User:Lindenb/Notebook/UMR915/20101103: Difference between revisions

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==Testing GigaBayes==
==Testing GigaBayes==
from http://bioinformatics.bc.edu/marthlab/Software_Release
from http://bioinformatics.bc.edu/marthlab/Software_Release
I cannot get a correct archive. Both 64 & 32 said:
<pre>gzip: stdin: unexpected end of file
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now</pre>


==Testing GEM==
==Testing GEM==

Revision as of 06:39, 3 November 2010

20101102        Top        20101104       


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

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:

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)...
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