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 ------------------------------------------------------------------------------ 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
