Daniel:Notebook/HiResChrPaint/2014-6-19

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Revision as of 22:09, 19 June 2014 by >Djacobse
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Probe Design (Started 06/17/2014)

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Probe Mining

The OligoArray script might actually need the blast database broken up into 1kb chunks for some reason. So, let's try that.

  1. Create BLAST database from fragmented genome
    1. formatdb -i in_hg38.fas -p T -o F
[formatdb] WARNING: Cannot add sequence number 1953021 (lcl|range=hg38:1953020000-1953020999) because it has zero-length.
[formatdb] FATAL ERROR: Fatal error when adding sequence to BLAST database.

So that's a fatal error.

The instructions call for concatenating all the fasta files into one. I did this step using cat, but they suggest using their java script, so I'll try that.

  1. Concatenate fasta files
    1. java ConcatenateFiles hg38_cat.fas *.fa
  2. Fragment genome into pieces
    1. python ../bin/input_blocks.py
    2. Please enter the filename, "chr2R_sorted_oligo.txt" or "chr2R_intersect.bed" etc.: hg38_cat.fas
    3. Please enter the chromosome or assembly, "chr1 or ch2R, etc.: hg38
Killed

Couldn't have said it better myself.

Trying again using the Wu lab (Oligopaints) version of the fasta file. This is an older version (hg19/gr37, not gr38), but it'll have to do.

  1. Format BLAST database
    1. formatdb -i hg19.fas -p F -o T
  2. Run OligoArray2
    1. java -Xmx8192m -jar /home/djacobse/blastdb_hg38/OligoArray2_1/OligoArray2.jar -i in_caskgene.fas -d hg19.fas -o oligo_caskgene.txt -r rejected_oligo.fas -R caskgene.log -n 30 -l 60 -L 60 -D 1000 -t 55 -T 65 -s 70 -x 70 -p 35 -P 80 -m "CCCC;GGGG;TTTTT;AAAAA" -g 2
Start range=chrX:1157000-1157999
Running Blast (-e 0.0)... For sequence range=chrX:1157000-1157999, the following exception was caugth:
java.io.IOException: Cannot run program "blastall": java.io.IOException: error=12, Cannot allocate memory

New problem, sort of. Looks like it can run OligoArray for a little while (gets through about 5000 bp or so), then says it can't allocate memory. Not sure what that's all about.

I may be allocating more memory than is available for allocation with this command, so I'll try again without the memory allocation flag. I may also need to try again using a different (smaller) memory allocation flag.

  1. Run OligoArray2
    1. java -jar /home/djacobse/blastdb_hg38/OligoArray2_1/OligoArray2.jar -i in_caskgene.fas -d hg19.fas -o oligo_caskgene.txt -r rejected_oligo.fas -R caskgene.log -n 30 -l 60 -L 60 -D 1000 -t 55 -T 65 -s 70 -x 70 -p 35 -P 80 -m "CCCC;GGGG;TTTTT;AAAAA" -g 2