Daniel:Notebook/HiResChrPaint/2014-6-18: Difference between revisions

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Well, it took all day (and much of the night), but I managed to get the above.  Since I allocated a whopping 8 GB to this particular run, I'm going to review what I've put in so far, and see if there's something I'm missing.
Well, it took all day (and much of the night), but I managed to get the above.  Since I allocated a whopping 8 GB to this particular run, I'm going to review what I've put in so far, and see if there's something I'm missing.
[[Category:HRCP]] [[Category:Probe Mining]] [[Category:OligoArray]]

Latest revision as of 17:57, 2 July 2014

Probe Design (Started 06/17/2014)[edit]

Back to Calendar

Probe Mining[edit]

  1. Run OligoArray2 with greater memory allocation
    1. java -Xmx8192m -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
Start range=chrX:14000-14999
Start range=chrX:15000-15999
Start range=chrX:16000-16999
Start range=chrX:17000-17999
Start range=chrX:18000-18999
Start range=chrX:19000-19999
Start range=chrX:20000-20999
Start range=chrX:21000-21999
Start range=chrX:22000-22999
Start range=chrX:23000-23999
Start range=chrX:24000-24999
Start range=chrX:25000-25999
Start range=chrX:26000-26999
Start range=chrX:27000-27999
Start range=chrX:28000-28999
Start range=chrX:29000-29999
The Blast crashed because there is not enought memory allowed to the application (java.lang.OutOfMemoryError: GC overhead limit exceeded).
You may want to allow more memory to java by using the java option -Xmx256m (will allow 256 M RAM)
Start range=chrX:30000-30999
Start range=chrX:31000-31999
Start range=chrX:32000-32999
Start range=chrX:33000-33999
Start range=chrX:34000-34999
Start range=chrX:35000-35999
Start range=chrX:36000-36999
Start range=chrX:37000-37999
Start range=chrX:38000-38999
Start range=chrX:39000-39999
The Blast crashed because there is not enought memory allowed to the application (java.lang.OutOfMemoryError: GC overhead limit exceeded).
You may want to allow more memory to java by using the java option -Xmx256m (will allow 256 M RAM)
Start range=chrX:40000-40999
The process crashed due to an error (java.io.IOException: Cannot run program "blastall": java.io.IOException: error=12, Cannot allocate memory).
Start range=chrX:41000-41999
Start range=chrX:42000-42999

Well, it took all day (and much of the night), but I managed to get the above. Since I allocated a whopping 8 GB to this particular run, I'm going to review what I've put in so far, and see if there's something I'm missing.