search

lh3 / seqtk

Toolkit for processing sequences in FASTA/Q formats
MIT License
1.35k stars 311 forks source link

seqtk: command not found #121

Open Roopali24 opened 5 years ago

Roopali24 commented 5 years ago

Hi,

So I installed seqtk using the instructions before:

git clone https://github.com/lh3/seqtk.git; cd seqtk; make

This works fine. But now when I try using a command for downsampling:

seqtk sample -s100 sra_data.fq 10000 > sample1.fq

I get error: "seqtk: command not found"

Please help.

yzhernand commented 5 years ago

That only builds the binary, so the Readme is a little misleading. Also run sudo make install in the seqtk directory to install the binary into /usr/local/bin. The binary should be in your path after that.

Roopali24 commented 5 years ago

So apparently the problem was that I needed to call the path to the function seqtk i.e. /Users/roopali/ncbi/seqtk/seqtk rather than just seqtk, even if I was in that directory.

yzhernand commented 5 years ago

That works too, but installing it, or just copying the binary to any directory in your path, avoids the extra typing :)

Roopali24 commented 5 years ago

oh. Thanks :)

abusalah85 commented 4 years ago

Hi there,

I have installed seqtk using the instructions given as it show bellow git clone https://github.com/lh3/seqtk.git; cd seqtk; make install

however I want to use Fastq TO Fasta command as showing bellow

mohamedalbulushi@Mohameds-MacBook-Pro seqtk % seqtk seq -a in /Users/mohamedalbulushi/Desktop/OM-1901_1.fastq > out OM-1901_1.fa

I get the following error

[E::stk_seq] failed to open the input file/stream.

yzhernand commented 4 years ago

Remove "in" and "out" in your command:

seqtk seq -a /Users/mohamedalbulushi/Desktop/OM-1901_1.fastq > OM-1901_1.fa
abusalah85 commented 4 years ago

Thank you Dear Yozen

it was helpful

I am beginner in using and understanding those command

Abu Salah