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.
