Question: HISAT2 Error: Encountered internal HISAT2 exception (#1)
0
gravatar for ja4123
8 months ago by
ja41230
ja41230 wrote:

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.

hisat2 • 968 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by ja41230
1

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.

ADD REPLYlink modified 8 months ago • written 8 months ago by genomax89k

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"

ADD REPLYlink modified 8 months ago • written 8 months ago by ja41230

Are you using the latest hisat version available?

ADD REPLYlink written 8 months ago by genomax89k

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

ADD REPLYlink modified 8 months ago • written 8 months ago by ja41230

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

ADD REPLYlink modified 8 months ago • written 8 months ago by genomax89k
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
ADD REPLYlink modified 8 months ago • written 8 months ago by ja41230

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
ADD REPLYlink written 8 months ago by genomax89k

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

ADD REPLYlink modified 8 months ago • written 8 months ago by ja41230

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

ADD REPLYlink written 8 months ago by genomax89k
0
gravatar for ATpoint
8 months ago by
ATpoint38k
Germany
ATpoint38k wrote:

I guess the problem is that you try to directly run the aligner via the hisat2-align-s executable rather than using the recommended wrapper function hisat2 (which is apparently not in PATH). When I run it directly I get a warning:

'hisat2-align' was run directly. It is recommended that you run the wrapper script 'hisat2' instead.

I suggest you put your hisat2 executable into PATH and try to run the whole command again. Also please show output of zcat input1.fastq.gz | head

Pro tip: Do not save SAM files, instead pipe into samtools to get BAM right away: hisat2 (options...) | samtools view -o aligned.bam

ADD COMMENTlink written 8 months ago by ATpoint38k
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