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--- archive:bioinformatic_tools:abyss [2010/05/19 17:46]
jstjohn
+++ archive:bioinformatic_tools:abyss [2010/05/19 20:55]
jstjohn
@@ Line 278: / Line 278: @@
 Near the height I have observed this is eating up about 50G of ram, but the issue appears to be in available space for the sort algorithm in kolossus's /tmp/ directory. I am trying this again so I can copy down the error and send it to cluster-admin because kolossus should have around 400GB free of local HD space on top of its 1.1TB of ram. (kolossus has more ram than HD space: 1.1TB of ram vs 750GB hd)
+To get around the issue of sort running out of memory in its temp directory, I found an alternate command where you can supply your own temp directory to sort. Since there is plenty of room left on the hive I issue the following command to generate the files myself. The nice thing is that since this is a makefile, once I have done this I can simply re-start the assembler, and it will see the files I have manually generated and move on to the next step.
+<code>
+KAligner   -j4 -k35 /scratch/galt/bananaSlug/slug_1.fastq /scratch/galt/bananaSlug/slug_2.fastq slugAbyss3-3.fa \
+                |ParseAligns  -k35 -h lib1-3.hist \
+                |sort -T /hive/users/jstjohn/slugAssembly/tmp -nk2,2 \
+                |gzip >lib1-3.pair.gz
+</code>

Banana Slug Genomics