Entering edit mode
3.0 years ago
Xiaoyun
▴
10
Hi all,
I am really struggling with hisat2 recently and getting confused. I'm trying to run hisat2:
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
This is my error:
File "/home/yun/Downloads/hisat2-2.2.0/hisat2_read_statistics.py", line 182
length_map = sorted(length_map.iteritems(), key=lambda (k,v):(v,k), reverse=True)
^
SyntaxError: invalid syntax
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
Any help is appreciated!
There is an ongoing thread here: hisat SyntaxError: invalid syntax
It is not clear if this is an ongoing iteration of problems OP is experiencing.
Answered here. Not sure why you are creating new threads for the same problem. Without the context in that previous thread, specifically what changes you made already, I doubt that anyone can answer the question as you posed it here.
Thanks a lot! I have figured it out.
Maybe share your solution in one of the threads to help others with a similar problem?