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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


download SOAPAligner from

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..
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...
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


download from

scp on server 2,3,4

Testing GigaBayes


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


downloaded binaries for linux from

$ 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

( )

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 <>
* WARNING: this is a beta version, provided for testing purposes only; *
*  check for updates at <>.     *
Creating sequence and location files...
<<<WARNING>>> This index can only be generated in external memory.
              Proceeding, with --external-memory-prefix='gemhg18'
Computing BWT in external memory (likely to take very long)...
Cleaning up... done.

> 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