How to save BamUtil stats result as text file

Question

[ttsutsui1028]

Dear all,

I am in trouble to export BamUtil stats result as text file. Could anyone suggest me to solve this problem?

I have tried following

Path/to/bamutil stats --basic --in my.bam > stats.txt
Path/to/bamutil stats --basic --in my.bam | echo > stats.txt

Both couldn't write statistics in text file.

Thank you for your answer,

[WouterDeCoster]

Both couldn't write statistics in text file.

What happens then? Please be as informative as possible since we cannot see what happens on your screen.

[Tm]

Even I have experienced the same problem but then you can always use 'nohup' to get output appended in 'nohup.out'.

i.e you can use below command:

nohup Path/to/bamutil stats --basic --in my.bam

And you can find the stats written in nohup.out file

[cpad0112]

try @ ttsutsui1028 :

$ bamutil/bam stats --basic --in my.bam |& tee >stats.txt

or

$ bamutil/bam stats --basic --in my.bam 2>&1| tee >stats.txt

Answer 1

[h.mon]

bamUtil redirects --stats (also --phred and --qual) to sdterr, not to stdout. So if you want to redirect those stats to a file, you have to redirect stderr with 2>stats.txt:

bam stats --basic --in my.bam 2>stats.txt

[lakhujanivijay]

I would say , learn and understand the difference between stderr and stdout. Check out this link and never get messed up

https://www.jstorimer.com/blogs/workingwithcode/7766119-when-to-use-stderr-instead-of-stdout