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

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  Start range=chrX:42000-42999
  Start range=chrX:42000-42999


Well, it took all day (and much of the night), but I managed to get the above.
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.