hisat2 SyntaxError: invalid syntax
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5 weeks 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!

hisat2 error alignment • 417 views
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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.

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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.

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Thanks a lot! I have figured it out.

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Maybe share your solution in one of the threads to help others with a similar problem?

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