Hi all,
I am really struggling with hisat2 recently and getting confused. I'm trying to run hisat2
python2 /home/yun/Downloads/hisat2-2.2.0/hisat2 -t -p 2 -x shiryn\ RNAseq\ data/reference/grch38_genome/grch38 -1 shiryn\ RNAseq\ data/trimmed\ data/ly1_paired_1.trim.fq.gz shiryn\ RNAseq\ data/trimmed\ data/ly1_paired_2.trim.fq.gz -S shiryn\ RNAseq\ data/alighed/ly1.sam
Heie is my error:
File "/home/yun/Downloads/hisat2-2.2.0/hisat2", line 31
use strict;
^
SyntaxError: invalid syntax
Any help is appreciated.
hisat2 is a wrapper script. You need to run it simply as is. Do not run it using python2.
$ hisat2 -h
HISAT2 version 2.2.0 by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo)
Usage:
hisat2 [options]* -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <sam>]
the OP has problems like so hisat2 /usr/bin/env: ‘python’: No such file or directory
After I run the command
hisat2 -t -p 2 -x shiryn\ RNAseq\ data/reference/grch38_genome/grch38 -1 shiryn\ RNAseq\ data/trimmed\ data/ly1_paired_1.trim.fq.gz shiryn\ RNAseq\ data/trimmed\ data/ly1_paired_2.trim.fq.gz -S shiryn\ RNAseq\ data/alighed/ly1.sam
The output is
/usr/bin/env: ‘python’: No such file or directory
Extra parameter(s) specified: "data/reference/grch38_genome/grch38", "shiryn", "RNAseq", "data/trimmed", "data/ly1_paired_2.trim.fq.gz", "RNAseq", "data/alighed/ly1.sam"
Overall time: 00:00:00
Error: Encountered internal HISAT2 exception (#1)
Command: /home/yun/Downloads/hisat2-2.2.0/hisat2-align-s --wrapper basic-0 -t -p 2 -x shiryn -S shiryn RNAseq data/reference/grch38_genome/grch38 shiryn RNAseq data/trimmed data/ly1_paired_2.trim.fq.gz RNAseq data/alighed/ly1.sam
(ERR): hisat2-align exited with value 1
It may be much simpler to re-install hisat2 using conda. Please use the directions here: Creating workflows with snakemake and conda (use the conda part of this tutorial). It should, I think, install all necessary dependencies in your user space.
Please do NOT use spaces in folder/file names (shiryn\ RNAseq\). While it may work it would cause strange issues with programs like what you are seeing here.
Don't run hisat2 through Python, it is not written in Python.
You could run it via Perl, but there should be no need to do so.
Invoke it directly as
hisat2
Edit: now I see that you also had a problem here
hisat2 /usr/bin/env: ‘python’: No such file or directory
as it turns out the two programs were written in different languages
So how should I do？ After I run the command
hisat2 -t -p 2 -x shiryn\ RNAseq\ data/reference/grch38_genome/grch38 -1 shiryn\ RNAseq\ data/trimmed\ data/ly1_paired_1.trim.fq.gz shiryn\ RNAseq\ data/trimmed\ data/ly1_paired_2.trim.fq.gz -S shiryn\ RNAseq\ data/alighed/ly1.sam
The output is
/usr/bin/env: ‘python’: No such file or directory
Extra parameter(s) specified: "data/reference/grch38_genome/grch38", "shiryn", "RNAseq", "data/trimmed", "data/ly1_paired_2.trim.fq.gz", "RNAseq", "data/alighed/ly1.sam"
Overall time: 00:00:00
Error: Encountered internal HISAT2 exception (#1)
Command: /home/yun/Downloads/hisat2-2.2.0/hisat2-align-s --wrapper basic-0 -t -p 2 -x shiryn -S shiryn RNAseq data/reference/grch38_genome/grch38 shiryn RNAseq data/trimmed data/ly1_paired_2.trim.fq.gz RNAseq data/alighed/ly1.sam
(ERR): hisat2-align exited with value 1
I have installed python2 and python3. But it desn't work at all.
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This was already indirectly answered in your other thread. Try typing
python3instead ofpython2.I see the problem actually, amusing
hisat2 runs via perl
hisat2-build runs via python
Serves me right for trying to answer the question in general without knowing the inner workings of the program. Xiaoyun, please ignore my response.