Thanks for the response. I guess I hadn't fully understood this seed file field. I've now set it to 4 (since I have gap.txt, plus chromosomal RM, TRF files and no since files are needed for AMB masks) and the function is running now. Elisabetta --- On Mon, 10 Oct 2011, Hervé Pagès wrote: > Hi Elisabetta, > > Handling of missing nmask_per_seq field was broken (should have been > set to 0 when missing). I just fixed this in BSgenome release (1.20.1) > and devel (1.21.7). Anyway, in your case, it seems like you *do* have > masks, so you need to have the nmask_per_seq field explicitly set > to a non-zero value in your seed file. For example, if you have the 4 > "standard" masks: > > nmask_per_seq: 4 > > You can look at the seed file for hg19 in the BSgenome package > (BSgenome/inst/extdata/GentlemanLab/BSgenome.Hsapiens.UCSC.hg19-seed) > for an example. > > Please let me know if you have further questions about this. > > Cheers, > H. > > > On 11-10-07 11:21 AM, Elisabetta Manduchi wrote: >> >> Hello, >> I'm trying to build a data package for Sus scrofa with BSgenome (R >> version 2.13.2 and BSgenome version 1.20.0). >> At the bottom of this email I've copied my seed file. >> I've downloaded the sequence files from UCSC and checked the md5sums. >> I've also downloaded the gap.txt and masks files (chr*.fa.out and >> chr*.bed) from UCSC (but no md5sums were provided). >> I've followed the instructions from >> http://bioconductor.org/packages/2.8/bioc/vignettes/BSgenome/inst/d oc/BSgenomeForge.pdf >> >> and I'm getting the following error >> >> --- >>> forgeBSgenomeDataPkg("./BSgenome.Sscrofa.UCSC.susScr2-seed") >> Error in forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, masks_srcdir >> = masks_srcdir, : >> values for symbols NMASKPERSEQ are not single strings >> --- >> >> Can you advice on what the problem might be? >> Thanks, >> Elisabetta >> >> >> *SEED file BSgenome.Sscrofa.UCSC.susScr2-seed* >> >> Package: BSgenome.Sscrofa.UCSC.susScr2 >> Title: Sus scrofa (Pig) full genome (UCSC version susScr2) >> Description: Sus scrofa (Pig) full genome as provided by UCSC (susScr2, >> Nov. 2009) >> Version: 0.1-0 >> Author: Elisabetta Manduchi <manduchi at="" pcbi.upenn.edu=""> >> Maintainer: Elisabetta Manduchi <manduchi at="" pcbi.upenn.edu=""> >> License: GPL-3 >> organism: Sus scrofa >> species: Pig >> provider: UCSC >> provider_version: susScr2 >> release_date: Nov. 2009 >> release_name: SGSC Sscrofa9.2 >> source_url: http://hgdownload.cse.ucsc.edu/goldenPath/susScr2/ >> organism_biocview: Sus_scrofa >> BSgenomeObjname: Sscrofa >> seqnames: paste("chr", c(1:18, "X", "M"), sep="") >> circ_seqs: "chrM" >> SrcDataFiles1: sequences: all the chr*.fa.gz files from >> ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/chromosomes/ >> SrcDataFiles2: AGAPS masks: the gap.txt.gz file from >> http://hgdownload.cse.ucsc.edu/golden >> Path/susScr2/database/; RM masks: >> http://hgdownload.cse.ucsc.edu/goldenPath/susScr2/bigZip >> s/chromOut.tar.gz;TRF masks: >> http://hgdownload.cse.ucsc.edu/goldenPath/susScr2/bigZips/chr >> omTrf.tar.gz >> seqs_srcdir: >> /mnt/files/cbil/data/cbil/UHTS/Davies/AAvsDT_DNAmethyl/working_dir/ MEDIPS/BSgenome.Sscrofa.UCSC.susScr2/seqs >> >> masks_srcdir: >> /mnt/files/cbil/data/cbil/UHTS/Davies/AAvsDT_DNAmethyl/working_dir/ MEDIPS/BS >> >> genome.Sscrofa.UCSC.susScr2/masks >> AGAPSfiles_type: gap >> AGAPSfiles_name: gap.txt >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages at fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 >