9:15 am – 6:00pm, 8:00pm – 8:55 pm
Library building
- goal: building 10 kb tiling regions of BX-C probes against genome
- approach: adapt new OligoArray-free pipeline from transcriptome libraries to design genome libraries
Problems
- crashed Morgan when all 256 GB of RAM got paged during penalty calculations
- this may have happened because the target sequences are all included in the off-target table (the whole genome)
- tested this hypothesis by running against chr2L only (currently constructing for BX-C on 2R)
- this runs quickly without any sign of crashing.
- (might have been a mis-interpretation — code is written to load an existing trDesigner rather than rerun. May not have attempted to use this off-target library at all.)
- indeed this appears to have been the case, now rerunning.
- wrote new function to remove regions probed from the genome sequence and create a new offTarget fasta file database of the genome for this library construction
- writing whole-genome fasta files is not fast, even for Drosophila (nor is loading them, though the fly fasta loads pretty quickly)
- building OTtable to whole genome duplicated to plus and minus strands, (with BXC removed) goes pretty fast — less than 400 seconds
- this goes MUCH faster with local databases, read-write speed pretty important, doesn’t work well over network.
- moved to new folder on MorganData (ChromatinLibraries/Library7)
- (originally had data on Monet in Chromatin/OligoLibraries/Library7)
- calculating penalties is pretty slow
- this is the step that caused the memory to destroy the computer running (maxed out).
- currently have 29 GB paged, now calc’ penalities with the chr2L_plus strand only. We’ll see how much it eats and whether this destroys the system again. (started 8:45 pm).
- even without BX-C this does indeed use tons of memory. aside from that it’s not killer slow.