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. |
Revision as of 17:49, 19 June 2014
Probe Design (Started 06/17/2014)
Probe Mining
- Run OligoArray2 with greater memory allocation
- 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.