As I recall, there's some condition that the decompression library incorrectly decides means there's something wrong with the input file, and it returns a value that the calling routine can't distinguish from an end of file. The calling routine then reports that the file is truncated but continues to try to read the rest of the file, and might be successful.
I believe I reported this a few months back but I really got no response from the samtools folks. I think/guess the basic problem is that the decompression library doesn't originate with this project, so there's resistance to making any changes to it. The change I suggested at the time *looked* simple enough, but it would involve a change to how that library reports errors. All that may have nothing to do with why your file isn't being sorted though. Bob H On Sep 19, 2014, at 8:04 PM, Vickie S <[email protected]> wrote: > Hi > I am trying to sort the bam file by using the sort command: > samtools sort -n aln.bam aln.qsort > [W::sam_hdr_read] bgzf_check_EOF: Value too large for defined data type > [bam_sort_core] truncated file. Continue anyway. > > I am not sure if "continue anyway" means it continues to sort or just aborts. > I checked the file size. > $ du -hs * > 113G aln.bam > 8.4M aln.bam.bai > 28K aln.qsort.bam > > So it does not seem like file is sorted. I have checked one previous thread > about this bug but could not find any solution. Anyone comments ? Suggestion > for any other tool ? > > Thanks > > ------------------------------------------------------------------------------ > Slashdot TV. Video for Nerds. Stuff that Matters. > http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg.clktrk > _______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help > ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
