Daniel:Notebook/HiResChrPaint/2014-6-17: Difference between revisions
Jump to navigation
Jump to search
>Djacobse (Created page with "=Probe Design (Started 06/17/2014)= Back to Calendar ==Probe Mining== From [[Daniel:Notebook/H...") |
>Djacobse No edit summary |
||
(3 intermediate revisions by the same user not shown) | |||
Line 11: | Line 11: | ||
##make | ##make | ||
##make install | ##make install | ||
# | #Run OligoArray2 using the blast available on genome miner | ||
##java -jar /home/djacobse/blastdb_hg38/OligoArray2_1/OligoArray2.jar -i in_caskgene.fas -d hg38.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 | |||
Can OligoArray read/write specified files? NO | |||
Data initialization: DONE | |||
Is hg38.fas a valid Blast database? NO | |||
Is OligoArrayAux installed? YES | |||
So something is still up. I'm going to try rewriting the Blast database using formatdb, which is available on this version of blast. | |||
#Create blast database | |||
##formatdb -i hg38.fas -p F -o T | |||
#Run OligoArray2 using new blast database | |||
##java -jar /home/djacobse/blastdb_hg38/OligoArray2_1/OligoArray2.jar -i in_caskgene.fas -d hg38.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 | |||
This command runs for a long time. This command didn't work either. The memory allocation by java was too small. As such, I will run the command again using larger memory allocation. | |||
[[Category:HRCP]] [[Category:OligoArray]] [[Category:Probe Mining]] |
Latest revision as of 17:56, 2 July 2014
Probe Design (Started 06/17/2014)[edit]
Probe Mining[edit]
From yesterday's results I know that I need to move the files and programs to genome miner to run.
- Install oligoarrayaux
- ./configure --prefix=$HOME
- make
- make install
- Run OligoArray2 using the blast available on genome miner
- java -jar /home/djacobse/blastdb_hg38/OligoArray2_1/OligoArray2.jar -i in_caskgene.fas -d hg38.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
Can OligoArray read/write specified files? NO Data initialization: DONE Is hg38.fas a valid Blast database? NO Is OligoArrayAux installed? YES
So something is still up. I'm going to try rewriting the Blast database using formatdb, which is available on this version of blast.
- Create blast database
- formatdb -i hg38.fas -p F -o T
- Run OligoArray2 using new blast database
- java -jar /home/djacobse/blastdb_hg38/OligoArray2_1/OligoArray2.jar -i in_caskgene.fas -d hg38.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
This command runs for a long time. This command didn't work either. The memory allocation by java was too small. As such, I will run the command again using larger memory allocation.