HISAT2 Error: Encountered internal HISAT2 exception (#1)

Question

[ja4123]

Hello, I am using HISAT2 for aligning transcripts to the reference genome. I have build the indexes first. And try the command as follows:

hisat2-build -p 8 --dta -x name_tran -1 input1.fastq.gz -2 input2.fastq.gz -S out.sam

However, I am getting the following error:

Error: Encountered internal HISAT2 exception (#1)

Kindly help.

[GenoMax]

Command you posted has a typo/is incorrect (hisat2-bulit -p 8 --dta -x name_tran -1 input1.fastq.gz -2 input2.fastq.gz -S out.sam). It is not a command that you would use for the alignment.

[ja4123]

I am useing this procedure:

Align the RNA-seq reads to the genome
Map the reads for each sample to the reference genome:
$ hisat2 -p 8 --dta -x chrX_data/indexes/chrX_tran -1 
chrX_data/samples/ERR188044_chrX_1.fastq.gz -2 
chrX_data/samples/ERR188044_chrX_2.fastq.gz -S ERR188044_chrX.sam

That is an example

From Nature protocol "Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown"

[GenoMax]

Are you using the latest hisat version available?

[ja4123]

You know, I have change the command:

hisat2-align-s -p 8 --dta -x name_tran -1 input1.fastq.gz -2 input2.fastq.gz -S out.sam

And now I have error like this:

Error: reads file does not look like a FASTQ file
terminate called after throwing an instance of 'int'
Aborted (core dumped)

But they are fastq files ..

Answering youre question: No, I have hisat2-2.0.1 beta

[GenoMax]

What do you get when you run these commands file input1.fastq.gz and file input2.fastq.gz?

[ja4123]

input1.fastq.gz: gzip compressed data, was "input1.fastq", last modified: Fri Jan  3 10:46:39 2020, from Unix

input2.fastq.gz: gzip compressed data, was "input2.fastq", last modified: Fri Jan  3 10:45:58 2020, from Unix

[GenoMax]

Ok. So these files appear to be in the right format. How much memory do you have available on your machine?

Are you able to successfully run:

hisat2 --dta -x name_tran -1 input1.fastq.gz -2 input2.fastq.gz -S out.sam

[ja4123]

Output of youre command:

Command 'hisat2' not found

After mine change:

hisat2-align-s --dta -x name_tran -1 input1.fastq.gz -2 input2.fastq.gz -S out.sam

I get the same error:

Error: reads file does not look like a FASTQ file

Memory is about 80 GB

[GenoMax]

It is puzzling that you are not able to find the hisat2 wrapper. You are not supposed to run hisat-align directly.