This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to save a terminal output in a txt file?

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

fastxtoolkit
• 4,984 views • link
updated by Ram Ram • written by silas008 silas008

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!

• 0 views • link
written by Michael Dondrup Michael Dondrup

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

• 0 views • link
updated by Ram Ram • written by Brian Bushnell Brian Bushnell

2 answers

">" directs standard output into a file:

fastq_quality_utility > output.txt

• 0 views • link
written by novice novice

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.

• 0 views • link
updated by Ram Ram • written by Brian Bushnell Brian Bushnell

&> also works:

command &> out.txt
• 0 views • link
updated by Ram Ram • written by novice novice

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

• 0 views • link
written by 5heikki 5heikki

Ok... Thank you

• 0 views • link
written by silas008 silas008

Why no "thank you" to me? :(

• 0 views • link
updated by Ram Ram • written by novice novice

I'm 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

• 0 views • link
updated by Ram Ram • written by silas008 silas008

Log in to answer this question.

More posts like this