samtools fixmate: what's wrong with the terminal?

Question

[npavliukovec]

What is wrong with my terminal? Why it could look like on the picture? The command which I use:

samtools fixmate -m file_nSorted -@ 6 -0 BAM -path/file_fixmated.bam

Terminal during script processing:

Answer 1

[Ram]

The output format parameter is -O, not -0. Also, there's a - before the path/ which makes samtools thing ath/file_fixmated.bam is the value passed to -p but -p doesn't expect an input parameter. Speaking of, -m doesn't expect an input parameter as well, so I'm not sure what the file_nSorted value is doing there. Also, there's only one positional argument supplied so BAM output is being written to STDOUT. It looks like you did not read the extremely brief manual at all. Please read it and fix all of that - nothing is wrong with your terminal. PEBCAK.

Answer 2

[Pierre Lindenbaum]

1) your standard output is redirected to the terminal instead of a file.

2) there is no such option -0 (zero) . your want -O (letter)

3) -path/file_fixmated.bam is a source of error as -p is a flag, you shouldn't concatenate it with a filename . Disable FR proper pair check 4) what is file_nSorted ?

etc...

all in one, you should have a look at the samtools manual. http://www.htslib.org/doc/samtools-fixmate.html

[Pierre Lindenbaum]

oh , Ram was too fast ! :-D

[Ram]

Lol I started writing first, then discovered each issue as I was writing. All I saw was the -0 but then oh my goodness, so many problems!