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How to save BamUtil stats result as text file

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,

bamutil
• 2,622 views • link
updated by h.mon h.mon • written by ttsutsui1028 • ttsutsui1028

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.

• 1 views • link
written by WouterDeCoster WouterDeCoster

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

• 1 views • link
written by Tm Tm

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
• 1 views • link
written by cpad0112 cpad0112

1 answer

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
• 1 views • link
written by h.mon h.mon

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