On May 14, 2009, at 2:31 AM, michel bellis wrote:
>
> pygr.cnestedlist.NLMSA.IntervalDB.buildFromUnsortedFile
> MemoryError: pygr\intervaldb.c, line 311: memory request failed: NAME
> [57936509]
Hi Michel,
you're running out of memory. It is requesting 58MB and your OS is
returning NULL.
By the way, Michel, I should have asked this a long time ago: could
you just use one of our pre-built NLMSA? These were designed to help
precisely for this situation where someone has insufficient memory to
build it themselves. To get pygr to download the NLMSA and sequence
data for you (rather than just connecting to it as an XMLRPC client),
just give the download=True flag. For example
>>> from pygr import worldbase
>>> worldbase.dir('Bio.MSA') # this shows what's available as XMLRPC
client
['Bio.MSA.UCSC.bosTau2ToBostau3', 'Bio.MSA.UCSC.bosTau3ToBostau4',
'Bio.MSA.UCSC.bosTau4_multiz5way', 'Bio.MSA.UCSC.calJac1_multiz9way',
'Bio.MSA.UCSC.canFam2_multiz4way', 'Bio.MSA.UCSC.ce2ToCe4',
'Bio.MSA.UCSC.danRer2ToDanrer3', 'Bio.MSA.UCSC.danRer3ToDanrer2',
'Bio.MSA.UCSC.danRer3ToDanrer4', 'Bio.MSA.UCSC.danRer3_multiz5way',
'Bio.MSA.UCSC.danRer4ToDanrer3', 'Bio.MSA.UCSC.danRer4ToDanrer5',
'Bio.MSA.UCSC.danRer4_multiz7way', 'Bio.MSA.UCSC.danRer5ToDanrer4',
'Bio.MSA.UCSC.dm2ToDm3', 'Bio.MSA.UCSC.dm2_multiz15way',
'Bio.MSA.UCSC.dm2_multiz9way', 'Bio.MSA.UCSC.dm3_multiz15way',
'Bio.MSA.UCSC.felCat3_multiz4way', 'Bio.MSA.UCSC.fr2_multiz5way',
'Bio.MSA.UCSC.galGal2ToGalgal3', 'Bio.MSA.UCSC.galGal2_multiz7way',
'Bio.MSA.UCSC.galGal3_multiz7way', 'Bio.MSA.UCSC.gasAcu1_multiz8way',
'Bio.MSA.UCSC.hg17ToHg18', 'Bio.MSA.UCSC.hg17_multiz17way',
'Bio.MSA.UCSC.hg18ToHg17', 'Bio.MSA.UCSC.hg18_multiz17way',
'Bio.MSA.UCSC.hg18_multiz28way', 'Bio.MSA.UCSC.mm5ToMm6',
'Bio.MSA.UCSC.mm5ToMm7', 'Bio.MSA.UCSC.mm5ToMm8',
'Bio.MSA.UCSC.mm7ToMm5', 'Bio.MSA.UCSC.mm7ToMm6',
'Bio.MSA.UCSC.mm7ToMm8', 'Bio.MSA.UCSC.mm7_multiz17way',
'Bio.MSA.UCSC.mm8ToMm7', 'Bio.MSA.UCSC.mm8ToMm9',
'Bio.MSA.UCSC.mm8_multiz17way', 'Bio.MSA.UCSC.mm9ToMm8',
'Bio.MSA.UCSC.mm9_multiz30way', 'Bio.MSA.UCSC.monDom4_multiz7way',
'Bio.MSA.UCSC.ornAna1_multiz6way', 'Bio.MSA.UCSC.oryLat1_multiz5way',
'Bio.MSA.UCSC.panTro1ToPantro2', 'Bio.MSA.UCSC.panTro2ToPantro1',
'Bio.MSA.UCSC.ponAbe2_multiz8way', 'Bio.MSA.UCSC.rn3ToRn4',
'Bio.MSA.UCSC.rn4ToRn3', 'Bio.MSA.UCSC.rn4_multiz9way',
'Bio.MSA.UCSC.xenTro1ToXentro2', 'Bio.MSA.UCSC.xenTro1_multiz5way']
>>> worldbase.dir('Bio.MSA', download=True) # this shows what's
available for download
['Bio.MSA.UCSC.bosTau2ToBostau3', 'Bio.MSA.UCSC.bosTau2ToBostau3.txt',
'Bio.MSA.UCSC.bosTau3ToBostau4', 'Bio.MSA.UCSC.bosTau3ToBostau4.txt',
'Bio.MSA.UCSC.bosTau4_multiz5way',
'Bio.MSA.UCSC.bosTau4_multiz5way.txt',
'Bio.MSA.UCSC.calJac1_multiz9way',
'Bio.MSA.UCSC.calJac1_multiz9way.txt',
'Bio.MSA.UCSC.canFam2_multiz4way',
'Bio.MSA.UCSC.canFam2_multiz4way.txt', 'Bio.MSA.UCSC.ce2ToCe4',
'Bio.MSA.UCSC.ce2ToCe4.txt', 'Bio.MSA.UCSC.danRer2ToDanrer3',
'Bio.MSA.UCSC.danRer2ToDanrer3.txt', 'Bio.MSA.UCSC.danRer3ToDanrer2',
'Bio.MSA.UCSC.danRer3ToDanrer2.txt', 'Bio.MSA.UCSC.danRer3ToDanrer4',
