Hi Chris, We are still having trouble with the MSA. We were able to build it without any errors using pygr/0.8.2
However when we try to load and query it, we get the following error. In [1]: from pygr import worldbase In [2]: genome = worldbase.Bio.Seq.Genome.MOUSE.mm10() In [3]: msa = worldbase.Bio.Seq.Alignments.MOUSE.mm10.multiz60way() In [4]: slice = genome['chrY'] In [5]: res = msa[slice] --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-5-628143efd160> in <module>() ----> 1 res = msa[slice] pygr/msa-builder/build/lib.linux-x86_64-2.6/pygr/cnestedlist.so in pygr.cnestedlist.NLMSA.__getitem__() pygr/msa-builder/build/lib.linux-x86_64-2.6/pygr/cnestedlist.so in pygr.cnestedlist.NLMSASlice.__cinit__() AttributeError: 'pygr.cnestedlist.NLMSA' object has no attribute 'doSlice' Any clue? Vishal On Thursday, April 25, 2013 10:23:33 AM UTC-7, Vishal Patel wrote: > > Hi, > > We usually download the pygr NLMSA from the UCLA server. However, the > latest mm10 - multiz60way alignment does not exist there so we decided to > build it. > > First I ran into issues with max size, > > * 1 msa = cnestedlist.NLMSA(pathstem=pathstem,* > * 2 seqDict=genomeUnion,* > *----> 3 mafFiles=maflist, mode="w")* > * > * > *site-packages/pygr-0.8.2-py2.7-linux-x86_64.egg/pygr/cnestedlist.so in > pygr.cnestedlist.NLMSA.__init__()* > *site-packages/pygr-0.8.2-py2.7-linux-x86_64.egg/pygr/cnestedlist.so in > pygr.cnestedlist.NLMSA.readMAFfiles() > * > * > * > *ValueError: MAF block too long! Increase max size* > > Setting the maxlen and maxint to a billion also did not help so I set it > to sys.maxint. > > However this code still fails because it open 1000's of ".build" files and > fails because it does not have "write permission" on the next file handle > it tries to open. Basically hits the max open files limit. I increased the > ulimit to 10,000 files at which point it fails with "Segmentation fault > (core dumped)" > > Here is lsof out every 0.1 s when it failed, > 170 # these are file handles to genome files > 170 > 170 > 170 > 170 > 170 > 170 > 726 # starts creating .build files > 1682 > 2443 > 3706 > 6300 > 7209 > 9160 # hits the upper limit again and fails with a core dump. > > I have tried this with py2.6/pygr0.8.1 and py2.7/pygr0.8.2 and get the > same error. > > Has anyone experienced this? > What are the .build files? > > Vishal > > > > > > > > > -- You received this message because you are subscribed to the Google Groups "pygr-dev" group. To unsubscribe from this group and stop receiving emails from it, send an email to pygr-dev+unsubscr...@googlegroups.com. To post to this group, send email to pygr-dev@googlegroups.com. Visit this group at http://groups.google.com/group/pygr-dev?hl=en. For more options, visit https://groups.google.com/groups/opt_out.