weird samtools tview errors

[iwtwb8]

I give the following command:

samtools tview <chrom5_23MB_to_end.sorted.bam> chrom5_23MB_to_end.fas

and receive the following error:

Usage: bamtk tview <aln.bam> [ref.fasta]

In addition, my chrom5_23MB_to_end.fas reference file has been overwritten and now has a size of 0 KB.

Anyone have any suggestions or ideas?

[gaffa]

The "<" signs are not supposed to be included, they are only placed around the file name to signify that it's a single file or unit or whatever. It's a convention sometimes used in these contexts.

So what's happening is that these signs have a different meaning in UNIX, namely to re-direct output. That's why your .fas file is overwritten - the ">" means to write the output of the previous command to file, but there's nothing to write so the file is empty.

[iwtwb8]

Well now I feel like an idiot but at least I understand what happened. Thank you!