Perhaps the length of the header text is longer than 2G or 4G. Heng
On Oct 23, 2014, at 8:51, Alexis Bertrand <abertr...@genoscope.cns.fr> wrote: > Hello, > > I’m using samtools view –H (version : 0.1.18) to retrieve the header only and > getting the following error : > > samtools view –H data.bam > data_header.sam > [samopen] inconsistent number of target sequences. Output the text header. > > The header of data.bam contains 117130845 sequences but only 30216898 > sequences are written in my output file (data_header.sam). > > The last line of the output file is “@SQ > SN:ARC11SUR1QQSS14UUU.ASY1CTG177062.1 LN:1” instead of “@SQ > SN:ARC11SUR1QQSS14UUU.ASY1CTG177062.1 LN:138”. > > Is there a known issue regarding this? > > Thanks, > > Alexis Bertrand > > > > > ------------------------------------------------------------------------------ > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
