HISAT2 software installation

Question

[saj98]

Hello everyone

I am trying to install HISAT2, so I used the following command: wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.4-Linux_x86_64.zip Then I used: unzip hisat2-2.0.4-Linux_x86_64.zip then I used cd hisat2-2.0.4 Then I used ./hisat2. It came fine, but at the end it gave the following error: (ERR): hisat2-align exited with value 1

Any help or suggestion I appreciate your time Shaima

[GenoMax]

You need to provide a valid input for hisat2 command that is complete or if you just want to see the in-line help then ./hisat2 -h will work for that purpose. Running ./hisat2 prints the in-line help (but there is more than a screen full) and then generates that error at the end.

[saj98]

Sorry, I am new to to HISAT2. What do you mean a valid input? Could you explain? I used hisat2 -h, but it gave me hisat2: command not found

[GenoMax]

If you scroll up in the terminal you will see this message

./hisat2
No index, query, or output file specified!
HISAT2 version 2.1.0 by Daehwan Kim ([e-mail], www.ccb.jhu.edu/people/infphilo)
Usage: 
  hisat2 [options]* -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]

  <ht2-idx>  Index filename prefix (minus trailing .X.ht2).
  <m1>       Files with #1 mates, paired with files in <m2>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <m2>       Files with #2 mates, paired with files in <m1>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <r>        Files with unpaired reads.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <sam>      File for SAM output (default: stdout)

  <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
  specified many times.  E.g. '-U file1.fq,file2.fq -U file3.fq'.

[output truncated for space reasons]

HISAT2 is trying to let you know that you need to provide a minimum number of valid options for the command to work. In this case name of the index, a query and an output file name.

[sooyoung16]

Did you resolve this all issues? Actually, when I wrote all pathways, hisat seems be working. I'm using M2 Mac. I tried to change zshrc, but not working or I do not know how to change properly. Please give me advice Thanks, S

[GenoMax]

Actually, when I wrote all pathways, hisat seems be working. I'm using M2 Mac. I tried to change zshrc, but not working or I do not know how to change properly.

What does this mean?

Answer 1

[nancydong20]

First, this doesn't seem to be an installation issue. You can try installing hisat2 using conda, which will give a more hassle-free installation.

Is the hisat2 folder in your PATH? If not, then just typing hisat2 -h would likely give you "command not found". I see in your first post that you used ./hisat2 while in the hisat2 folder, which worked fine. Does entering "./hisat2 -h" while in the hisat2 folder work?

[ddeemer]

That conda install hisat2 is the way to go.

[saj98]

Hello Does conda work with linux? Thanks for your help

[nancydong20]

Yes, conda works with Linux. You can think of it as kinda like perlbrew for python. But it really doesn't seem like an installation issue if your original ./hista2 command worked.

You can download and install Miniconda on Linux from here: https://conda.io/miniconda.html

After installing Miniconda (it should automatically add itself to your PATH), you can install hisat2 using the command conda install -c bioconda hisat2 .

In fact, once you have Miniconda installed, you can google "conda install program" ("program" being the name of your program of choice), and see if there is a bioconda package already available. Most of the commonly used programs can be installed this way. I think it makes installation a lot easier. One caveat is that sometimes the bioconda package may not be the most recent version of the program (most of the time it is), so you should check on which version is being installed using the bioconda package.