouldn't.
>
> I'm using a regular SequenceFileDB, and a regular NLMSA.
>
> --titus
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