Dear Devon, Thank you very much for your reply.
best, Sung-Huan Quoting Devon Ryan <[email protected]>: > Hi Sung-Huan, > > Upon further inspection, your BAM file is actually a bit malformed (you can > get around this with the --ignore-RG option, but you shouldn't have to). > The problem is that the auxiliary data is set as being larger than needed > and so skip_aux ends up finding a bunch of nulls, which cause it to abort. > Interestingly, this is still the case if remake the BAM file after > converting to a proper SAM file, so there is a bug here, just not one > directly in the mpileup code. > > I'll look into this a bit more since, if correct, it would seem like this > would affect a lot of the rest of us too. > > Best, > Devon > > -- > Devon Ryan, Ph.D. > Email: [email protected] > Laboratory for Molecular and Cellular Cognition > German Centre for Neurodegenerative Diseases (DZNE) > Ludwig-Erhard-Allee 2 > 53175 Bonn > Germany > <[email protected]> > > On Mon, Sep 22, 2014 at 12:08 PM, Sung-Huan Yu < > [email protected]> wrote: > >> Hi, >> >> I already uploaded the genome fasta file here. >> >> https://data.imib-zinf.net/Staphylococcus_aureus_HG003.zip >> >> please refer to it. >> >> Best, >> >> Sung-Huan >> >> >> Quoting Devon Ryan <[email protected]>: >> >> Hi Sung-Huan, >>> >>> At least on my laptop I can't reproduce this (I get the expected bcf file >>> output), though since I don't have your fasta file perhaps that's why. >>> Could you post that somewhere as well? >>> >>> Best, >>> Devon >>> >>> ____________________________________________ >>> Devon Ryan, Ph.D. >>> Email: [email protected] >>> Tel: +49 (0)178 298-6067 >>> Molecular and Cellular Cognition Lab >>> German Centre for Neurodegenerative Diseases (DZNE) >>> Ludwig-Erhard-Allee 2 >>> 53175 Bonn, Germany >>> >>> On Sep 19, 2014, at 2:19 PM, Sung-Huan Yu wrote: >>> >>> Dear all, >>>> >>>> I would like to use samtools to call SNP. I use the latest version 1.0. >>>> First, I have to generate bcf file. >>>> I run the following command. >>>> >>>> samtools mpileup -t DP -ugf my.fasta my.bam >>>> >>>> the result is always like this: >>>> >>>> [mpileup] 1 samples in 1 input files >>>> Set max per-file depth to 8000 >>>> Aborted >>>> >>>> If I just run >>>> >>>> samtools mpileup -f my.fasta my.bam >>>> >>>> it works fine. >>>> I have no idea what happens. >>>> If I go back to use samtools-0.1.19 to run >>>> >>>> samtools mpileup -uD -f my.fasta my.bam >>>> >>>> everything is okay. >>>> Could anyone helps me? Thank you. >>>> >>>> I also parsed the BAM file to short one. I found when the line comes to >>>> 88, it will aborted. Before line 88, everythin is fine. But I checked the >>>> file, I didn't see anything wrong. Please refer the attachment. >>>> Sung-Huan >>>> >>>> >>>> <short.bam>------------------------------------------------- >>>> ----------------------------- >>>> 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 >>>> >>> >>> >>> >> >> >> > ------------------------------------------------------------------------------ Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
