Question: (Closed) How to save a terminal output in a txt file?
0
gravatar for silas008
2.7 years ago by
silas00870
Brazil
silas00870 wrote:

Hi,

I am using Fastx Tool Kit and i need to save the output of command line. For example, if I use the fastq_quality_filter command, the output in the terminal is:

Quality cut-off: 20
Minimum percentage: 50
Input: 24038429 reads.
Output: 23792466 reads.
discarded 245963 (1%) low-quality reads.

How can I save the output in a txt file to see later if I need to do that?

Thank you so much

 

 

fastxtool kit • 1.8k views
ADD COMMENTlink modified 2.7 years ago by 5heikki7.6k • written 2.7 years ago by silas00870

Hello silas008!

We believe that this post does not fit the main topic of this site.

Not a bioinformatics question. This is basic unix, use google.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 2.7 years ago by Michael Dondrup44k

Friends don't let friends use Fastx Toolkit.  Virtually any alternative would be superior.  I am biased, but I recommend BBDuk.

ADD REPLYlink written 2.7 years ago by Brian Bushnell15k
5
gravatar for novice
2.7 years ago by
novice830
United States
novice830 wrote:

">" directs standard output into a file:

fastq_quality_utility > output.txt

ADD COMMENTlink written 2.7 years ago by novice830

And for the record, some programs output to both standard out and standard error.  So the most universal way to record all screen output is like this:

foo 1>out.txt 2>&1

..where "foo" is the complete program command line.

ADD REPLYlink written 2.7 years ago by Brian Bushnell15k
2

&> also works:
command &> out.txt 

 

ADD REPLYlink written 2.7 years ago by novice830
1

Neat, thanks for sharing!

ADD REPLYlink written 2.7 years ago by Brian Bushnell15k
2
gravatar for 5heikki
2.7 years ago by
5heikki7.6k
Finland
5heikki7.6k wrote:

Is this stdout? If yes, just > file.txt

ADD COMMENTlink written 2.7 years ago by 5heikki7.6k

Ok... Thank you

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by silas00870

Why no "thank you" to me? :( 

ADD REPLYlink written 2.7 years ago by novice830
1

Im sorry...

I did a idiot question to 5eikki and then I edited the question to: Ok... thank you.  :) 

But I gave a "like" to you answer too. And thank you so much

ADD REPLYlink written 2.7 years ago by silas00870
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