On Fri, Mar 18, 2016 at 5:24 AM, Robert May <[email protected]> wrote: > ioLinux Mint Desktop mate > > samtools depth -b -q -Q -r <chrY:1-30000000> in.bam > samtools depth -b -q -Q -r<chrY:1-30000000> in.bam > samtools depth -q -Q -r <chrY:1-30000000> in.bam > samtools depth -q -Q -r <chrY:1-30000000> in.bam > samtools depth -Q -r <chrY:1-30000000> in.bam > samtools depth -r <chrY:1-30000000> in.bam > samtools depth <chrY:1-30000000> in.bam > > bash: chrY:1-30000000: No such file or directory >
Don't type the < and > signs, which mean something special to the Unix shell (here specifically the bash shell), see below. Either remove the greater and less-than signs, or you can use the double quote character instead. > samtools depth -b -q -Q -r <chrY:1-30000000> in.bam > samtools depth -Q in.bam > open: No such file or directory > Segmentation fault Same mistake. > samtools depth -b -q -Q in.bam > samtools depth -b in.bam > samtools depth -q in.bam > samtools depth -Q in.bam > usage and options menu > > samtools depth -b -q in.bam > samtools depth -b in.bam > prints to screen > > How do I get it to print to file The greater than sign is for redirecting the output from the screen to a file (Google for Unix piping and stdout), e.g. samtools dept -b in.bam > example.txt Peter ------------------------------------------------------------------------------ Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140 _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
