User:Lindenb/Notebook/UMR915/20101103: Difference between revisions
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<pre>sudo /usr/local/package/soap2.20release/2bwt-builder hg18.fa | <pre>sudo /usr/local/package/soap2.20release/2bwt-builder hg18.fa | ||
Parsing FASTA file.. | Parsing FASTA file.. | ||
</pre> | Finished. Parsed 45 sequences. | ||
Elapsed time = 127.31 s | |||
Building Look-Up.. | |||
Finished. | |||
Elapsed time = 266.45 s | |||
Building BWT.. | |||
Finished constructing BWT in 289 iterations. Elapsed time = 1852.57 s | |||
Saving BWT.. | |||
Finished saving BWT. Elapsed time = 2.48 s | |||
Building Reversed BWT.. | |||
Finished constructing Reversed BWT in 289 iterations. Elapsed time = 1810.43 s | |||
Saving BWT.. | |||
Finished saving BWT. Elapsed time = 1.54 s | |||
Loading BWT... | |||
Finished loading BWT. Elapsed time = 1.20 s | |||
Building SA value... | |||
Finished building SA value. Elapsed time = 1396.13 s | |||
Building High-Occ Hash Table... | |||
Finished. | |||
Elapsed time = 938.02 s | |||
Building SA index... | |||
Finished building SA index. Elapsed time = 14.20 s | |||
Index building is completed. | |||
Total elapsed time = 6410.68 s</pre> | |||
==Hadoop== | ==Hadoop== |
Revision as of 01:41, 4 November 2010
Polyphen
Does polyphen discard the stop codon ? Testing polyphen with a stop codon: chr22:40053278 C/G should create a stop codon UA.G
result: pph2-snps.txt contains:
## Totals: ## lines input 1 ## lines skipped 0 ## alleles annotated 2 ## missense 0 ## nonsense 2 ## coding-synon 0 ## intron 0 ## utr-3 0 ## utr-5 0
but pph2-full.txt is empty
SOAPAligner
download SOAPAligner from http://soap.genomics.org.cn/soapaligner.html
sudo /usr/local/package/soap2.20release/2bwt-builder hg18.fa Parsing FASTA file.. Finished. Parsed 45 sequences. Elapsed time = 127.31 s Building Look-Up.. Finished. Elapsed time = 266.45 s Building BWT.. Finished constructing BWT in 289 iterations. Elapsed time = 1852.57 s Saving BWT.. Finished saving BWT. Elapsed time = 2.48 s Building Reversed BWT.. Finished constructing Reversed BWT in 289 iterations. Elapsed time = 1810.43 s Saving BWT.. Finished saving BWT. Elapsed time = 1.54 s Loading BWT... Finished loading BWT. Elapsed time = 1.20 s Building SA value... Finished building SA value. Elapsed time = 1396.13 s Building High-Occ Hash Table... Finished. Elapsed time = 938.02 s Building SA index... Finished building SA index. Elapsed time = 14.20 s Index building is completed. Total elapsed time = 6410.68 s
Hadoop
download from http://apache.multidist.com//hadoop/core/stable/hadoop-0.20.2.tar.gz
scp on server 2,3,4
Testing GigaBayes
from http://bioinformatics.bc.edu/marthlab/Software_Release
I cannot get a correct archive. Both 64 & 32 said:
gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now
Testing GEM
cf:
- http://sourceforge.net/apps/mediawiki/gemlibrary/index.php?title=The_GEM_library
- http://sourceforge.net/apps/mediawiki/gemlibrary/index.php?title=Gem_mapper_man_page
- http://sourceforge.net/apps/mediawiki/gemlibrary/index.php?title=Installation_instructions
downloaded binaries for linux from SF.net
$ ls gem-2-sam gem-do-index_fm_dna_64b gem-mappability gem-mapper gem-split-mapper gem-do-bwt_32b gem-do-index_fm_general_32b gem-mappability_fm_dna_32b gem-mapper_fm_dna_32b gem-split-mapper_fm_dna_32b gem-do-bwt_64b gem-do-index_fm_general_64b gem-mappability_fm_dna_64b gem-mapper_fm_dna_64b gem-split-mapper_fm_dna_64b gem-do-dna-bwt gem-dump-magic gem-mappability_fm_general_32b gem-mapper_fm_general_32b gem-split-mapper_fm_general_32b gem-do-index gem-fasta2loc_cont_32b gem-mappability_fm_general_64b gem-mapper_fm_general_64b gem-split-mapper_fm_general_64b gem-do-index_fm_dna_32b gem-fasta2loc_cont_64b gem-mappability-retriever gem-retriever
Creating an index
( http://sourceforge.net/apps/mediawiki/gemlibrary/index.php?title=Gem_do_index_man_page )
gem-do-index -i ${HG18} -o gemhg18 Welcome to GEM-do-index build 156 (beta) - (2009/10/07 02:50:12 GMT) (c) 2008-2010 Paolo Ribeca <paolo.ribeca@gmail.com> ************************************************************************ * WARNING: this is a beta version, provided for testing purposes only; * * check for updates at <http://www.paoloribeca.net/software/GEM>. * ************************************************************************ Creating sequence and location files... <<<WARNING>>> This index can only be generated in external memory. Proceeding, with --external-memory-prefix='gemhg18' done. Computing BWT in external memory (likely to take very long)...