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
