lecture_notes:04-28-2010
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lecture_notes:04-28-2010 [2010/05/02 05:42] galt |
lecture_notes:04-28-2010 [2010/05/02 16:22] (current) karplus added workaround for campusrocks filesystem problem |
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| === Misc Notes: === | === Misc Notes: === | ||
| - | **campusrocks is broken!** | + | **campusrocks is broken!** The head node has the file system mounted as /campusdata, but the client nodes have it mounted as /campus. The workaround is to use the trick in assemblies/Pog/map-colorspace5/Makefile |
| + | <code> | ||
| + | CWD ?= $(subst campusdata,campus,$(shell pwd)) | ||
| + | </code> | ||
| + | Then instead of | ||
| + | <code> | ||
| + | qsub -cwd | ||
| + | </code> use | ||
| + | <code> | ||
| + | qsub -wd ${CWD} | ||
| + | </code> | ||
| //Pog// has 2 repeats: ~1k & 1.1k \\ | //Pog// has 2 repeats: ~1k & 1.1k \\ | ||
| Line 122: | Line 133: | ||
| Took about 50 minutes for all.\\ | Took about 50 minutes for all.\\ | ||
| - | For comparison, Newbler took 18 minutes and about 40 contigs. | + | For comparison, Newbler took 18 minutes and 31 non-overlapping contigs. |
| - | Just qsub them with no arguments, and it runs everything.\\ | + | Just qsub them with no arguments, and it runs everything. ("Them"? "it"? What does this sentence mean? FIXME --- //[[karplus@soe.ucsc.edu|Kevin Karplus]] 2010/05/02 09:14//) |
lecture_notes/04-28-2010.1272778937.txt.gz · Last modified: 2010/05/02 05:42 by galt
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