User:Lindenb/Notebook/UMR915/20101103

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:
 * 1) Totals:
 * 2)   lines input               1
 * 3)   lines skipped             0
 * 4)   alleles annotated         2
 * 5)     missense                0
 * 6)     nonsense                2
 * 7)     coding-synon            0
 * 8)     intron                  0
 * 9)     utr-3                   0
 * 10)     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  Creating sequence and location files... <<>> 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)... Cleaning up... done.
 * WARNING: this is a beta version, provided for testing purposes only; *
 * check for updates at .    *
 * check for updates at .    *

> ls gemhg18.blf     gemhg18.bwt.bl1  gemhg18.bwt.bl3  gemhg18.csa  gemhg18.loc gemhg18.bwt.bl0 gemhg18.bwt.bl2  gemhg18.bwt.toc  gemhg18.gem  gemhg18.log

size: 3Go