Will do, thanks!

--t

On Feb 7, 2013, at 12:32 PM, Michael Lawrence <lawrence.michael@gene.com> wrote:

> I've asked Tom Wu and he pointed out that your genome index may be truncated, since there should be more than 2,990,309,376 bytes for an hg18 index. More like 3,841,790,404 bytes. Perhaps you could try rebuilding the genome index?
> 
> Thanks,
> Michael
> 
> 
> 
> 
> On Tue, Feb 5, 2013 at 11:43 AM, Tim Triche, Jr. <tim.triche@gmail.com> wrote:
>> I was interested in comparing gsnap to subread, so I followed the
>> instructions provided in the gmapR vignette (BioC-2.11, stable version) and
>> created an hg18 genome, etc. to realign some ChIP-seq data.
>> 
>> Unfortunately, the aligner did not seem to like any of the reads I fed it
>> (I tried several, including SRA archives SRR094809 and SRR350216).  Do the
>> following error messages set off red flags for anyone?
>> 
>> Looking for index files in directory /home/ttriche/FASTQ/gmapR/Hsapiens/hg18
>>   Gammaptrs file is hg18.ref12153gammaptrs
>>   Offsetscomp file is hg18.ref12153offsetscomp
>>   Positions file is hg18.ref12153positions
>> Allocating memory for ref gammaptrs, kmer 15, interval 3...done (67,108,868
>> bytes, 0.78 sec)
>> Allocating memory for ref offsets, kmer 15, interval 3...done (349,702,436
>> bytes, 3.86 sec)
>> Pre-loading ref positions, kmer 15, interval 3... done  (2,990,309,376
>> bytes, 730056 pages, 32.16 sec).
>> GMAP modes: pairsearch, terminal, improvement
>> Starting alignment
>> Signal received: Segmentation fault
>> Problem sequence: CD133.H3K79me2.41 (36 bp)
>> >CD133.H3K79me2.41
>> NCCAACATGTTAAAACCCTTTCTCTACTAAAAACAC
>> sh: line 1: 13517 Aborted
>> /home/ttriche/R/x86_64-unknown-linux-gnu-library/2.15/gmapR/usr/bin/gsnap
>> --db=hg18 --dir=/home/ttriche/FASTQ/gmapR/Hsapiens --nthreads=12
>> --npaths=10 --quiet-if-excessive --nofails --format=sam
>> CD133.H3K79me2.fastq > CD133.H3K79me2.sam
>> GSNAP version 2011-12-28 called with args:
>> /home/ttriche/R/x86_64-unknown-linux-gnu-library/2.15/gmapR/usr/bin/gsnap
>> --db= --version
>> A GsnapOutput Object
>> path: CD133.H3K79me2.sam
>> 
>> I'm running the stable version:
>> 
>> R> packageVersion('gmapR')
>> [1] ‘1.0.0’
>> 
>> And here is the rest...
>> 
>> R> sessionInfo()
>> R version 2.15.2 (2012-10-26)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>> 
>> locale:
>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>  [7] LC_PAPER=C                 LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices datasets  utils     methods   base
>> 
>> other attached packages:
>> [1] GmapGenome.Hsapiens.UCSC.hg18_1.0.0 BSgenome.Hsapiens.UCSC.hg18_1.3.19
>> [3] BSgenome_1.26.1                     Biostrings_2.26.2
>> [5] gmapR_1.0.0                         GenomicRanges_1.10.6
>> [7] IRanges_1.16.4                      BiocGenerics_0.4.0
>> 
>> loaded via a namespace (and not attached):
>>  [1] AnnotationDbi_1.20.3    Biobase_2.18.0          biomaRt_2.14.0
>>  [4] bitops_1.0-5            DBI_0.2-5               GenomicFeatures_1.10.1
>>  [7] parallel_2.15.2         RCurl_1.95-3            Rsamtools_1.10.2
>> [10] RSQLite_0.11.2          rtracklayer_1.18.2      stats4_2.15.2
>> [13] tools_2.15.2            VariantAnnotation_1.4.8 XML_3.95-0.1
>> [16] zlibbioc_1.4.0
>> 
>> 
>> Thanks for any assistance,
>> 
>> --t
>> 
>> --
>> *A model is a lie that helps you see the truth.*
>> *
>> *
>> Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>> 
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>> 
>> 
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