'Bio.MSA.UCSC.danRer3ToDanrer4.txt',
'Bio.MSA.UCSC.danRer3_multiz5way',
'Bio.MSA.UCSC.danRer3_multiz5way.txt',
'Bio.MSA.UCSC.danRer4ToDanrer3', 'Bio.MSA.UCSC.danRer4ToDanrer3.txt',
'Bio.MSA.UCSC.danRer4ToDanrer5', 'Bio.MSA.UCSC.danRer4ToDanrer5.txt',
'Bio.MSA.UCSC.danRer4_multiz7way',
'Bio.MSA.UCSC.danRer4_multiz7way.txt',
'Bio.MSA.UCSC.danRer5ToDanrer4', 'Bio.MSA.UCSC.danRer5ToDanrer4.txt',
'Bio.MSA.UCSC.dm2ToDm3', 'Bio.MSA.UCSC.dm2ToDm3.txt',
'Bio.MSA.UCSC.dm2_multiz15way', 'Bio.MSA.UCSC.dm2_multiz15way.txt',
'Bio.MSA.UCSC.dm2_multiz9way', 'Bio.MSA.UCSC.dm2_multiz9way.txt',
'Bio.MSA.UCSC.dm3_multiz15way', 'Bio.MSA.UCSC.dm3_multiz15way.txt',
'Bio.MSA.UCSC.felCat3_multiz4way',
'Bio.MSA.UCSC.felCat3_multiz4way.txt', 'Bio.MSA.UCSC.fr2_multiz5way',
'Bio.MSA.UCSC.fr2_multiz5way.txt', 'Bio.MSA.UCSC.galGal2ToGalgal3',
'Bio.MSA.UCSC.galGal2ToGalgal3.txt',
'Bio.MSA.UCSC.galGal2_multiz7way',
'Bio.MSA.UCSC.galGal2_multiz7way.txt',
'Bio.MSA.UCSC.galGal3_multiz7way',
'Bio.MSA.UCSC.galGal3_multiz7way.txt',
'Bio.MSA.UCSC.gasAcu1_multiz8way',
'Bio.MSA.UCSC.gasAcu1_multiz8way.txt', 'Bio.MSA.UCSC.hg17ToHg18',
'Bio.MSA.UCSC.hg17ToHg18.txt', 'Bio.MSA.UCSC.hg17_multiz17way',
'Bio.MSA.UCSC.hg17_multiz17way.txt', 'Bio.MSA.UCSC.hg18ToHg17',
'Bio.MSA.UCSC.hg18ToHg17.txt', 'Bio.MSA.UCSC.hg18_multiz17way',
'Bio.MSA.UCSC.hg18_multiz17way.txt', 'Bio.MSA.UCSC.hg18_multiz28way',
'Bio.MSA.UCSC.hg18_multiz28way.txt', 'Bio.MSA.UCSC.mm5ToMm6',
'Bio.MSA.UCSC.mm5ToMm6.txt', 'Bio.MSA.UCSC.mm5ToMm7',
'Bio.MSA.UCSC.mm5ToMm7.txt', 'Bio.MSA.UCSC.mm5ToMm8',
'Bio.MSA.UCSC.mm5ToMm8.txt', 'Bio.MSA.UCSC.mm7ToMm5',
'Bio.MSA.UCSC.mm7ToMm5.txt', 'Bio.MSA.UCSC.mm7ToMm6',
'Bio.MSA.UCSC.mm7ToMm6.txt', 'Bio.MSA.UCSC.mm7ToMm8',
'Bio.MSA.UCSC.mm7ToMm8.txt', 'Bio.MSA.UCSC.mm7_multiz17way',
'Bio.MSA.UCSC.mm7_multiz17way.txt', 'Bio.MSA.UCSC.mm8ToMm7',
'Bio.MSA.UCSC.mm8ToMm7.txt', 'Bio.MSA.UCSC.mm8ToMm9',
'Bio.MSA.UCSC.mm8ToMm9.txt', 'Bio.MSA.UCSC.mm8_multiz17way',
'Bio.MSA.UCSC.mm8_multiz17way.txt', 'Bio.MSA.UCSC.mm9ToMm8',
'Bio.MSA.UCSC.mm9ToMm8.txt', 'Bio.MSA.UCSC.mm9_multiz30way',
'Bio.MSA.UCSC.mm9_multiz30way.txt', 'Bio.MSA.UCSC.monDom4_multiz7way',
'Bio.MSA.UCSC.monDom4_multiz7way.txt',
'Bio.MSA.UCSC.ornAna1_multiz6way',
'Bio.MSA.UCSC.ornAna1_multiz6way.txt',
'Bio.MSA.UCSC.oryLat1_multiz5way',
'Bio.MSA.UCSC.oryLat1_multiz5way.txt',
'Bio.MSA.UCSC.panTro1ToPantro2', 'Bio.MSA.UCSC.panTro1ToPantro2.txt',
'Bio.MSA.UCSC.panTro2ToPantro1', 'Bio.MSA.UCSC.panTro2ToPantro1.txt',
'Bio.MSA.UCSC.ponAbe2_multiz8way',
'Bio.MSA.UCSC.ponAbe2_multiz8way.txt', 'Bio.MSA.UCSC.rn3ToRn4',
'Bio.MSA.UCSC.rn3ToRn4.txt', 'Bio.MSA.UCSC.rn4ToRn3',
'Bio.MSA.UCSC.rn4ToRn3.txt', 'Bio.MSA.UCSC.rn4_multiz9way',
'Bio.MSA.UCSC.rn4_multiz9way.txt', 'Bio.MSA.UCSC.xenTro1ToXentro2',
'Bio.MSA.UCSC.xenTro1ToXentro2.txt',
'Bio.MSA.UCSC.xenTro1_multiz5way',
'Bio.MSA.UCSC.xenTro1_multiz5way.txt']
>>> msa = worldbase. Bio.MSA.UCSC.hg18_multiz28way(download=True)
The last statement downloads and installs the data on your local
computer, ready to use ... which of course will take a while.
-- Chris
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